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+ + + + + + + + + + \ No newline at end of file diff --git a/ANATOMICALDIRECTION/index.html b/ANATOMICALDIRECTION/index.html new file mode 100644 index 00000000..a0ef7d21 --- /dev/null +++ b/ANATOMICALDIRECTION/index.html @@ -0,0 +1,689 @@ + + + + + + + + + + + + + + + + + + + Enum: ANATOMICALDIRECTION - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Enum: ANATOMICALDIRECTION

+

A controlled vocabulary term defining axis direction in terms of anatomical direction.

+

URI: ANATOMICALDIRECTION

+

Permissible Values

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ValueMeaningDescription
left_to_rightNone
posterior_to_anteriorNone
inferior_to_superiorNone
superior_to_inferiorNone
anterior_to_posteriorNone
+

Slots

+ + + + + + + + + + + + + + + + + + + + + +
NameDescription
x_directionA controlled vocabulary attribute defining the x axis direction in terms of a...
y_directionA controlled vocabulary attribute defining the y axis direction in terms of a...
z_directionA controlled vocabulary attribute defining the z axis direction in terms of a...
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/my-org/anatomical-structure-schema
    • +
+

LinkML Source

+
+ +
name: ANATOMICAL_DIRECTION
+description: A controlled vocabulary term defining axis direction in terms of anatomical
+  direction.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+rank: 1000
+permissible_values:
+  left_to_right:
+    text: left_to_right
+    title: left-to-right
+  posterior_to_anterior:
+    text: posterior_to_anterior
+    title: posterior-to-anterior
+  inferior_to_superior:
+    text: inferior_to_superior
+    title: inferior-to-superior
+  superior_to_inferior:
+    text: superior_to_inferior
+    title: superior-to-inferior
+  anterior_to_posterior:
+    text: anterior_to_posterior
+    title: anterior-to-posterior
+
+
+ +
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
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+ + + + + + + + + + \ No newline at end of file diff --git a/Activity/index.html b/Activity/index.html new file mode 100644 index 00000000..b5ac789c --- /dev/null +++ b/Activity/index.html @@ -0,0 +1,1037 @@ + + + + + + + + + +Class: Activity - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
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+

Class: Activity

+

An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.

+

URI: biolink:Activity

+
classDiagram + class Activity + click Activity href "../Activity" + ActivityAndBehavior <|-- Activity + click ActivityAndBehavior href "../ActivityAndBehavior" + NamedThing <|-- Activity + click NamedThing href "../NamedThing" + + Activity : category + + Activity : deprecated + + Activity : description + + Activity : full_name + + Activity : has_attribute + + + + + Activity --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + Activity : id + + Activity : iri + + Activity : name + + Activity : provided_by + + Activity : synonym + + Activity : type + + Activity : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
id1
String		A unique identifier for an entitydirect
iri0..1
IriType		An IRI for an entitydirect
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizeddirect
type*
String		direct
name0..1
LabelType		A human-readable name for an attribute or entitydirect
description0..1
NarrativeText		a human-readable description of an entitydirect
has_attribute*
Attribute		connects any entity to an attributedirect
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...direct
provided_by*
String		The value in this node property represents the knowledge provider that create...direct
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...direct
full_name0..1
LabelType		a long-form human readable name for a thingdirect
synonym*
LabelType		Alternate human-readable names for a thingdirect
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:Activity
nativebican:Activity
exactprov:Activity, NCIT:C43431, STY:T052
narrowSTY:T056, STY:T057, STY:T064, STY:T066, STY:T062, STY:T065, STY:T058
+

LinkML Source

+ +

Direct

+
+
name: activity
+definition_uri: https://w3id.org/biolink/vocab/Activity
+description: An activity is something that occurs over a period of time and acts upon
+  or with entities; it may include consuming, processing, transforming, modifying,
+  relocating, using, or generating entities.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- prov:Activity
+- NCIT:C43431
+- STY:T052
+narrow_mappings:
+- STY:T056
+- STY:T057
+- STY:T064
+- STY:T066
+- STY:T062
+- STY:T065
+- STY:T058
+is_a: named thing
+mixins:
+- activity and behavior
+slots:
+- id
+- iri
+- category
+- type
+- name
+- description
+- has attribute
+- deprecated
+- provided by
+- xref
+- full name
+- synonym
+class_uri: biolink:Activity
+
+
+
+

Induced

+
+
name: activity
+definition_uri: https://w3id.org/biolink/vocab/Activity
+description: An activity is something that occurs over a period of time and acts upon
+  or with entities; it may include consuming, processing, transforming, modifying,
+  relocating, using, or generating entities.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- prov:Activity
+- NCIT:C43431
+- STY:T052
+narrow_mappings:
+- STY:T056
+- STY:T057
+- STY:T064
+- STY:T066
+- STY:T062
+- STY:T065
+- STY:T058
+is_a: named thing
+mixins:
+- activity and behavior
+attributes:
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: activity
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: activity
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: activity
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: activity
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: activity
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: activity
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: activity
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: activity
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: activity
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: activity
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: activity
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: activity
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+class_uri: biolink:Activity
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/ActivityAndBehavior/index.html b/ActivityAndBehavior/index.html new file mode 100644 index 00000000..f64aab97 --- /dev/null +++ b/ActivityAndBehavior/index.html @@ -0,0 +1,448 @@ + + + + + + + + + +Class: ActivityAndBehavior - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: ActivityAndBehavior

+

Activity or behavior of any independent integral living, organization or mechanical actor in the world

+

URI: biolink:ActivityAndBehavior

+
classDiagram + class ActivityAndBehavior + click ActivityAndBehavior href "../ActivityAndBehavior" + Occurrent <|-- ActivityAndBehavior + click Occurrent href "../Occurrent" + + + ActivityAndBehavior <|-- Activity + click Activity href "../Activity" + ActivityAndBehavior <|-- Procedure + click Procedure href "../Procedure" + + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
+

Mixin Usage

+ + + + + + + + + + + + + + + + + +
mixed intodescription
ActivityAn activity is something that occurs over a period of time and acts upon or w...
ProcedureA series of actions conducted in a certain order or manner
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:ActivityAndBehavior
nativebican:ActivityAndBehavior
exactUMLSSG:ACTI
+

LinkML Source

+ +

Direct

+
+
name: activity and behavior
+definition_uri: https://w3id.org/biolink/vocab/ActivityAndBehavior
+description: Activity or behavior of any independent integral living, organization
+  or mechanical actor in the world
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- UMLSSG:ACTI
+is_a: occurrent
+mixin: true
+class_uri: biolink:ActivityAndBehavior
+
+
+
+

Induced

+
+
name: activity and behavior
+definition_uri: https://w3id.org/biolink/vocab/ActivityAndBehavior
+description: Activity or behavior of any independent integral living, organization
+  or mechanical actor in the world
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- UMLSSG:ACTI
+is_a: occurrent
+mixin: true
+class_uri: biolink:ActivityAndBehavior
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/AgeAtDeathReferencePoint/index.html b/AgeAtDeathReferencePoint/index.html new file mode 100644 index 00000000..7d8052fa --- /dev/null +++ b/AgeAtDeathReferencePoint/index.html @@ -0,0 +1,688 @@ + + + + + + + + + + + + + + + + + + + Enum: AgeAtDeathReferencePoint - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
+
+ + + +
+
+
+ + + + + +
+
+
+ + + +
+
+
+ + + +
+
+
+ + + +
+
+ + + + + + + +

Enum: AgeAtDeathReferencePoint

+

URI: AgeAtDeathReferencePoint

+

Permissible Values

+ + + + + + + + + + + + + + + + + + + + +
ValueMeaningDescription
birthNIMP:PD-RARAGG39birth
conceptionNIMP:PD-RARAGG39conception
+

Slots

+ + + + + + + + + + + + + +
NameDescription
age_at_death_reference_pointThe reference point for an age interval; for example, birth or conception
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:3bed1f94-9d82-4ed7-afdf-79d896b24dbb
nativebican:age_at_death_reference_point
exactNIMP:PD-RARAGG39
+

LinkML Source

+
+ +
name: age_at_death_reference_point
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+rank: 1000
+permissible_values:
+  birth:
+    text: birth
+    description: birth
+    meaning: NIMP:PD-RARAGG39
+  conception:
+    text: conception
+    description: conception
+    meaning: NIMP:PD-RARAGG39
+
+
+ +
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/AgeAtDeathUnit/index.html b/AgeAtDeathUnit/index.html new file mode 100644 index 00000000..919ccd3f --- /dev/null +++ b/AgeAtDeathUnit/index.html @@ -0,0 +1,697 @@ + + + + + + + + + + + + + + + + + + + Enum: AgeAtDeathUnit - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
+
+ + + +
+
+
+ + + + + +
+
+
+ + + +
+
+
+ + + +
+
+
+ + + +
+
+ + + + + + + +

Enum: AgeAtDeathUnit

+

URI: AgeAtDeathUnit

+

Permissible Values

+ + + + + + + + + + + + + + + + + + + + + + + + + +
ValueMeaningDescription
daysNIMP:PD-AVAVEV39days
monthsNIMP:PD-AVAVEV39months
yearsNIMP:PD-AVAVEV39years
+

Slots

+ + + + + + + + + + + + + +
NameDescription
age_at_death_unitThe unit used for representing the donor age from the reference point
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:b5436e99-f0a7-4c30-825d-56b88ee2ac1d
nativebican:age_at_death_unit
exactNIMP:PD-AVAVEV39
+

LinkML Source

+
+ +
name: age_at_death_unit
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+rank: 1000
+permissible_values:
+  days:
+    text: days
+    description: days
+    meaning: NIMP:PD-AVAVEV39
+  months:
+    text: months
+    description: months
+    meaning: NIMP:PD-AVAVEV39
+  years:
+    text: years
+    description: years
+    meaning: NIMP:PD-AVAVEV39
+
+
+ +
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/Alignment/index.html b/Alignment/index.html new file mode 100644 index 00000000..81b9d1fd --- /dev/null +++ b/Alignment/index.html @@ -0,0 +1,574 @@ + + + + + + + + + + + + + + + + + + + Subset: Alignment - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
+
+ + + +
+
+
+ + + + + +
+
+
+ + + +
+
+
+ + + +
+
+
+ + + +
+
+ + + + + + + +

Subset: Alignment

+

A subset of slots/attributes that are required for alignment.

+

URI: Alignment

+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/AmplifiedCdna/index.html b/AmplifiedCdna/index.html new file mode 100644 index 00000000..ed73cfa6 --- /dev/null +++ b/AmplifiedCdna/index.html @@ -0,0 +1,1354 @@ + + + + + + + + + +Class: AmplifiedCdna - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: AmplifiedCdna

+

A collection of cDNA molecules derived and amplified from an input barcoded cell sample. These cDNA molecules represent the gene expression of each cell, with all cDNA molecules from a given cell retaining that cell's unique barcode from the cell barcoding step. This is a necessary step for GEX methods but is not used for ATAC methods.

+

URI: bican:AmplifiedCdna

+
classDiagram + class AmplifiedCdna + click AmplifiedCdna href "../AmplifiedCdna" + ProvEntity <|-- AmplifiedCdna + click ProvEntity href "../ProvEntity" + MaterialSample <|-- AmplifiedCdna + click MaterialSample href "../MaterialSample" + + AmplifiedCdna : category + + AmplifiedCdna : deprecated + + AmplifiedCdna : description + + AmplifiedCdna : full_name + + AmplifiedCdna : has_attribute + + + + + AmplifiedCdna --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + AmplifiedCdna : id + + AmplifiedCdna : iri + + AmplifiedCdna : name + + AmplifiedCdna : pass_fail_result + + + + + AmplifiedCdna --> "0..1" AmplifiedCdnaRnaAmplificationPassFail : pass_fail_result + click AmplifiedCdnaRnaAmplificationPassFail href "../AmplifiedCdnaRnaAmplificationPassFail" + + + AmplifiedCdna : percent_cdna_longer_than_400bp + + AmplifiedCdna : provided_by + + AmplifiedCdna : quantity_ng + + AmplifiedCdna : synonym + + AmplifiedCdna : type + + AmplifiedCdna : was_derived_from + + + + + AmplifiedCdna --> "0..1" BarcodedCellSample : was_derived_from + click BarcodedCellSample href "../BarcodedCellSample" + + + AmplifiedCdna : was_generated_by + + + + + AmplifiedCdna --> "0..1" CdnaAmplification : was_generated_by + click CdnaAmplification href "../CdnaAmplification" + + + AmplifiedCdna : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
was_generated_by0..1
CdnaAmplification		The cDNA amplification process from which the amplified cDNA was generated bydirect
was_derived_from0..1
BarcodedCellSample		The input barcoded cell sample from which amplified cDNA was derived fromdirect
name0..1
LabelType		Name of a collection of cDNA molecules derived and amplified from an input ba...direct
quantity_ng0..1
Float		Amount of cDNA produced after cDNA amplification measured in nanogramsdirect
pass_fail_result0..1
AmplifiedCdnaRnaAmplificationPassFail		Pass or Fail result based on qualitative assessment of cDNA yield and sizedirect
percent_cdna_longer_than_400bp0..1
Float		QC metric to measure mRNA degradation of cDNAdirect
id1
String		A unique identifier for an entityNamedThing, MaterialSample, PhysicalEntity, Entity
iri0..1
IriType		An IRI for an entityNamedThing, MaterialSample, PhysicalEntity, Entity
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizedNamedThing, MaterialSample, PhysicalEntity, Entity
type*
String		NamedThing, MaterialSample, PhysicalEntity, Entity
description0..1
NarrativeText		a human-readable description of an entityNamedThing, MaterialSample, PhysicalEntity, Entity
has_attribute*
Attribute		connects any entity to an attributeNamedThing, MaterialSample, PhysicalEntity, Entity
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...NamedThing, MaterialSample, PhysicalEntity, Entity
provided_by*
String		The value in this node property represents the knowledge provider that create...NamedThing, MaterialSample, PhysicalEntity
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...NamedThing, MaterialSample, PhysicalEntity
full_name0..1
LabelType		a long-form human readable name for a thingNamedThing, MaterialSample, PhysicalEntity
synonym*
LabelType		Alternate human-readable names for a thingNamedThing, MaterialSample, PhysicalEntity
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
Librarywas_derived_fromany_of[range]AmplifiedCdna
LibraryConstructionusedany_of[range]AmplifiedCdna
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:AmplifiedCdna
nativebican:AmplifiedCdna
exactNIMP:Amplified%20cDNA
+

LinkML Source

+ +

Direct

+
+
name: AmplifiedCdna
+description: A collection of cDNA molecules derived and amplified from an input barcoded
+  cell sample. These cDNA molecules represent the gene expression of each cell, with
+  all cDNA molecules from a given cell retaining that cell's unique barcode from the
+  cell barcoding step. This is a necessary step for GEX methods but is not used for
+  ATAC methods.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Amplified%20cDNA
+is_a: material sample
+mixins:
+- ProvEntity
+slots:
+- was_generated_by
+- was_derived_from
+- name
+slot_usage:
+  was_generated_by:
+    name: was_generated_by
+    description: The cDNA amplification process from which the amplified cDNA was
+      generated by.
+    range: CdnaAmplification
+  was_derived_from:
+    name: was_derived_from
+    description: The input barcoded cell sample from which amplified cDNA was derived
+      from.
+    exact_mappings:
+    - NIMP:has_parent
+    range: BarcodedCellSample
+  name:
+    name: name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: amplified_cdna_local_name
+    description: Name of a collection of cDNA molecules derived and amplified from
+      an input barcoded_cell_sample.  These cDNA molecules represent the gene expression
+      of each cell, with all cDNA molecules from a given cell retaining that cell's
+      unique barcode from the cell barcoding step.  This is a necessary step for GEX
+      methods but is not used for ATAC methods.
+    exact_mappings:
+    - NIMP:PD-YAAGGG39
+    slot_uri: bican:e2606a11-114e-472f-9e05-33f9b6fc3089
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  quantity_ng:
+    name: quantity_ng
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: amplified_cdna_amplified_quantity_ng
+    description: Amount of cDNA produced after cDNA amplification measured in nanograms.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-TITIIC26
+    rank: 1000
+    slot_uri: bican:0db79d05-8612-4896-b9d3-eb1558841449
+    alias: amplified cDNA amplified quantity ng
+    domain_of:
+    - AmplifiedCdna
+    - Library
+    range: float
+  pass_fail_result:
+    name: pass_fail_result
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: amplified_cdna_rna_amplification_pass_fail
+    description: Pass or Fail result based on qualitative assessment of cDNA yield
+      and size.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-XXXXFQ31
+    rank: 1000
+    slot_uri: bican:bc62bdb2-7dc8-4404-bb84-ce0bbcae59e5
+    alias: amplified cDNA RNA amplification pass-fail
+    domain_of:
+    - AmplifiedCdna
+    - Library
+    range: amplified_cdna_rna_amplification_pass_fail
+  percent_cdna_longer_than_400bp:
+    name: percent_cdna_longer_than_400bp
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: amplified_cdna_percent_cdna_longer_than_400bp
+    description: QC metric to measure mRNA degradation of cDNA.  Higher % is higher
+      quality starting material.  Over 400bp is used as a universal cutoff for intact
+      (full length) vs degraded cDNA and is a common output from Bioanalyzer and Fragment
+      Analyzer elecropheragrams.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-JJJJWD35
+    rank: 1000
+    slot_uri: bican:8d150467-f69e-461c-b54c-bcfd22f581e5
+    alias: amplified cDNA percent cDNA longer than 400bp
+    domain_of:
+    - AmplifiedCdna
+    range: float
+
+
+
+

Induced

+
+
name: AmplifiedCdna
+description: A collection of cDNA molecules derived and amplified from an input barcoded
+  cell sample. These cDNA molecules represent the gene expression of each cell, with
+  all cDNA molecules from a given cell retaining that cell's unique barcode from the
+  cell barcoding step. This is a necessary step for GEX methods but is not used for
+  ATAC methods.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Amplified%20cDNA
+is_a: material sample
+mixins:
+- ProvEntity
+slot_usage:
+  was_generated_by:
+    name: was_generated_by
+    description: The cDNA amplification process from which the amplified cDNA was
+      generated by.
+    range: CdnaAmplification
+  was_derived_from:
+    name: was_derived_from
+    description: The input barcoded cell sample from which amplified cDNA was derived
+      from.
+    exact_mappings:
+    - NIMP:has_parent
+    range: BarcodedCellSample
+  name:
+    name: name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: amplified_cdna_local_name
+    description: Name of a collection of cDNA molecules derived and amplified from
+      an input barcoded_cell_sample.  These cDNA molecules represent the gene expression
+      of each cell, with all cDNA molecules from a given cell retaining that cell's
+      unique barcode from the cell barcoding step.  This is a necessary step for GEX
+      methods but is not used for ATAC methods.
+    exact_mappings:
+    - NIMP:PD-YAAGGG39
+    slot_uri: bican:e2606a11-114e-472f-9e05-33f9b6fc3089
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  quantity_ng:
+    name: quantity_ng
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: amplified_cdna_amplified_quantity_ng
+    description: Amount of cDNA produced after cDNA amplification measured in nanograms.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-TITIIC26
+    rank: 1000
+    slot_uri: bican:0db79d05-8612-4896-b9d3-eb1558841449
+    alias: amplified cDNA amplified quantity ng
+    owner: AmplifiedCdna
+    domain_of:
+    - AmplifiedCdna
+    - Library
+    range: float
+  pass_fail_result:
+    name: pass_fail_result
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: amplified_cdna_rna_amplification_pass_fail
+    description: Pass or Fail result based on qualitative assessment of cDNA yield
+      and size.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-XXXXFQ31
+    rank: 1000
+    slot_uri: bican:bc62bdb2-7dc8-4404-bb84-ce0bbcae59e5
+    alias: amplified cDNA RNA amplification pass-fail
+    owner: AmplifiedCdna
+    domain_of:
+    - AmplifiedCdna
+    - Library
+    range: amplified_cdna_rna_amplification_pass_fail
+  percent_cdna_longer_than_400bp:
+    name: percent_cdna_longer_than_400bp
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: amplified_cdna_percent_cdna_longer_than_400bp
+    description: QC metric to measure mRNA degradation of cDNA.  Higher % is higher
+      quality starting material.  Over 400bp is used as a universal cutoff for intact
+      (full length) vs degraded cDNA and is a common output from Bioanalyzer and Fragment
+      Analyzer elecropheragrams.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-JJJJWD35
+    rank: 1000
+    slot_uri: bican:8d150467-f69e-461c-b54c-bcfd22f581e5
+    alias: amplified cDNA percent cDNA longer than 400bp
+    owner: AmplifiedCdna
+    domain_of:
+    - AmplifiedCdna
+    range: float
+  was_generated_by:
+    name: was_generated_by
+    description: The cDNA amplification process from which the amplified cDNA was
+      generated by.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: was_generated_by
+    owner: AmplifiedCdna
+    domain_of:
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryPool
+    - DissectionRoiPolygon
+    - ProvEntity
+    range: CdnaAmplification
+  was_derived_from:
+    name: was_derived_from
+    description: The input barcoded cell sample from which amplified cDNA was derived
+      from.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:has_parent
+    rank: 1000
+    alias: was_derived_from
+    owner: AmplifiedCdna
+    domain_of:
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DigitalAsset
+    - ProvEntity
+    range: BarcodedCellSample
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: amplified_cdna_local_name
+    description: Name of a collection of cDNA molecules derived and amplified from
+      an input barcoded_cell_sample.  These cDNA molecules represent the gene expression
+      of each cell, with all cDNA molecules from a given cell retaining that cell's
+      unique barcode from the cell barcoding step.  This is a necessary step for GEX
+      methods but is not used for ATAC methods.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - NIMP:PD-YAAGGG39
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: bican:e2606a11-114e-472f-9e05-33f9b6fc3089
+    alias: name
+    owner: AmplifiedCdna
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - Donor
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DissectionRoiPolygon
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: AmplifiedCdna
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: AmplifiedCdna
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: AmplifiedCdna
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+    pattern: ^bican:[A-Z][A-Za-z]+$
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: AmplifiedCdna
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: AmplifiedCdna
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: AmplifiedCdna
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: AmplifiedCdna
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: AmplifiedCdna
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: AmplifiedCdna
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: AmplifiedCdna
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: AmplifiedCdna
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/AmplifiedCdnaRnaAmplificationPassFail/index.html b/AmplifiedCdnaRnaAmplificationPassFail/index.html new file mode 100644 index 00000000..d4ebddfb --- /dev/null +++ b/AmplifiedCdnaRnaAmplificationPassFail/index.html @@ -0,0 +1,674 @@ + + + + + + + + + + + + + + + + + + + Enum: AmplifiedCdnaRnaAmplificationPassFail - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
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+ + + +
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+ + + + + +
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+ + + +
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+ + + +
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+ + + + + + + +

Enum: AmplifiedCdnaRnaAmplificationPassFail

+

URI: AmplifiedCdnaRnaAmplificationPassFail

+

Permissible Values

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ValueMeaningDescription
PassNIMP:PD-XXXXFQ31The RNA amplification passed the QA/QC
FailNIMP:PD-XXXXFQ31The RNA amplification failed the QA/QC
Low QCNIMP:PD-XXXXFQ31The RNA amplification low passed the QA/QC
Not evaluatedNIMP:PD-XXXXFQ31Library Prep not evaluated for QA/QC
+

Slots

+ + + + + + + + + + + + + +
NameDescription
pass_fail_resultPass or Fail result based on qualitative assessment of cDNA yield and size
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

LinkML Source

+
+ +
name: amplified_cdna_rna_amplification_pass_fail
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+rank: 1000
+permissible_values:
+  Pass:
+    text: Pass
+    description: The RNA amplification passed the QA/QC
+    meaning: NIMP:PD-XXXXFQ31
+  Fail:
+    text: Fail
+    description: The RNA amplification failed the QA/QC
+    meaning: NIMP:PD-XXXXFQ31
+  Low QC:
+    text: Low QC
+    description: The RNA amplification low passed the QA/QC
+    meaning: NIMP:PD-XXXXFQ31
+  Not evaluated:
+    text: Not evaluated
+    description: Library Prep not evaluated for QA/QC
+    meaning: NIMP:PD-XXXXFQ31
+
+
+ +
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/Analysis/index.html b/Analysis/index.html new file mode 100644 index 00000000..a56cd99e --- /dev/null +++ b/Analysis/index.html @@ -0,0 +1,654 @@ + + + + + + + + + + + + + + + + + + + Subset: Analysis - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
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+ + + + + + + +

Subset: Analysis

+

A subset of slots/attributes that are required for analysis.

+

URI: Analysis

+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Slots in subset

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
SlotDescription
average_size_bpAverage size of the library in terms of base pairs
cell_prep_typeThe type of cell preparation
enrichment_populationActual percentage of cells as a result of using set of fluorescent marker lab...
input_quantityNumber of enriched or dissociated cells/nuclei going into the barcoding proce...
input_quantity_ngAmount of cDNA going into library construction in nanograms
local_tube_idLibrary Pool Tube local name
number_of_expected_cellsExpected number of cells/nuclei of a barcoded_cell_sample that will be barcod...
pass_fail_resultPass or Fail result based on qualitative assessment of cDNA yield and size
pcr_cyclesNumber of PCR cycles used during cDNA amplification for this cDNA
percent_cdna_longer_than_400bpQC metric to measure mRNA degradation of cDNA
port_wellSpecific position of the loaded port of the 10x chip
quantity_fmolAmount of library generated in terms of femtomoles
quantity_ngAmount of cDNA produced after cDNA amplification measured in nanograms
r1_r2_indexName of the pair of library indexes used for sequencing
setcDNA amplification set, containing multiple amplified_cDNA_names that were pr...
+ + + + + + + + + + + + + +
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+ + + + + +
+ +
+ + + +
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+ + + + + + + + + + \ No newline at end of file diff --git a/AnatomicalAnnotationSet/index.html b/AnatomicalAnnotationSet/index.html new file mode 100644 index 00000000..c9f4acfb --- /dev/null +++ b/AnatomicalAnnotationSet/index.html @@ -0,0 +1,610 @@ + + + + + + + + + +Class: AnatomicalAnnotationSet - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
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+ +
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+ +
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+ +
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+

Class: AnatomicalAnnotationSet

+

An anatomical annotation set is a versioned release of a set of anatomical annotations anchored in the same anatomical space that divides the space into distinct segments following some annotation criteria or parcellation scheme. For example, the anatomical annotation set of 3D image based reference atlases (e.g. Allen Mouse CCF) can be expressed as a set of label indices of single multi-valued image annotations or as a set of segmentation masks (ref: ILX:0777108, RRID:SCR_023499)

+

URI: AnS:AnatomicalAnnotationSet

+
classDiagram + class AnatomicalAnnotationSet + click AnatomicalAnnotationSet href "../AnatomicalAnnotationSet" + VersionedNamedThing <|-- AnatomicalAnnotationSet + click VersionedNamedThing href "../VersionedNamedThing" + + AnatomicalAnnotationSet : category + + AnatomicalAnnotationSet : description + + AnatomicalAnnotationSet : id + + AnatomicalAnnotationSet : name + + AnatomicalAnnotationSet : parameterizes + + AnatomicalAnnotationSet : revision_of + + + + + AnatomicalAnnotationSet --> "0..1" VersionedNamedThing : revision_of + click VersionedNamedThing href "../VersionedNamedThing" + + + AnatomicalAnnotationSet : version + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
parameterizes1
String or 
AnatomicalSpace or 
String		Reference to the anatomical space for which the anatomical annotation set is ...direct
version1
String		VersionedNamedThing
revision_of0..1
VersionedNamedThing or 
AnatomicalAnnotationSet or 
String		VersionedNamedThing
id1
Uriorcurie		NamedThing
name1
String		NamedThing
description1
String		NamedThing
category*
Uriorcurie		NamedThing
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
AnatomicalAnnotationSetrevision_ofany_of[range]AnatomicalAnnotationSet
ParcellationAnnotationpart_of_anatomical_annotation_setany_of[range]AnatomicalAnnotationSet
ParcellationAtlashas_anatomical_annotation_setany_of[range]AnatomicalAnnotationSet
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/my-org/anatomical-structure-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfAnS:AnatomicalAnnotationSet
nativeAnS:AnatomicalAnnotationSet
+

LinkML Source

+ +

Direct

+
+
name: AnatomicalAnnotationSet
+description: 'An anatomical annotation set is a versioned release of a set of anatomical
+  annotations anchored  in the same anatomical space that divides the space into distinct
+  segments following some annotation  criteria or parcellation scheme. For example,
+  the anatomical annotation set of 3D image based  reference atlases (e.g. Allen Mouse
+  CCF) can be expressed as a set of label indices of single  multi-valued image annotations
+  or as a set of segmentation masks (ref: ILX:0777108, RRID:SCR_023499)'
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: VersionedNamedThing
+slot_usage:
+  revision_of:
+    name: revision_of
+    any_of:
+    - range: AnatomicalAnnotationSet
+    - range: string
+attributes:
+  parameterizes:
+    name: parameterizes
+    description: Reference to the anatomical space for which the anatomical annotation
+      set is anchored
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - AnatomicalAnnotationSet
+    required: true
+    any_of:
+    - range: AnatomicalSpace
+    - range: string
+
+
+
+

Induced

+
+
name: AnatomicalAnnotationSet
+description: 'An anatomical annotation set is a versioned release of a set of anatomical
+  annotations anchored  in the same anatomical space that divides the space into distinct
+  segments following some annotation  criteria or parcellation scheme. For example,
+  the anatomical annotation set of 3D image based  reference atlases (e.g. Allen Mouse
+  CCF) can be expressed as a set of label indices of single  multi-valued image annotations
+  or as a set of segmentation masks (ref: ILX:0777108, RRID:SCR_023499)'
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: VersionedNamedThing
+slot_usage:
+  revision_of:
+    name: revision_of
+    any_of:
+    - range: AnatomicalAnnotationSet
+    - range: string
+attributes:
+  parameterizes:
+    name: parameterizes
+    description: Reference to the anatomical space for which the anatomical annotation
+      set is anchored
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: parameterizes
+    owner: AnatomicalAnnotationSet
+    domain_of:
+    - AnatomicalAnnotationSet
+    range: string
+    required: true
+    any_of:
+    - range: AnatomicalSpace
+    - range: string
+  version:
+    name: version
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: version
+    owner: AnatomicalAnnotationSet
+    domain_of:
+    - VersionedNamedThing
+    range: string
+    required: true
+  revision_of:
+    name: revision_of
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: revision_of
+    owner: AnatomicalAnnotationSet
+    domain_of:
+    - VersionedNamedThing
+    range: VersionedNamedThing
+    any_of:
+    - range: AnatomicalAnnotationSet
+    - range: string
+  id:
+    name: id
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    identifier: true
+    alias: id
+    owner: AnatomicalAnnotationSet
+    domain_of:
+    - NamedThing
+    range: uriorcurie
+    required: true
+  name:
+    name: name
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: name
+    owner: AnatomicalAnnotationSet
+    domain_of:
+    - NamedThing
+    range: string
+    required: true
+  description:
+    name: description
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: description
+    owner: AnatomicalAnnotationSet
+    domain_of:
+    - NamedThing
+    range: string
+    required: true
+  category:
+    name: category
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    designates_type: true
+    alias: category
+    owner: AnatomicalAnnotationSet
+    domain_of:
+    - NamedThing
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/AnatomicalSpace/index.html b/AnatomicalSpace/index.html new file mode 100644 index 00000000..afab5863 --- /dev/null +++ b/AnatomicalSpace/index.html @@ -0,0 +1,608 @@ + + + + + + + + + +Class: AnatomicalSpace - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
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+ +
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+ +
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+ +
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+

Class: AnatomicalSpace

+

An anatomical space is versioned release of a mathematical space with a defined mapping between the anatomical axes and the mathematical axes. An anatomical space may be defined by a reference image chosen as the biological reference for an anatomical structure of interest derived from a single or multiple specimens (ref: ILX:0777106, RRID:SCR_023499)

+

URI: AnS:AnatomicalSpace

+
classDiagram + class AnatomicalSpace + click AnatomicalSpace href "../AnatomicalSpace" + VersionedNamedThing <|-- AnatomicalSpace + click VersionedNamedThing href "../VersionedNamedThing" + + AnatomicalSpace : category + + AnatomicalSpace : description + + AnatomicalSpace : id + + AnatomicalSpace : measures + + AnatomicalSpace : name + + AnatomicalSpace : revision_of + + + + + AnatomicalSpace --> "0..1" VersionedNamedThing : revision_of + click VersionedNamedThing href "../VersionedNamedThing" + + + AnatomicalSpace : version + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
measures1
String or 
ImageDataset or 
String		Reference to the specific image dataset used to define the anatomical spacedirect
version1
String		VersionedNamedThing
revision_of0..1
VersionedNamedThing or 
AnatomicalSpace or 
String		VersionedNamedThing
id1
Uriorcurie		NamedThing
name1
String		NamedThing
description1
String		NamedThing
category*
Uriorcurie		NamedThing
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
AnatomicalSpacerevision_ofany_of[range]AnatomicalSpace
AnatomicalAnnotationSetparameterizesany_of[range]AnatomicalSpace
ParcellationAtlashas_anatomical_spaceany_of[range]AnatomicalSpace
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/my-org/anatomical-structure-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfAnS:AnatomicalSpace
nativeAnS:AnatomicalSpace
+

LinkML Source

+ +

Direct

+
+
name: AnatomicalSpace
+description: 'An anatomical space is versioned release of a mathematical space with
+  a defined mapping  between the anatomical axes and the mathematical axes. An anatomical
+  space may be defined by  a reference image chosen as the biological reference for
+  an anatomical structure of interest  derived from a single or multiple specimens
+  (ref: ILX:0777106, RRID:SCR_023499)'
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: VersionedNamedThing
+slot_usage:
+  revision_of:
+    name: revision_of
+    any_of:
+    - range: AnatomicalSpace
+    - range: string
+attributes:
+  measures:
+    name: measures
+    description: Reference to the specific image dataset used to define the anatomical
+      space.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - AnatomicalSpace
+    required: true
+    any_of:
+    - range: ImageDataset
+    - range: string
+
+
+
+

Induced

+
+
name: AnatomicalSpace
+description: 'An anatomical space is versioned release of a mathematical space with
+  a defined mapping  between the anatomical axes and the mathematical axes. An anatomical
+  space may be defined by  a reference image chosen as the biological reference for
+  an anatomical structure of interest  derived from a single or multiple specimens
+  (ref: ILX:0777106, RRID:SCR_023499)'
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: VersionedNamedThing
+slot_usage:
+  revision_of:
+    name: revision_of
+    any_of:
+    - range: AnatomicalSpace
+    - range: string
+attributes:
+  measures:
+    name: measures
+    description: Reference to the specific image dataset used to define the anatomical
+      space.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: measures
+    owner: AnatomicalSpace
+    domain_of:
+    - AnatomicalSpace
+    range: string
+    required: true
+    any_of:
+    - range: ImageDataset
+    - range: string
+  version:
+    name: version
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: version
+    owner: AnatomicalSpace
+    domain_of:
+    - VersionedNamedThing
+    range: string
+    required: true
+  revision_of:
+    name: revision_of
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: revision_of
+    owner: AnatomicalSpace
+    domain_of:
+    - VersionedNamedThing
+    range: VersionedNamedThing
+    any_of:
+    - range: AnatomicalSpace
+    - range: string
+  id:
+    name: id
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    identifier: true
+    alias: id
+    owner: AnatomicalSpace
+    domain_of:
+    - NamedThing
+    range: uriorcurie
+    required: true
+  name:
+    name: name
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: name
+    owner: AnatomicalSpace
+    domain_of:
+    - NamedThing
+    range: string
+    required: true
+  description:
+    name: description
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: description
+    owner: AnatomicalSpace
+    domain_of:
+    - NamedThing
+    range: string
+    required: true
+  category:
+    name: category
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    designates_type: true
+    alias: category
+    owner: AnatomicalSpace
+    domain_of:
+    - NamedThing
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/Annotation/index.html b/Annotation/index.html new file mode 100644 index 00000000..a009c65a --- /dev/null +++ b/Annotation/index.html @@ -0,0 +1,403 @@ + + + + + + + + + +Class: Annotation - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
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+ +
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+ +
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+
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+ +
+
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+
+
+

Class: Annotation

+

Biolink Model root class for entity annotations.

+
    +
  • NOTE: this is an abstract class and should not be instantiated directly
    • +
+

URI: biolink:Annotation

+
classDiagram + class Annotation + click Annotation href "../Annotation" + Annotation <|-- QuantityValue + click QuantityValue href "../QuantityValue" + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:Annotation
nativebican:Annotation
+

LinkML Source

+ +

Direct

+
+
name: annotation
+definition_uri: https://w3id.org/biolink/vocab/Annotation
+description: Biolink Model root class for entity annotations.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+abstract: true
+class_uri: biolink:Annotation
+
+
+
+

Induced

+
+
name: annotation
+definition_uri: https://w3id.org/biolink/vocab/Annotation
+description: Biolink Model root class for entity annotations.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+abstract: true
+class_uri: biolink:Annotation
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/AnnotationCollection/index.html b/AnnotationCollection/index.html new file mode 100644 index 00000000..8e364da6 --- /dev/null +++ b/AnnotationCollection/index.html @@ -0,0 +1,484 @@ + + + + + + + + + +Class: AnnotationCollection - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
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+ +
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+ +
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+
+ +
+
+
+
+
+

Class: AnnotationCollection

+

URI: bican:AnnotationCollection

+
classDiagram + class AnnotationCollection + click AnnotationCollection href "../AnnotationCollection" + AnnotationCollection : annotations + + + + + AnnotationCollection --> "*" GeneAnnotation : annotations + click GeneAnnotation href "../GeneAnnotation" + + + AnnotationCollection : genome_annotations + + + + + AnnotationCollection --> "*" GenomeAnnotation : genome_annotations + click GenomeAnnotation href "../GenomeAnnotation" + + + AnnotationCollection : genome_assemblies + + + + + AnnotationCollection --> "*" GenomeAssembly : genome_assemblies + click GenomeAssembly href "../GenomeAssembly" + + + +
+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
annotations*
GeneAnnotation		direct
genome_annotations*
GenomeAnnotation		direct
genome_assemblies*
GenomeAssembly		direct
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:AnnotationCollection
nativebican:AnnotationCollection
+

LinkML Source

+ +

Direct

+
+
name: annotation collection
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+attributes:
+  annotations:
+    name: annotations
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    domain_of:
+    - annotation collection
+    range: gene annotation
+    multivalued: true
+    inlined: true
+    inlined_as_list: true
+  genome_annotations:
+    name: genome_annotations
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    domain_of:
+    - annotation collection
+    range: genome annotation
+    multivalued: true
+    inlined: true
+    inlined_as_list: true
+  genome_assemblies:
+    name: genome_assemblies
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    domain_of:
+    - annotation collection
+    range: genome assembly
+    multivalued: true
+    inlined: true
+    inlined_as_list: true
+tree_root: true
+
+
+
+

Induced

+
+
name: annotation collection
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+attributes:
+  annotations:
+    name: annotations
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    alias: annotations
+    owner: annotation collection
+    domain_of:
+    - annotation collection
+    range: gene annotation
+    multivalued: true
+    inlined: true
+    inlined_as_list: true
+  genome_annotations:
+    name: genome_annotations
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    alias: genome_annotations
+    owner: annotation collection
+    domain_of:
+    - annotation collection
+    range: genome annotation
+    multivalued: true
+    inlined: true
+    inlined_as_list: true
+  genome_assemblies:
+    name: genome_assemblies
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    alias: genome_assemblies
+    owner: annotation collection
+    domain_of:
+    - annotation collection
+    range: genome assembly
+    multivalued: true
+    inlined: true
+    inlined_as_list: true
+tree_root: true
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/Attribute/index.html b/Attribute/index.html new file mode 100644 index 00000000..5ff734c4 --- /dev/null +++ b/Attribute/index.html @@ -0,0 +1,1362 @@ + + + + + + + + + +Class: Attribute - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: Attribute

+

A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material.

+

URI: biolink:Attribute

+
classDiagram + class Attribute + click Attribute href "../Attribute" + OntologyClass <|-- Attribute + click OntologyClass href "../OntologyClass" + NamedThing <|-- Attribute + click NamedThing href "../NamedThing" + + Attribute : attribute_name + + Attribute : category + + Attribute : deprecated + + Attribute : description + + Attribute : full_name + + Attribute : has_attribute + + + + + Attribute --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + Attribute : has_attribute_type + + + + + Attribute --> "1" OntologyClass : has_attribute_type + click OntologyClass href "../OntologyClass" + + + Attribute : has_qualitative_value + + + + + Attribute --> "0..1" NamedThing : has_qualitative_value + click NamedThing href "../NamedThing" + + + Attribute : has_quantitative_value + + + + + Attribute --> "*" QuantityValue : has_quantitative_value + click QuantityValue href "../QuantityValue" + + + Attribute : id + + Attribute : iri + + Attribute : name + + Attribute : provided_by + + Attribute : synonym + + Attribute : type + + Attribute : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
id1
String		A unique identifier for an entitydirect
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizeddirect
type*
String		direct
description0..1
NarrativeText		a human-readable description of an entitydirect
has_attribute*
Attribute		connects any entity to an attributedirect
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...direct
provided_by*
String		The value in this node property represents the knowledge provider that create...direct
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...direct
full_name0..1
LabelType		a long-form human readable name for a thingdirect
synonym*
LabelType		Alternate human-readable names for a thingdirect
attribute_name0..1
LabelType		The human-readable 'attribute name' can be set to a string which reflects its...direct
has_attribute_type1
OntologyClass		connects an attribute to a class that describes itdirect
has_quantitative_value*
QuantityValue		connects an attribute to a valuedirect
has_qualitative_value0..1
NamedThing		connects an attribute to a valuedirect
iri0..1
IriType		An IRI for an entitydirect
name0..1
LabelType		The human-readable 'attribute name' can be set to a string which reflects its...NamedThing, Entity, Attribute
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
GeneAnnotationhas_attributerangeAttribute
GenomeAnnotationhas_attributerangeAttribute
GenomeAssemblyhas_attributerangeAttribute
Attributehas_attributerangeAttribute
Attributeattribute_namedomainAttribute
Attributehas_attribute_typedomainAttribute
Attributehas_quantitative_valuedomainAttribute
Attributehas_qualitative_valuedomainAttribute
Entityhas_attributerangeAttribute
NamedThinghas_attributerangeAttribute
OrganismTaxonhas_attributerangeAttribute
InformationContentEntityhas_attributerangeAttribute
Datasethas_attributerangeAttribute
PhysicalEntityhas_attributerangeAttribute
Activityhas_attributerangeAttribute
Procedurehas_attributerangeAttribute
MaterialSamplehas_attributerangeAttribute
BiologicalEntityhas_attributerangeAttribute
Genehas_attributerangeAttribute
Genomehas_attributerangeAttribute
Checksumhas_attributerangeAttribute
+

Identifier and Mapping Information

+

Valid ID Prefixes

+

Instances of this class should have identifiers with one of the following prefixes:

+
    +
  • +

    EDAM-DATA

    +
    • +
  • +

    EDAM-FORMAT

    +
    • +
  • +

    EDAM-OPERATION

    +
    • +
  • +

    EDAM-TOPIC

    +
    • +
+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:Attribute
nativebican:Attribute
exactSIO:000614
+

LinkML Source

+ +

Direct

+
+
name: attribute
+id_prefixes:
+- EDAM-DATA
+- EDAM-FORMAT
+- EDAM-OPERATION
+- EDAM-TOPIC
+definition_uri: https://w3id.org/biolink/vocab/Attribute
+description: A property or characteristic of an entity. For example, an apple may
+  have properties such as color, shape, age, crispiness. An environmental sample may
+  have attributes such as depth, lat, long, material.
+in_subset:
+- samples
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- SIO:000614
+is_a: named thing
+mixins:
+- ontology class
+slots:
+- id
+- category
+- type
+- description
+- has attribute
+- deprecated
+- provided by
+- xref
+- full name
+- synonym
+- attribute_name
+- has attribute type
+- has quantitative value
+- has qualitative value
+- iri
+slot_usage:
+  name:
+    name: name
+    description: The human-readable 'attribute name' can be set to a string which
+      reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence
+      annotation or it can default to the name associated with the 'has attribute
+      type' slot ontology term.
+class_uri: biolink:Attribute
+
+
+
+

Induced

+
+
name: attribute
+id_prefixes:
+- EDAM-DATA
+- EDAM-FORMAT
+- EDAM-OPERATION
+- EDAM-TOPIC
+definition_uri: https://w3id.org/biolink/vocab/Attribute
+description: A property or characteristic of an entity. For example, an apple may
+  have properties such as color, shape, age, crispiness. An environmental sample may
+  have attributes such as depth, lat, long, material.
+in_subset:
+- samples
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- SIO:000614
+is_a: named thing
+mixins:
+- ontology class
+slot_usage:
+  name:
+    name: name
+    description: The human-readable 'attribute name' can be set to a string which
+      reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence
+      annotation or it can default to the name associated with the 'has attribute
+      type' slot ontology term.
+attributes:
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: attribute
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: attribute
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: attribute
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: attribute
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: attribute
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: attribute
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: attribute
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: attribute
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: attribute
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: attribute
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+  attribute_name:
+    name: attribute_name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: The human-readable 'attribute name' can be set to a string which
+      reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence
+      annotation or it can default to the name associated with the 'has attribute
+      type' slot ontology term.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    is_a: name
+    domain: attribute
+    slot_uri: rdfs:label
+    alias: name
+    owner: attribute
+    domain_of:
+    - attribute
+    is_usage_slot: true
+    usage_slot_name: name
+    range: label type
+  has attribute type:
+    name: has attribute type
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute_type
+    description: connects an attribute to a class that describes it
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    narrow_mappings:
+    - LOINC:has_modality_type
+    - LOINC:has_view_type
+    rank: 1000
+    domain: attribute
+    slot_uri: biolink:has_attribute_type
+    alias: has_attribute_type
+    owner: attribute
+    domain_of:
+    - attribute
+    range: ontology class
+    required: true
+    multivalued: false
+  has quantitative value:
+    name: has quantitative value
+    definition_uri: https://w3id.org/biolink/vocab/has_quantitative_value
+    description: connects an attribute to a value
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - qud:quantityValue
+    narrow_mappings:
+    - SNOMED:has_concentration_strength_numerator_value
+    - SNOMED:has_presentation_strength_denominator_value
+    - SNOMED:has_presentation_strength_numerator_value
+    rank: 1000
+    domain: attribute
+    slot_uri: biolink:has_quantitative_value
+    alias: has_quantitative_value
+    owner: attribute
+    domain_of:
+    - attribute
+    range: quantity value
+    multivalued: true
+    inlined: true
+  has qualitative value:
+    name: has qualitative value
+    definition_uri: https://w3id.org/biolink/vocab/has_qualitative_value
+    description: connects an attribute to a value
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    domain: attribute
+    slot_uri: biolink:has_qualitative_value
+    alias: has_qualitative_value
+    owner: attribute
+    domain_of:
+    - attribute
+    range: named thing
+    multivalued: false
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: attribute
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: The human-readable 'attribute name' can be set to a string which
+      reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence
+      annotation or it can default to the name associated with the 'has attribute
+      type' slot ontology term.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: attribute
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+class_uri: biolink:Attribute
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/AuthorityType/index.html b/AuthorityType/index.html new file mode 100644 index 00000000..2fb84d26 --- /dev/null +++ b/AuthorityType/index.html @@ -0,0 +1,652 @@ + + + + + + + + + + + + + + + + + + + Enum: AuthorityType - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
+
+ + + +
+
+
+ + + + + +
+
+
+ + + +
+
+
+ + + +
+
+
+ + + +
+
+ + + + + + + +

Enum: AuthorityType

+

URI: AuthorityType

+

Permissible Values

+ + + + + + + + + + + + + + + + + + + + +
ValueMeaningDescription
ENSEMBLNone
NCBINone
+

Slots

+ + + + + + + + + + + + + +
NameDescription
authorityThe organization responsible for publishing the data
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

LinkML Source

+
+ +
name: AuthorityType
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+rank: 1000
+permissible_values:
+  ENSEMBL:
+    text: ENSEMBL
+  NCBI:
+    text: NCBI
+
+
+ +
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/BarcodedCellSample/index.html b/BarcodedCellSample/index.html new file mode 100644 index 00000000..32d89e52 --- /dev/null +++ b/BarcodedCellSample/index.html @@ -0,0 +1,1269 @@ + + + + + + + + + +Class: BarcodedCellSample - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: BarcodedCellSample

+

A collection of molecularly barcoded cells. Input will be either dissociated cell sample or enriched cell sample. Cell barcodes are only guaranteed to be unique within this one collection. One dissociated cell sample or enriched cell sample can lead to multiple barcoded cell samples. The sequences of the molecular barcodes are revealed during alignment of the resulting fastq files for the barcoded cell sample. The barcoded cell sample name and the cell level molecular barcode together uniquely identify a single cell.

+

URI: bican:BarcodedCellSample

+
classDiagram + class BarcodedCellSample + click BarcodedCellSample href "../BarcodedCellSample" + ProvEntity <|-- BarcodedCellSample + click ProvEntity href "../ProvEntity" + MaterialSample <|-- BarcodedCellSample + click MaterialSample href "../MaterialSample" + + BarcodedCellSample : category + + BarcodedCellSample : deprecated + + BarcodedCellSample : description + + BarcodedCellSample : full_name + + BarcodedCellSample : has_attribute + + + + + BarcodedCellSample --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + BarcodedCellSample : id + + BarcodedCellSample : iri + + BarcodedCellSample : name + + BarcodedCellSample : number_of_expected_cells + + BarcodedCellSample : provided_by + + BarcodedCellSample : synonym + + BarcodedCellSample : type + + BarcodedCellSample : was_derived_from + + BarcodedCellSample : was_generated_by + + + + + BarcodedCellSample --> "0..1" CellBarcoding : was_generated_by + click CellBarcoding href "../CellBarcoding" + + + BarcodedCellSample : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
was_generated_by0..1
CellBarcoding		The barcoding process from which the barcoded cell sample is generated fromdirect
was_derived_from*
String or 
DissociatedCellSample or 
EnrichedCellSample		The input dissociated or enriched cell sample(s) from which the barcoded cell...direct
name0..1
LabelType		Name of a collection of barcoded cellsdirect
number_of_expected_cells0..1
Integer		Expected number of cells/nuclei of a barcoded_cell_sample that will be barcod...direct
id1
String		A unique identifier for an entityNamedThing, MaterialSample, PhysicalEntity, Entity
iri0..1
IriType		An IRI for an entityNamedThing, MaterialSample, PhysicalEntity, Entity
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizedNamedThing, MaterialSample, PhysicalEntity, Entity
type*
String		NamedThing, MaterialSample, PhysicalEntity, Entity
description0..1
NarrativeText		a human-readable description of an entityNamedThing, MaterialSample, PhysicalEntity, Entity
has_attribute*
Attribute		connects any entity to an attributeNamedThing, MaterialSample, PhysicalEntity, Entity
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...NamedThing, MaterialSample, PhysicalEntity, Entity
provided_by*
String		The value in this node property represents the knowledge provider that create...NamedThing, MaterialSample, PhysicalEntity
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...NamedThing, MaterialSample, PhysicalEntity
full_name0..1
LabelType		a long-form human readable name for a thingNamedThing, MaterialSample, PhysicalEntity
synonym*
LabelType		Alternate human-readable names for a thingNamedThing, MaterialSample, PhysicalEntity
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
AmplifiedCdnawas_derived_fromrangeBarcodedCellSample
Librarywas_derived_fromany_of[range]BarcodedCellSample
CdnaAmplificationusedrangeBarcodedCellSample
LibraryConstructionusedany_of[range]BarcodedCellSample
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:BarcodedCellSample
nativebican:BarcodedCellSample
exactNIMP:Barcoded%20Cell%20Sample
+

LinkML Source

+ +

Direct

+
+
name: BarcodedCellSample
+description: A collection of molecularly barcoded cells. Input will be either dissociated
+  cell sample or enriched cell sample. Cell barcodes are only guaranteed to be unique
+  within this one collection. One dissociated cell sample or enriched cell sample
+  can lead to multiple barcoded cell samples.  The sequences of the molecular barcodes
+  are revealed during alignment of the resulting fastq files for the barcoded cell
+  sample. The barcoded cell sample name and the cell level molecular barcode together
+  uniquely identify a single cell.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Barcoded%20Cell%20Sample
+is_a: material sample
+mixins:
+- ProvEntity
+slots:
+- was_generated_by
+- was_derived_from
+- name
+slot_usage:
+  was_generated_by:
+    name: was_generated_by
+    description: The barcoding process from which the barcoded cell sample is generated
+      from.
+    range: CellBarcoding
+  was_derived_from:
+    name: was_derived_from
+    description: The input dissociated or enriched cell sample(s) from which the barcoded
+      cell sample was derived from.
+    exact_mappings:
+    - NIMP:has_parent
+    multivalued: true
+    exactly_one_of:
+    - range: DissociatedCellSample
+    - range: EnrichedCellSample
+  name:
+    name: name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: barcoded_cell_sample_local_name
+    description: Name of a collection of barcoded cells.  Input will be either dissociated_cell_sample
+      or enriched_cell_sample.  Cell barcodes are only guaranteed to be unique within
+      this one collection. One dissociated_cell_sample or enriched_cell_sample can
+      lead to multiple barcoded_cell_samples.
+    exact_mappings:
+    - NIMP:PD-XEMDJF38
+    slot_uri: bican:4c0e6380-e53f-4173-a474-d41e836fefe3
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  number_of_expected_cells:
+    name: number_of_expected_cells
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: barcoded_cell_sample_number_of_expected_cells
+    description: Expected number of cells/nuclei of a barcoded_cell_sample that will
+      be barcoded and available for sequencing.  This is a derived number from 'Barcoded
+      cell input quantity count' that is dependent on the "capture rate" of the barcoding
+      method.  It is usually a calculated fraction of the 'Barcoded cell input quantity
+      count' going into the barcoding method.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-ONONEV39
+    rank: 1000
+    slot_uri: bican:f10e928d-5a2b-4943-af18-d8fe5d05528d
+    alias: expected cell capture
+    domain_of:
+    - BarcodedCellSample
+    range: integer
+
+
+
+

Induced

+
+
name: BarcodedCellSample
+description: A collection of molecularly barcoded cells. Input will be either dissociated
+  cell sample or enriched cell sample. Cell barcodes are only guaranteed to be unique
+  within this one collection. One dissociated cell sample or enriched cell sample
+  can lead to multiple barcoded cell samples.  The sequences of the molecular barcodes
+  are revealed during alignment of the resulting fastq files for the barcoded cell
+  sample. The barcoded cell sample name and the cell level molecular barcode together
+  uniquely identify a single cell.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Barcoded%20Cell%20Sample
+is_a: material sample
+mixins:
+- ProvEntity
+slot_usage:
+  was_generated_by:
+    name: was_generated_by
+    description: The barcoding process from which the barcoded cell sample is generated
+      from.
+    range: CellBarcoding
+  was_derived_from:
+    name: was_derived_from
+    description: The input dissociated or enriched cell sample(s) from which the barcoded
+      cell sample was derived from.
+    exact_mappings:
+    - NIMP:has_parent
+    multivalued: true
+    exactly_one_of:
+    - range: DissociatedCellSample
+    - range: EnrichedCellSample
+  name:
+    name: name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: barcoded_cell_sample_local_name
+    description: Name of a collection of barcoded cells.  Input will be either dissociated_cell_sample
+      or enriched_cell_sample.  Cell barcodes are only guaranteed to be unique within
+      this one collection. One dissociated_cell_sample or enriched_cell_sample can
+      lead to multiple barcoded_cell_samples.
+    exact_mappings:
+    - NIMP:PD-XEMDJF38
+    slot_uri: bican:4c0e6380-e53f-4173-a474-d41e836fefe3
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  number_of_expected_cells:
+    name: number_of_expected_cells
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: barcoded_cell_sample_number_of_expected_cells
+    description: Expected number of cells/nuclei of a barcoded_cell_sample that will
+      be barcoded and available for sequencing.  This is a derived number from 'Barcoded
+      cell input quantity count' that is dependent on the "capture rate" of the barcoding
+      method.  It is usually a calculated fraction of the 'Barcoded cell input quantity
+      count' going into the barcoding method.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-ONONEV39
+    rank: 1000
+    slot_uri: bican:f10e928d-5a2b-4943-af18-d8fe5d05528d
+    alias: expected cell capture
+    owner: BarcodedCellSample
+    domain_of:
+    - BarcodedCellSample
+    range: integer
+  was_generated_by:
+    name: was_generated_by
+    description: The barcoding process from which the barcoded cell sample is generated
+      from.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: was_generated_by
+    owner: BarcodedCellSample
+    domain_of:
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryPool
+    - DissectionRoiPolygon
+    - ProvEntity
+    range: CellBarcoding
+  was_derived_from:
+    name: was_derived_from
+    description: The input dissociated or enriched cell sample(s) from which the barcoded
+      cell sample was derived from.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:has_parent
+    rank: 1000
+    alias: was_derived_from
+    owner: BarcodedCellSample
+    domain_of:
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DigitalAsset
+    - ProvEntity
+    range: string
+    multivalued: true
+    exactly_one_of:
+    - range: DissociatedCellSample
+    - range: EnrichedCellSample
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: barcoded_cell_sample_local_name
+    description: Name of a collection of barcoded cells.  Input will be either dissociated_cell_sample
+      or enriched_cell_sample.  Cell barcodes are only guaranteed to be unique within
+      this one collection. One dissociated_cell_sample or enriched_cell_sample can
+      lead to multiple barcoded_cell_samples.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - NIMP:PD-XEMDJF38
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: bican:4c0e6380-e53f-4173-a474-d41e836fefe3
+    alias: name
+    owner: BarcodedCellSample
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - Donor
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DissectionRoiPolygon
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: BarcodedCellSample
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: BarcodedCellSample
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: BarcodedCellSample
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+    pattern: ^bican:[A-Z][A-Za-z]+$
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: BarcodedCellSample
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: BarcodedCellSample
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: BarcodedCellSample
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: BarcodedCellSample
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: BarcodedCellSample
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: BarcodedCellSample
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: BarcodedCellSample
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: BarcodedCellSample
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/BarcodedCellSampleTechnique/index.html b/BarcodedCellSampleTechnique/index.html new file mode 100644 index 00000000..01dfd2be --- /dev/null +++ b/BarcodedCellSampleTechnique/index.html @@ -0,0 +1,674 @@ + + + + + + + + + + + + + + + + + + + Enum: BarcodedCellSampleTechnique - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
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+ + + + + + + +

Enum: BarcodedCellSampleTechnique

+

URI: BarcodedCellSampleTechnique

+

Permissible Values

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ValueMeaningDescription
MultiomeNIMP:PD-TDTDDF25Multiome
ATACOnlyNIMP:PD-TDTDDF25ATACOnly
GEXOnlyNIMP:PD-TDTDDF25GEXOnly
snm3C-seqNIMP:PD-TDTDDF25snm3C-seq
+

Slots

+ + + + + + + + + + + + + +
NameDescription
methodStandardized nomenclature to describe the general barcoding method used
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

LinkML Source

+
+ +
name: barcoded_cell_sample_technique
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+rank: 1000
+permissible_values:
+  Multiome:
+    text: Multiome
+    description: Multiome
+    meaning: NIMP:PD-TDTDDF25
+  ATACOnly:
+    text: ATACOnly
+    description: ATACOnly
+    meaning: NIMP:PD-TDTDDF25
+  GEXOnly:
+    text: GEXOnly
+    description: GEXOnly
+    meaning: NIMP:PD-TDTDDF25
+  snm3C-seq:
+    text: snm3C-seq
+    description: snm3C-seq
+    meaning: NIMP:PD-TDTDDF25
+
+
+ +
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
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+ + + + + + + + + + \ No newline at end of file diff --git a/Bican/index.html b/Bican/index.html new file mode 100644 index 00000000..d1203848 --- /dev/null +++ b/Bican/index.html @@ -0,0 +1,670 @@ + + + + + + + + + + + + + + + + + + + Subset: Bican - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
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Subset: Bican

+

A subset of classes that are associated with BICAN.

+

URI: Bican

+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Classes in subset

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ClassDescription
AmplifiedCdnaA collection of cDNA molecules derived and amplified from an input barcoded c...
BarcodedCellSampleA collection of molecularly barcoded cells
BrainSlabA thick flat piece of brain tissue obtained by slicing a whole brain, brain h...
CdnaAmplificationThe process of creating a collection of cDNA molecules derived and amplified ...
CellBarcodingThe process of adding a molecular barcode to individual cells in a sample
CellDissociationThe process of generating dissociated cells from an input tissue sample
CellEnrichmentThe process of enriching a dissociated cell sample by including or excluding ...
DissectionRoiDelineationThe process of outlining a region of interest on a brain slab image to guide ...
DissectionRoiPolygonA polygon annotated on a brain slab image delineating a region of interest (R...
DissociatedCellSampleA collection of dissociated cells or nuclei derived from dissociation of a ti...
EnrichedCellSampleA collection of enriched cells or nuclei after enrichment process, usually vi...
EnrichedCellSampleSplittingThe process of splitting an enriched cell sample into several portions
LibraryA collection of fragmented and barcode-indexed DNA molecules for sequencing
LibraryAliquotOne library in the library pool
LibraryConstructionThe process of constructing a library from input material (such as amplified ...
LibraryPoolA library pool is made up of library aliquots from multiple libraries
LibraryPoolingThe process of constructing of a libray pool by combining library aliquots fr...
TissueDissectionThe process of dissecting a tissue sample from a brain slab guided by a disse...
TissueSampleThe final intact piece of tissue before cell or nuclei prep
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+ + + + + + + + + + \ No newline at end of file diff --git a/BioType/index.html b/BioType/index.html new file mode 100644 index 00000000..6ec411de --- /dev/null +++ b/BioType/index.html @@ -0,0 +1,628 @@ + + + + + + + + + + + + + + + + + + + Enum: BioType - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
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Enum: BioType

+

URI: BioType

+

Permissible Values

+ + + + + + + + + + + + + + + + + + + + +
ValueMeaningDescription
protein_codingNone
noncodingNone
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

LinkML Source

+
+ +
name: BioType
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+rank: 1000
+permissible_values:
+  protein_coding:
+    text: protein_coding
+  noncoding:
+    text: noncoding
+
+
+ +
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/BiologicalEntity/index.html b/BiologicalEntity/index.html new file mode 100644 index 00000000..187d766a --- /dev/null +++ b/BiologicalEntity/index.html @@ -0,0 +1,1130 @@ + + + + + + + + + +Class: BiologicalEntity - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
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Class: BiologicalEntity

+
    +
  • NOTE: this is an abstract class and should not be instantiated directly
    • +
+

URI: biolink:BiologicalEntity

+
classDiagram + class BiologicalEntity + click BiologicalEntity href "../BiologicalEntity" + ThingWithTaxon <|-- BiologicalEntity + click ThingWithTaxon href "../ThingWithTaxon" + NamedThing <|-- BiologicalEntity + click NamedThing href "../NamedThing" + + + BiologicalEntity <|-- Gene + click Gene href "../Gene" + BiologicalEntity <|-- Genome + click Genome href "../Genome" + + + BiologicalEntity : category + + BiologicalEntity : deprecated + + BiologicalEntity : description + + BiologicalEntity : full_name + + BiologicalEntity : has_attribute + + + + + BiologicalEntity --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + BiologicalEntity : id + + BiologicalEntity : in_taxon + + + + + BiologicalEntity --> "*" OrganismTaxon : in_taxon + click OrganismTaxon href "../OrganismTaxon" + + + BiologicalEntity : in_taxon_label + + BiologicalEntity : iri + + BiologicalEntity : name + + BiologicalEntity : provided_by + + BiologicalEntity : synonym + + BiologicalEntity : type + + BiologicalEntity : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
id1
String		A unique identifier for an entitydirect
iri0..1
IriType		An IRI for an entitydirect
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizeddirect
type*
String		direct
name0..1
LabelType		A human-readable name for an attribute or entitydirect
description0..1
NarrativeText		a human-readable description of an entitydirect
has_attribute*
Attribute		connects any entity to an attributedirect
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...direct
provided_by*
String		The value in this node property represents the knowledge provider that create...direct
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...direct
full_name0..1
LabelType		a long-form human readable name for a thingdirect
synonym*
LabelType		Alternate human-readable names for a thingdirect
in_taxon*
OrganismTaxon		connects an entity to its taxonomic classificationdirect
in_taxon_label0..1
LabelType		The human readable scientific name for the taxon of the entitydirect
+

Aliases

+
    +
  • bioentity
    • +
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:BiologicalEntity
nativebican:BiologicalEntity
narrowWIKIDATA:Q28845870, STY:T050, SIO:010046, STY:T129
+

LinkML Source

+ +

Direct

+
+
name: biological entity
+definition_uri: https://w3id.org/biolink/vocab/BiologicalEntity
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+aliases:
+- bioentity
+narrow_mappings:
+- WIKIDATA:Q28845870
+- STY:T050
+- SIO:010046
+- STY:T129
+is_a: named thing
+abstract: true
+mixins:
+- thing with taxon
+slots:
+- id
+- iri
+- category
+- type
+- name
+- description
+- has attribute
+- deprecated
+- provided by
+- xref
+- full name
+- synonym
+- in taxon
+- in taxon label
+class_uri: biolink:BiologicalEntity
+
+
+
+

Induced

+
+
name: biological entity
+definition_uri: https://w3id.org/biolink/vocab/BiologicalEntity
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+aliases:
+- bioentity
+narrow_mappings:
+- WIKIDATA:Q28845870
+- STY:T050
+- SIO:010046
+- STY:T129
+is_a: named thing
+abstract: true
+mixins:
+- thing with taxon
+attributes:
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: biological entity
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: biological entity
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: biological entity
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: biological entity
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: biological entity
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: biological entity
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: biological entity
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: biological entity
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: biological entity
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: biological entity
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: biological entity
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: biological entity
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+  in taxon:
+    name: in taxon
+    definition_uri: https://w3id.org/biolink/vocab/in_taxon
+    annotations:
+      canonical_predicate:
+        tag: canonical_predicate
+        value: true
+    description: connects an entity to its taxonomic classification. Only certain
+      kinds of entities can be taxonomically classified; see 'thing with taxon'
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - instance of
+    - is organism source of gene product
+    - organism has gene
+    - gene found in organism
+    - gene product has organism source
+    exact_mappings:
+    - RO:0002162
+    - WIKIDATA_PROPERTY:P703
+    narrow_mappings:
+    - RO:0002160
+    rank: 1000
+    is_a: related to at instance level
+    domain: thing with taxon
+    slot_uri: biolink:in_taxon
+    inherited: true
+    alias: in_taxon
+    owner: biological entity
+    domain_of:
+    - thing with taxon
+    - biological entity
+    - gene
+    - genome
+    range: organism taxon
+    multivalued: true
+  in taxon label:
+    name: in taxon label
+    definition_uri: https://w3id.org/biolink/vocab/in_taxon_label
+    annotations:
+      denormalized:
+        tag: denormalized
+        value: true
+    description: The human readable scientific name for the taxon of the entity.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P225
+    rank: 1000
+    is_a: node property
+    domain: thing with taxon
+    slot_uri: biolink:in_taxon_label
+    alias: in_taxon_label
+    owner: biological entity
+    domain_of:
+    - thing with taxon
+    - biological entity
+    - gene
+    - genome
+    range: label type
+class_uri: biolink:BiologicalEntity
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/BiologicalSequence/index.html b/BiologicalSequence/index.html new file mode 100644 index 00000000..1897ed29 --- /dev/null +++ b/BiologicalSequence/index.html @@ -0,0 +1,612 @@ + + + + + + + + + + + + + + + + + + + Type: BiologicalSequence - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
+
+ + + +
+
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+ + + + + +
+
+
+ + + +
+
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+ + + +
+
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+ + + +
+
+ + + + + + + +

Type: BiologicalSequence

+

URI: xsd:string

+ +

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfxsd:string
nativebican:biological_sequence
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/Boolean/index.html b/Boolean/index.html new file mode 100644 index 00000000..4bf82a40 --- /dev/null +++ b/Boolean/index.html @@ -0,0 +1,617 @@ + + + + + + + + + + + + + + + + + + + Type: Boolean - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
+
+ + + +
+
+
+ + + + + +
+
+
+ + + +
+
+
+ + + +
+
+
+ + + +
+
+ + + + + + + +

Type: Boolean

+

A binary (true or false) value

+

URI: xsd:boolean

+
    +
  • +

    base: Bool

    +
    • +
  • +

    uri: xsd:boolean

    +
    • +
  • +

    repr: bool

    +
    • +
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfxsd:boolean
nativebican:boolean
exactschema:Boolean
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/BrainSlab/index.html b/BrainSlab/index.html new file mode 100644 index 00000000..e5750a3e --- /dev/null +++ b/BrainSlab/index.html @@ -0,0 +1,1178 @@ + + + + + + + + + +Class: BrainSlab - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
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+ +
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+ +
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+ +
+
+
+
+
+

Class: BrainSlab

+

A thick flat piece of brain tissue obtained by slicing a whole brain, brain hemisphere or subdivision with a blade at regular interval. When multiple brain slabs are obtained from the slicing process, an ordinal is assigned to provide information about the relative positioning of the slabs.

+

URI: bican:BrainSlab

+
classDiagram + class BrainSlab + click BrainSlab href "../BrainSlab" + ProvEntity <|-- BrainSlab + click ProvEntity href "../ProvEntity" + MaterialSample <|-- BrainSlab + click MaterialSample href "../MaterialSample" + + BrainSlab : category + + BrainSlab : deprecated + + BrainSlab : description + + BrainSlab : full_name + + BrainSlab : has_attribute + + + + + BrainSlab --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + BrainSlab : id + + BrainSlab : iri + + BrainSlab : name + + BrainSlab : provided_by + + BrainSlab : synonym + + BrainSlab : type + + BrainSlab : was_derived_from + + BrainSlab : was_generated_by + + BrainSlab : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
was_derived_from0..1
String or 
Donor or 
BrainSlab		The donor from which the brain slab was derived fromdirect
name0..1
LabelType		Name of a thick flat piece of brain tissue obtained by slicing a whole brain,...direct
was_generated_by0..1
String		ProvEntity
id1
String		A unique identifier for an entityNamedThing, MaterialSample, PhysicalEntity, Entity
iri0..1
IriType		An IRI for an entityNamedThing, MaterialSample, PhysicalEntity, Entity
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizedNamedThing, MaterialSample, PhysicalEntity, Entity
type*
String		NamedThing, MaterialSample, PhysicalEntity, Entity
description0..1
NarrativeText		a human-readable description of an entityNamedThing, MaterialSample, PhysicalEntity, Entity
has_attribute*
Attribute		connects any entity to an attributeNamedThing, MaterialSample, PhysicalEntity, Entity
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...NamedThing, MaterialSample, PhysicalEntity, Entity
provided_by*
String		The value in this node property represents the knowledge provider that create...NamedThing, MaterialSample, PhysicalEntity
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...NamedThing, MaterialSample, PhysicalEntity
full_name0..1
LabelType		a long-form human readable name for a thingNamedThing, MaterialSample, PhysicalEntity
synonym*
LabelType		Alternate human-readable names for a thingNamedThing, MaterialSample, PhysicalEntity
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
BrainSlabwas_derived_fromany_of[range]BrainSlab
DissectionRoiDelineationusedrangeBrainSlab
TissueDissectionusedrangeBrainSlab
DissectionRoiPolygonannotatesrangeBrainSlab
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:BrainSlab
nativebican:BrainSlab
exactNIMP:Slab
+

LinkML Source

+ +

Direct

+
+
name: BrainSlab
+description: A thick flat piece of brain tissue obtained by slicing a whole brain,
+  brain hemisphere or subdivision with a blade at regular interval.  When multiple
+  brain slabs are obtained from the slicing process, an ordinal is assigned to provide
+  information about the relative positioning of the slabs.
+in_subset:
+- bican
+- tissue_specimen
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Slab
+is_a: material sample
+mixins:
+- ProvEntity
+slots:
+- was_derived_from
+- name
+slot_usage:
+  was_derived_from:
+    name: was_derived_from
+    description: The donor from which the brain slab was derived from.
+    exact_mappings:
+    - NIMP:has_parent
+    any_of:
+    - range: Donor
+    - range: BrainSlab
+  name:
+    name: name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: local_name
+    description: Name of a thick flat piece of brain tissue obtained by slicing a
+      whole brain, brain hemisphere or subdivision with a blade at regular interval.  When
+      multiple brain slabs are obtained from the slicing process, an ordinal is assigned
+      to provide information about the relative positioning of the slabs.
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+
+
+
+

Induced

+
+
name: BrainSlab
+description: A thick flat piece of brain tissue obtained by slicing a whole brain,
+  brain hemisphere or subdivision with a blade at regular interval.  When multiple
+  brain slabs are obtained from the slicing process, an ordinal is assigned to provide
+  information about the relative positioning of the slabs.
+in_subset:
+- bican
+- tissue_specimen
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Slab
+is_a: material sample
+mixins:
+- ProvEntity
+slot_usage:
+  was_derived_from:
+    name: was_derived_from
+    description: The donor from which the brain slab was derived from.
+    exact_mappings:
+    - NIMP:has_parent
+    any_of:
+    - range: Donor
+    - range: BrainSlab
+  name:
+    name: name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: local_name
+    description: Name of a thick flat piece of brain tissue obtained by slicing a
+      whole brain, brain hemisphere or subdivision with a blade at regular interval.  When
+      multiple brain slabs are obtained from the slicing process, an ordinal is assigned
+      to provide information about the relative positioning of the slabs.
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  was_derived_from:
+    name: was_derived_from
+    description: The donor from which the brain slab was derived from.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:has_parent
+    rank: 1000
+    alias: was_derived_from
+    owner: BrainSlab
+    domain_of:
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DigitalAsset
+    - ProvEntity
+    range: string
+    any_of:
+    - range: Donor
+    - range: BrainSlab
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: local_name
+    description: Name of a thick flat piece of brain tissue obtained by slicing a
+      whole brain, brain hemisphere or subdivision with a blade at regular interval.  When
+      multiple brain slabs are obtained from the slicing process, an ordinal is assigned
+      to provide information about the relative positioning of the slabs.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: BrainSlab
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - Donor
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DissectionRoiPolygon
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  was_generated_by:
+    name: was_generated_by
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: was_generated_by
+    owner: BrainSlab
+    domain_of:
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryPool
+    - DissectionRoiPolygon
+    - ProvEntity
+    range: string
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: BrainSlab
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: BrainSlab
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: BrainSlab
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+    pattern: ^bican:[A-Z][A-Za-z]+$
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: BrainSlab
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: BrainSlab
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: BrainSlab
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: BrainSlab
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: BrainSlab
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: BrainSlab
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: BrainSlab
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: BrainSlab
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
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+ + Skip to content + +
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+

Class: CdnaAmplification

+

The process of creating a collection of cDNA molecules derived and amplified from an input barcoded cell sample. A large amount of cDNA is needed to have accurate and reliable sequencing detection of gene expression. This process generates multiple copies of each mRNA transcript (expressed gene) within each cell while retaining the cell's unique barcode from the barcoding step. This is a necessary step for GEX methods but is not used for ATAC methods.

+

URI: bican:CdnaAmplification

+
classDiagram + class CdnaAmplification + click CdnaAmplification href "../CdnaAmplification" + ProvActivity <|-- CdnaAmplification + click ProvActivity href "../ProvActivity" + Procedure <|-- CdnaAmplification + click Procedure href "../Procedure" + + CdnaAmplification : category + + CdnaAmplification : deprecated + + CdnaAmplification : description + + CdnaAmplification : full_name + + CdnaAmplification : has_attribute + + + + + CdnaAmplification --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + CdnaAmplification : id + + CdnaAmplification : iri + + CdnaAmplification : name + + CdnaAmplification : pcr_cycles + + CdnaAmplification : process_date + + CdnaAmplification : provided_by + + CdnaAmplification : set + + CdnaAmplification : synonym + + CdnaAmplification : type + + CdnaAmplification : used + + + + + CdnaAmplification --> "0..1" BarcodedCellSample : used + click BarcodedCellSample href "../BarcodedCellSample" + + + CdnaAmplification : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
used0..1
BarcodedCellSample		The input barcoded cell sample from which amplified cDNA was derived fromdirect
pcr_cycles0..1
Integer		Number of PCR cycles used during cDNA amplification for this cDNAdirect
process_date0..1
Date		Date of cDNA amplificationdirect
set0..1
String		cDNA amplification set, containing multiple amplified_cDNA_names that were pr...direct
id1
String		A unique identifier for an entityProcedure, NamedThing, Entity
iri0..1
IriType		An IRI for an entityProcedure, NamedThing, Entity
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizedProcedure, NamedThing, Entity
type*
String		Procedure, NamedThing, Entity
name0..1
LabelType		A human-readable name for an attribute or entityProcedure, NamedThing, Entity
description0..1
NarrativeText		a human-readable description of an entityProcedure, NamedThing, Entity
has_attribute*
Attribute		connects any entity to an attributeProcedure, NamedThing, Entity
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...Procedure, NamedThing, Entity
provided_by*
String		The value in this node property represents the knowledge provider that create...Procedure, NamedThing
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...Procedure, NamedThing
full_name0..1
LabelType		a long-form human readable name for a thingProcedure, NamedThing
synonym*
LabelType		Alternate human-readable names for a thingProcedure, NamedThing
+

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
AmplifiedCdnawas_generated_byrangeCdnaAmplification
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:CdnaAmplification
nativebican:CdnaAmplification
+

LinkML Source

+ +

Direct

+
+
name: CdnaAmplification
+description: The process of creating a collection of cDNA molecules derived and amplified
+  from an input barcoded cell sample.  A large amount of cDNA is needed to have accurate
+  and reliable sequencing detection of gene expression.  This process generates multiple
+  copies of each mRNA transcript (expressed gene) within each cell while retaining
+  the cell's unique barcode from the barcoding step. This is a necessary step for
+  GEX methods but is not used for ATAC methods.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slots:
+- used
+slot_usage:
+  used:
+    name: used
+    description: The input barcoded cell sample from which amplified cDNA was derived
+      from.
+    range: BarcodedCellSample
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  pcr_cycles:
+    name: pcr_cycles
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: amplified_cdna_pcr_cycles
+    description: Number of PCR cycles used during cDNA amplification for this cDNA.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-OKOKQD38
+    rank: 1000
+    slot_uri: bican:3827634c-3f8f-4760-b358-86ce4b030238
+    alias: amplified cDNA PCR cycles
+    domain_of:
+    - CdnaAmplification
+    range: integer
+  process_date:
+    name: process_date
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: amplified_cdna_preparation_date
+    description: Date of cDNA amplification.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-BYBYBY24
+    slot_uri: bican:6cc333e7-9b98-497f-b7b1-eae904db2400
+    alias: cDNA amplification process date
+    domain_of:
+    - CellDissociation
+    - CellEnrichment
+    - CellBarcoding
+    - CdnaAmplification
+    - LibraryConstruction
+    - LibraryPooling
+    range: date
+  set:
+    name: set
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: cdna_amplification_set
+    description: cDNA amplification set, containing multiple amplified_cDNA_names
+      that were processed at the same time.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-SCSCTM41
+    rank: 1000
+    slot_uri: bican:42e98a88-50b3-4ea2-871b-2142f6a0dfdd
+    alias: cDNA amplification set
+    domain_of:
+    - CdnaAmplification
+    - LibraryConstruction
+    range: string
+
+
+
+

Induced

+
+
name: CdnaAmplification
+description: The process of creating a collection of cDNA molecules derived and amplified
+  from an input barcoded cell sample.  A large amount of cDNA is needed to have accurate
+  and reliable sequencing detection of gene expression.  This process generates multiple
+  copies of each mRNA transcript (expressed gene) within each cell while retaining
+  the cell's unique barcode from the barcoding step. This is a necessary step for
+  GEX methods but is not used for ATAC methods.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slot_usage:
+  used:
+    name: used
+    description: The input barcoded cell sample from which amplified cDNA was derived
+      from.
+    range: BarcodedCellSample
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  pcr_cycles:
+    name: pcr_cycles
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: amplified_cdna_pcr_cycles
+    description: Number of PCR cycles used during cDNA amplification for this cDNA.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-OKOKQD38
+    rank: 1000
+    slot_uri: bican:3827634c-3f8f-4760-b358-86ce4b030238
+    alias: amplified cDNA PCR cycles
+    owner: CdnaAmplification
+    domain_of:
+    - CdnaAmplification
+    range: integer
+  process_date:
+    name: process_date
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: amplified_cdna_preparation_date
+    description: Date of cDNA amplification.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-BYBYBY24
+    slot_uri: bican:6cc333e7-9b98-497f-b7b1-eae904db2400
+    alias: cDNA amplification process date
+    owner: CdnaAmplification
+    domain_of:
+    - CellDissociation
+    - CellEnrichment
+    - CellBarcoding
+    - CdnaAmplification
+    - LibraryConstruction
+    - LibraryPooling
+    range: date
+  set:
+    name: set
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: cdna_amplification_set
+    description: cDNA amplification set, containing multiple amplified_cDNA_names
+      that were processed at the same time.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-SCSCTM41
+    rank: 1000
+    slot_uri: bican:42e98a88-50b3-4ea2-871b-2142f6a0dfdd
+    alias: cDNA amplification set
+    owner: CdnaAmplification
+    domain_of:
+    - CdnaAmplification
+    - LibraryConstruction
+    range: string
+  used:
+    name: used
+    description: The input barcoded cell sample from which amplified cDNA was derived
+      from.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: used
+    owner: CdnaAmplification
+    domain_of:
+    - DissectionRoiDelineation
+    - TissueDissection
+    - CellDissociation
+    - CellEnrichment
+    - EnrichedCellSampleSplitting
+    - CellBarcoding
+    - CdnaAmplification
+    - LibraryConstruction
+    - LibraryPooling
+    - ProvActivity
+    range: BarcodedCellSample
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: CdnaAmplification
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: CdnaAmplification
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: CdnaAmplification
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+    pattern: ^bican:[A-Z][A-Za-z]+$
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: CdnaAmplification
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: CdnaAmplification
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - Donor
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DissectionRoiPolygon
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: CdnaAmplification
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: CdnaAmplification
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: CdnaAmplification
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: CdnaAmplification
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: CdnaAmplification
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: CdnaAmplification
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: CdnaAmplification
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
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+ + + + \ No newline at end of file diff --git a/CellBarcoding/index.html b/CellBarcoding/index.html new file mode 100644 index 00000000..a56c7d5b --- /dev/null +++ b/CellBarcoding/index.html @@ -0,0 +1,1286 @@ + + + + + + + + + +Class: CellBarcoding - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
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Class: CellBarcoding

+

The process of adding a molecular barcode to individual cells in a sample. The input will be either dissociated cell sample or enriched cell sample. Cell barcodes are only guaranteed to be unique within this one collection. One dissociated cell sample or enriched cell sample can lead to multiple barcoded cell samples.

+

URI: bican:CellBarcoding

+
classDiagram + class CellBarcoding + click CellBarcoding href "../CellBarcoding" + ProvActivity <|-- CellBarcoding + click ProvActivity href "../ProvActivity" + Procedure <|-- CellBarcoding + click Procedure href "../Procedure" + + CellBarcoding : category + + CellBarcoding : deprecated + + CellBarcoding : description + + CellBarcoding : full_name + + CellBarcoding : has_attribute + + + + + CellBarcoding --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + CellBarcoding : id + + CellBarcoding : input_quantity + + CellBarcoding : iri + + CellBarcoding : method + + + + + CellBarcoding --> "0..1" BarcodedCellSampleTechnique : method + click BarcodedCellSampleTechnique href "../BarcodedCellSampleTechnique" + + + CellBarcoding : name + + CellBarcoding : port_well + + CellBarcoding : process_date + + CellBarcoding : provided_by + + CellBarcoding : synonym + + CellBarcoding : type + + CellBarcoding : used + + CellBarcoding : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
used*
String or 
DissociatedCellSample or 
EnrichedCellSample		The input dissociated or enriched cell sample(s) from which the barcoded cell...direct
port_well0..1
String		Specific position of the loaded port of the 10x chipdirect
input_quantity0..1
Integer		Number of enriched or dissociated cells/nuclei going into the barcoding proce...direct
process_date0..1
String		Date of cell barcoding processdirect
method0..1
BarcodedCellSampleTechnique		Standardized nomenclature to describe the general barcoding method useddirect
id1
String		A unique identifier for an entityProcedure, NamedThing, Entity
iri0..1
IriType		An IRI for an entityProcedure, NamedThing, Entity
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizedProcedure, NamedThing, Entity
type*
String		Procedure, NamedThing, Entity
name0..1
LabelType		A human-readable name for an attribute or entityProcedure, NamedThing, Entity
description0..1
NarrativeText		a human-readable description of an entityProcedure, NamedThing, Entity
has_attribute*
Attribute		connects any entity to an attributeProcedure, NamedThing, Entity
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...Procedure, NamedThing, Entity
provided_by*
String		The value in this node property represents the knowledge provider that create...Procedure, NamedThing
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...Procedure, NamedThing
full_name0..1
LabelType		a long-form human readable name for a thingProcedure, NamedThing
synonym*
LabelType		Alternate human-readable names for a thingProcedure, NamedThing
+

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
BarcodedCellSamplewas_generated_byrangeCellBarcoding
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:CellBarcoding
nativebican:CellBarcoding
+

LinkML Source

+ +

Direct

+
+
name: CellBarcoding
+description: The process of adding a molecular barcode to individual cells in a sample.
+  The input will be either dissociated cell sample or enriched cell sample. Cell barcodes
+  are only guaranteed to be unique within this one collection. One dissociated cell
+  sample or enriched cell sample can lead to multiple barcoded cell samples.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slots:
+- used
+slot_usage:
+  used:
+    name: used
+    description: The input dissociated or enriched cell sample(s) from which the barcoded
+      cell sample was derived from.
+    multivalued: true
+    exactly_one_of:
+    - range: DissociatedCellSample
+    - range: EnrichedCellSample
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  port_well:
+    name: port_well
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: barcoded_cell_sample_port_well
+    description: Specific position of the loaded port of the 10x chip.  An Enriched
+      or Dissociated Cell Sample is loaded into a port on a chip (creating a Barcoded
+      Cell Sample). Can be left null for non-10x methods.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-KJKJZK32
+    rank: 1000
+    slot_uri: bican:aca38100-d245-4be4-9be3-ba27192779fe
+    alias: barcoded cell sample port well
+    domain_of:
+    - CellBarcoding
+    range: string
+  input_quantity:
+    name: input_quantity
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: barcoded_cell_input_quantity_count
+    description: Number of enriched or dissociated cells/nuclei going into the barcoding
+      process.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-ZZZZWQ40
+    rank: 1000
+    slot_uri: bican:aa534269-7c9b-4b63-b990-eea8cda56d0e
+    alias: barcoded cell input quantity count
+    domain_of:
+    - CellBarcoding
+    range: integer
+  process_date:
+    name: process_date
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: barcoded_cell_sample_preparation_date
+    description: Date of cell barcoding process.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-SHSHZS25
+    domain_of:
+    - CellDissociation
+    - CellEnrichment
+    - CellBarcoding
+    - CdnaAmplification
+    - LibraryConstruction
+    - LibraryPooling
+  method:
+    name: method
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: barcoded_cell_sample_technique
+    description: 'Standardized nomenclature to describe the general barcoding method
+      used.  For example: Multiome, ATAC Only, GEX Only or snm3C-seq.'
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-TDTDDF25
+    rank: 1000
+    domain_of:
+    - CellBarcoding
+    - LibraryConstruction
+    range: barcoded_cell_sample_technique
+
+
+
+

Induced

+
+
name: CellBarcoding
+description: The process of adding a molecular barcode to individual cells in a sample.
+  The input will be either dissociated cell sample or enriched cell sample. Cell barcodes
+  are only guaranteed to be unique within this one collection. One dissociated cell
+  sample or enriched cell sample can lead to multiple barcoded cell samples.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slot_usage:
+  used:
+    name: used
+    description: The input dissociated or enriched cell sample(s) from which the barcoded
+      cell sample was derived from.
+    multivalued: true
+    exactly_one_of:
+    - range: DissociatedCellSample
+    - range: EnrichedCellSample
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  port_well:
+    name: port_well
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: barcoded_cell_sample_port_well
+    description: Specific position of the loaded port of the 10x chip.  An Enriched
+      or Dissociated Cell Sample is loaded into a port on a chip (creating a Barcoded
+      Cell Sample). Can be left null for non-10x methods.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-KJKJZK32
+    rank: 1000
+    slot_uri: bican:aca38100-d245-4be4-9be3-ba27192779fe
+    alias: barcoded cell sample port well
+    owner: CellBarcoding
+    domain_of:
+    - CellBarcoding
+    range: string
+  input_quantity:
+    name: input_quantity
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: barcoded_cell_input_quantity_count
+    description: Number of enriched or dissociated cells/nuclei going into the barcoding
+      process.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-ZZZZWQ40
+    rank: 1000
+    slot_uri: bican:aa534269-7c9b-4b63-b990-eea8cda56d0e
+    alias: barcoded cell input quantity count
+    owner: CellBarcoding
+    domain_of:
+    - CellBarcoding
+    range: integer
+  process_date:
+    name: process_date
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: barcoded_cell_sample_preparation_date
+    description: Date of cell barcoding process.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-SHSHZS25
+    alias: process_date
+    owner: CellBarcoding
+    domain_of:
+    - CellDissociation
+    - CellEnrichment
+    - CellBarcoding
+    - CdnaAmplification
+    - LibraryConstruction
+    - LibraryPooling
+    range: string
+  method:
+    name: method
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: barcoded_cell_sample_technique
+    description: 'Standardized nomenclature to describe the general barcoding method
+      used.  For example: Multiome, ATAC Only, GEX Only or snm3C-seq.'
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-TDTDDF25
+    rank: 1000
+    alias: method
+    owner: CellBarcoding
+    domain_of:
+    - CellBarcoding
+    - LibraryConstruction
+    range: barcoded_cell_sample_technique
+  used:
+    name: used
+    description: The input dissociated or enriched cell sample(s) from which the barcoded
+      cell sample was derived from.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: used
+    owner: CellBarcoding
+    domain_of:
+    - DissectionRoiDelineation
+    - TissueDissection
+    - CellDissociation
+    - CellEnrichment
+    - EnrichedCellSampleSplitting
+    - CellBarcoding
+    - CdnaAmplification
+    - LibraryConstruction
+    - LibraryPooling
+    - ProvActivity
+    range: string
+    multivalued: true
+    exactly_one_of:
+    - range: DissociatedCellSample
+    - range: EnrichedCellSample
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: CellBarcoding
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: CellBarcoding
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: CellBarcoding
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+    pattern: ^bican:[A-Z][A-Za-z]+$
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: CellBarcoding
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: CellBarcoding
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - Donor
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DissectionRoiPolygon
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: CellBarcoding
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: CellBarcoding
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: CellBarcoding
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: CellBarcoding
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: CellBarcoding
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: CellBarcoding
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: CellBarcoding
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
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+ + + + \ No newline at end of file diff --git a/CellDissociation/index.html b/CellDissociation/index.html new file mode 100644 index 00000000..1494b2a2 --- /dev/null +++ b/CellDissociation/index.html @@ -0,0 +1,1141 @@ + + + + + + + + + +Class: CellDissociation - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
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+

Class: CellDissociation

+

The process of generating dissociated cells from an input tissue sample. This process could also introduce a tissue-source barcode (eg cell hashing), allowing mixing of cell dissociation samples at the cell barcoding step.

+

URI: bican:CellDissociation

+
classDiagram + class CellDissociation + click CellDissociation href "../CellDissociation" + ProvActivity <|-- CellDissociation + click ProvActivity href "../ProvActivity" + Procedure <|-- CellDissociation + click Procedure href "../Procedure" + + CellDissociation : category + + CellDissociation : deprecated + + CellDissociation : description + + CellDissociation : full_name + + CellDissociation : has_attribute + + + + + CellDissociation --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + CellDissociation : id + + CellDissociation : iri + + CellDissociation : name + + CellDissociation : process_date + + CellDissociation : provided_by + + CellDissociation : synonym + + CellDissociation : type + + CellDissociation : used + + + + + CellDissociation --> "*" TissueSample : used + click TissueSample href "../TissueSample" + + + CellDissociation : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
used*
TissueSample		The input tissue sample(s) from which the dissociated cell sample was derived...direct
process_date0..1
String		Date of cell dissociation processdirect
id1
String		A unique identifier for an entityProcedure, NamedThing, Entity
iri0..1
IriType		An IRI for an entityProcedure, NamedThing, Entity
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizedProcedure, NamedThing, Entity
type*
String		Procedure, NamedThing, Entity
name0..1
LabelType		A human-readable name for an attribute or entityProcedure, NamedThing, Entity
description0..1
NarrativeText		a human-readable description of an entityProcedure, NamedThing, Entity
has_attribute*
Attribute		connects any entity to an attributeProcedure, NamedThing, Entity
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...Procedure, NamedThing, Entity
provided_by*
String		The value in this node property represents the knowledge provider that create...Procedure, NamedThing
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...Procedure, NamedThing
full_name0..1
LabelType		a long-form human readable name for a thingProcedure, NamedThing
synonym*
LabelType		Alternate human-readable names for a thingProcedure, NamedThing
+

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
DissociatedCellSamplewas_generated_byrangeCellDissociation
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:CellDissociation
nativebican:CellDissociation
+

LinkML Source

+ +

Direct

+
+
name: CellDissociation
+description: The process of generating dissociated cells from an input tissue sample.
+  This process could also introduce a tissue-source barcode (eg cell hashing), allowing
+  mixing of cell dissociation samples at the cell barcoding step.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slots:
+- used
+slot_usage:
+  used:
+    name: used
+    description: The input tissue sample(s) from which the dissociated cell sample
+      was derived from.
+    range: TissueSample
+    multivalued: true
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  process_date:
+    name: process_date
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: dissociated_cell_sample_preparation_date
+    description: Date of cell dissociation process.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-BUBUFE27
+    rank: 1000
+    domain_of:
+    - CellDissociation
+    - CellEnrichment
+    - CellBarcoding
+    - CdnaAmplification
+    - LibraryConstruction
+    - LibraryPooling
+
+
+
+

Induced

+
+
name: CellDissociation
+description: The process of generating dissociated cells from an input tissue sample.
+  This process could also introduce a tissue-source barcode (eg cell hashing), allowing
+  mixing of cell dissociation samples at the cell barcoding step.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slot_usage:
+  used:
+    name: used
+    description: The input tissue sample(s) from which the dissociated cell sample
+      was derived from.
+    range: TissueSample
+    multivalued: true
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  process_date:
+    name: process_date
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: dissociated_cell_sample_preparation_date
+    description: Date of cell dissociation process.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-BUBUFE27
+    rank: 1000
+    alias: process_date
+    owner: CellDissociation
+    domain_of:
+    - CellDissociation
+    - CellEnrichment
+    - CellBarcoding
+    - CdnaAmplification
+    - LibraryConstruction
+    - LibraryPooling
+    range: string
+  used:
+    name: used
+    description: The input tissue sample(s) from which the dissociated cell sample
+      was derived from.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: used
+    owner: CellDissociation
+    domain_of:
+    - DissectionRoiDelineation
+    - TissueDissection
+    - CellDissociation
+    - CellEnrichment
+    - EnrichedCellSampleSplitting
+    - CellBarcoding
+    - CdnaAmplification
+    - LibraryConstruction
+    - LibraryPooling
+    - ProvActivity
+    range: TissueSample
+    multivalued: true
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: CellDissociation
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: CellDissociation
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: CellDissociation
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+    pattern: ^bican:[A-Z][A-Za-z]+$
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: CellDissociation
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: CellDissociation
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - Donor
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DissectionRoiPolygon
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: CellDissociation
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: CellDissociation
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: CellDissociation
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: CellDissociation
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: CellDissociation
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: CellDissociation
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: CellDissociation
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/CellEnrichment/index.html b/CellEnrichment/index.html new file mode 100644 index 00000000..f183d200 --- /dev/null +++ b/CellEnrichment/index.html @@ -0,0 +1,1141 @@ + + + + + + + + + +Class: CellEnrichment - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
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+ +
+
+
+
+
+
+
+ +
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+
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+ +
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+
+
+

Class: CellEnrichment

+

The process of enriching a dissociated cell sample by including or excluding cells of different types based on an enrichment plan using techniques such as fluorescence-activated cell sorting (FACS). This process could also introduce a tissue-source barcode (eg cell hashing), allowing mixing of cell enriched samples at the cell barcoding step.

+

URI: bican:CellEnrichment

+
classDiagram + class CellEnrichment + click CellEnrichment href "../CellEnrichment" + ProvActivity <|-- CellEnrichment + click ProvActivity href "../ProvActivity" + Procedure <|-- CellEnrichment + click Procedure href "../Procedure" + + CellEnrichment : category + + CellEnrichment : deprecated + + CellEnrichment : description + + CellEnrichment : full_name + + CellEnrichment : has_attribute + + + + + CellEnrichment --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + CellEnrichment : id + + CellEnrichment : iri + + CellEnrichment : name + + CellEnrichment : process_date + + CellEnrichment : provided_by + + CellEnrichment : synonym + + CellEnrichment : type + + CellEnrichment : used + + + + + CellEnrichment --> "*" DissociatedCellSample : used + click DissociatedCellSample href "../DissociatedCellSample" + + + CellEnrichment : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
used*
DissociatedCellSample		The input dissociated cell sample(s) from which the enriched cell sample was ...direct
process_date0..1
String		Date of cell enrichment processdirect
id1
String		A unique identifier for an entityProcedure, NamedThing, Entity
iri0..1
IriType		An IRI for an entityProcedure, NamedThing, Entity
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizedProcedure, NamedThing, Entity
type*
String		Procedure, NamedThing, Entity
name0..1
LabelType		A human-readable name for an attribute or entityProcedure, NamedThing, Entity
description0..1
NarrativeText		a human-readable description of an entityProcedure, NamedThing, Entity
has_attribute*
Attribute		connects any entity to an attributeProcedure, NamedThing, Entity
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...Procedure, NamedThing, Entity
provided_by*
String		The value in this node property represents the knowledge provider that create...Procedure, NamedThing
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...Procedure, NamedThing
full_name0..1
LabelType		a long-form human readable name for a thingProcedure, NamedThing
synonym*
LabelType		Alternate human-readable names for a thingProcedure, NamedThing
+

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
EnrichedCellSamplewas_generated_byany_of[range]CellEnrichment
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:CellEnrichment
nativebican:CellEnrichment
+

LinkML Source

+ +

Direct

+
+
name: CellEnrichment
+description: The process of enriching a dissociated cell sample by including or excluding
+  cells of different types based on an enrichment plan using techniques such as fluorescence-activated
+  cell sorting (FACS). This process could also introduce a tissue-source barcode (eg
+  cell hashing), allowing mixing of cell enriched samples at the cell barcoding step.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slots:
+- used
+slot_usage:
+  used:
+    name: used
+    description: The input dissociated cell sample(s) from which the enriched cell
+      sample was derived from.
+    range: DissociatedCellSample
+    multivalued: true
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  process_date:
+    name: process_date
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: enriched_cell_sample_preparation_date
+    description: Date of cell enrichment process.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-PFPFFC28
+    domain_of:
+    - CellDissociation
+    - CellEnrichment
+    - CellBarcoding
+    - CdnaAmplification
+    - LibraryConstruction
+    - LibraryPooling
+
+
+
+

Induced

+
+
name: CellEnrichment
+description: The process of enriching a dissociated cell sample by including or excluding
+  cells of different types based on an enrichment plan using techniques such as fluorescence-activated
+  cell sorting (FACS). This process could also introduce a tissue-source barcode (eg
+  cell hashing), allowing mixing of cell enriched samples at the cell barcoding step.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slot_usage:
+  used:
+    name: used
+    description: The input dissociated cell sample(s) from which the enriched cell
+      sample was derived from.
+    range: DissociatedCellSample
+    multivalued: true
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  process_date:
+    name: process_date
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: enriched_cell_sample_preparation_date
+    description: Date of cell enrichment process.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-PFPFFC28
+    alias: process_date
+    owner: CellEnrichment
+    domain_of:
+    - CellDissociation
+    - CellEnrichment
+    - CellBarcoding
+    - CdnaAmplification
+    - LibraryConstruction
+    - LibraryPooling
+    range: string
+  used:
+    name: used
+    description: The input dissociated cell sample(s) from which the enriched cell
+      sample was derived from.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: used
+    owner: CellEnrichment
+    domain_of:
+    - DissectionRoiDelineation
+    - TissueDissection
+    - CellDissociation
+    - CellEnrichment
+    - EnrichedCellSampleSplitting
+    - CellBarcoding
+    - CdnaAmplification
+    - LibraryConstruction
+    - LibraryPooling
+    - ProvActivity
+    range: DissociatedCellSample
+    multivalued: true
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: CellEnrichment
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: CellEnrichment
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: CellEnrichment
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+    pattern: ^bican:[A-Z][A-Za-z]+$
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: CellEnrichment
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: CellEnrichment
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - Donor
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DissectionRoiPolygon
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: CellEnrichment
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: CellEnrichment
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: CellEnrichment
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: CellEnrichment
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: CellEnrichment
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: CellEnrichment
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: CellEnrichment
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/Checksum/index.html b/Checksum/index.html new file mode 100644 index 00000000..faa04399 --- /dev/null +++ b/Checksum/index.html @@ -0,0 +1,891 @@ + + + + + + + + + +Class: Checksum - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: Checksum

+

Checksum values associated with digital entities.

+

URI: bican:Checksum

+
classDiagram + class Checksum + click Checksum href "../Checksum" + Entity <|-- Checksum + click Entity href "../Entity" + + Checksum : category + + Checksum : checksum_algorithm + + + + + Checksum --> "0..1" DigestType : checksum_algorithm + click DigestType href "../DigestType" + + + Checksum : deprecated + + Checksum : description + + Checksum : has_attribute + + + + + Checksum --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + Checksum : id + + Checksum : iri + + Checksum : name + + Checksum : type + + Checksum : value + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
checksum_algorithm0..1
DigestType		The type of cryptographic hash function used to calculate the checksum valuedirect
value0..1
String		The checksum value obtained from a specific cryotographic hash functiondirect
id1
String		A unique identifier for an entityEntity
iri0..1
IriType		An IRI for an entityEntity
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizedEntity
type*
String		Entity
name0..1
LabelType		A human-readable name for an attribute or entityEntity
description0..1
NarrativeText		a human-readable description of an entityEntity
has_attribute*
Attribute		connects any entity to an attributeEntity
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...Entity
+

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
GenomeAnnotationdigestany_of[range]Checksum
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:Checksum
nativebican:Checksum
+

LinkML Source

+ +

Direct

+
+
name: checksum
+description: Checksum values associated with digital entities.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: entity
+slots:
+- checksum algorithm
+attributes:
+  value:
+    name: value
+    description: The checksum value obtained from a specific cryotographic hash function.
+    from_schema: https://identifiers.org/brain-bican/bican-core-schema
+    rank: 1000
+    domain_of:
+    - checksum
+
+
+
+

Induced

+
+
name: checksum
+description: Checksum values associated with digital entities.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: entity
+attributes:
+  value:
+    name: value
+    description: The checksum value obtained from a specific cryotographic hash function.
+    from_schema: https://identifiers.org/brain-bican/bican-core-schema
+    rank: 1000
+    alias: value
+    owner: checksum
+    domain_of:
+    - checksum
+    range: string
+  checksum algorithm:
+    name: checksum algorithm
+    description: The type of cryptographic hash function used to calculate the checksum
+      value.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    alias: checksum_algorithm
+    owner: checksum
+    domain_of:
+    - checksum
+    range: DigestType
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: checksum
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: checksum
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: checksum
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: checksum
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: checksum
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: checksum
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: checksum
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: checksum
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/ChemicalEntityOrGeneOrGeneProduct/index.html b/ChemicalEntityOrGeneOrGeneProduct/index.html new file mode 100644 index 00000000..7548e0ae --- /dev/null +++ b/ChemicalEntityOrGeneOrGeneProduct/index.html @@ -0,0 +1,413 @@ + + + + + + + + + +Class: ChemicalEntityOrGeneOrGeneProduct - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
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+ +
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+ +
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+ +
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+

Class: ChemicalEntityOrGeneOrGeneProduct

+

A union of chemical entities and children, and gene or gene product. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities.

+

URI: biolink:ChemicalEntityOrGeneOrGeneProduct

+
classDiagram + class ChemicalEntityOrGeneOrGeneProduct + click ChemicalEntityOrGeneOrGeneProduct href "../ChemicalEntityOrGeneOrGeneProduct" + ChemicalEntityOrGeneOrGeneProduct <|-- Gene + click Gene href "../Gene" + + +
+ +

Slots

+ + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
+

Mixin Usage

+ + + + + + + + + + + + + +
mixed intodescription
GeneA region (or regions) that includes all of the sequence elements necessary to...
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:ChemicalEntityOrGeneOrGeneProduct
nativebican:ChemicalEntityOrGeneOrGeneProduct
+

LinkML Source

+ +

Direct

+
+
name: chemical entity or gene or gene product
+definition_uri: https://w3id.org/biolink/vocab/ChemicalEntityOrGeneOrGeneProduct
+description: A union of chemical entities and children, and gene or gene product.
+  This mixin is helpful to use when searching across chemical entities that must include
+  genes and their children as chemical entities.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+mixin: true
+class_uri: biolink:ChemicalEntityOrGeneOrGeneProduct
+
+
+
+

Induced

+
+
name: chemical entity or gene or gene product
+definition_uri: https://w3id.org/biolink/vocab/ChemicalEntityOrGeneOrGeneProduct
+description: A union of chemical entities and children, and gene or gene product.
+  This mixin is helpful to use when searching across chemical entities that must include
+  genes and their children as chemical entities.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+mixin: true
+class_uri: biolink:ChemicalEntityOrGeneOrGeneProduct
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/ChemicalFormulaValue/index.html b/ChemicalFormulaValue/index.html new file mode 100644 index 00000000..ea39d807 --- /dev/null +++ b/ChemicalFormulaValue/index.html @@ -0,0 +1,610 @@ + + + + + + + + + + + + + + + + + + + Type: ChemicalFormulaValue - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
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+ +
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+ + + +
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+ + + + + + + +

Type: ChemicalFormulaValue

+

A chemical formula

+

URI: xsd:string

+
    +
  • +

    base: str

    +
    • +
  • +

    uri: xsd:string

    +
    • +
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfxsd:string
nativebican:chemical_formula_value
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/Curie/index.html b/Curie/index.html new file mode 100644 index 00000000..bff8a4fd --- /dev/null +++ b/Curie/index.html @@ -0,0 +1,627 @@ + + + + + + + + + + + + + + + + + + + Type: Curie - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
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+ + + + + +
+
+
+ + + +
+
+
+ + + +
+
+
+ + + +
+
+ + + + + + + +

Type: Curie

+

a compact URI

+

URI: xsd:string

+
    +
  • +

    base: Curie

    +
    • +
  • +

    uri: xsd:string

    +
    • +
  • +

    repr: str

    +
    • +
+

Comments

+
    +
  • in RDF serializations this MUST be expanded to a URI
    • +
  • in non-RDF serializations MAY be serialized as the compact representation
    • +
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfxsd:string
nativebican:curie
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/DISTANCEUNIT/index.html b/DISTANCEUNIT/index.html new file mode 100644 index 00000000..cd470a70 --- /dev/null +++ b/DISTANCEUNIT/index.html @@ -0,0 +1,662 @@ + + + + + + + + + + + + + + + + + + + Enum: DISTANCEUNIT - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
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+ +
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+ + + + + + + +

Enum: DISTANCEUNIT

+

URI: DISTANCEUNIT

+

Permissible Values

+ + + + + + + + + + + + + + + + + + + + + + + + + +
ValueMeaningDescription
mmNone
umNone
mNone
+

Slots

+ + + + + + + + + + + + + +
NameDescription
unitA controlled vocabulary attribute defining the length unit of the x, y, and z...
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/my-org/anatomical-structure-schema
    • +
+

LinkML Source

+
+ +
name: DISTANCE_UNIT
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+rank: 1000
+permissible_values:
+  mm:
+    text: mm
+    title: millimeter
+  um:
+    text: um
+    title: micrometer
+  m:
+    text: m
+    title: meter
+
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+ +
+ + + + + + + + + + + + + +
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+ + + + + +
+ +
+ + + +
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+ + + + + + + + + + \ No newline at end of file diff --git a/Dataset/index.html b/Dataset/index.html new file mode 100644 index 00000000..f22d91ef --- /dev/null +++ b/Dataset/index.html @@ -0,0 +1,1152 @@ + + + + + + + + + +Class: Dataset - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
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+ +
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+ +
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+ +
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+

Class: Dataset

+

an item that refers to a collection of data from a data source.

+

URI: biolink:Dataset

+
classDiagram + class Dataset + click Dataset href "../Dataset" + InformationContentEntity <|-- Dataset + click InformationContentEntity href "../InformationContentEntity" + + Dataset : category + + Dataset : creation_date + + Dataset : deprecated + + Dataset : description + + Dataset : format + + Dataset : full_name + + Dataset : has_attribute + + + + + Dataset --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + Dataset : id + + Dataset : iri + + Dataset : license + + Dataset : name + + Dataset : provided_by + + Dataset : rights + + Dataset : synonym + + Dataset : type + + Dataset : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
id1
String		A unique identifier for an entitydirect
iri0..1
IriType		An IRI for an entitydirect
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizeddirect
type*
String		direct
name0..1
LabelType		A human-readable name for an attribute or entitydirect
description0..1
NarrativeText		a human-readable description of an entitydirect
has_attribute*
Attribute		connects any entity to an attributedirect
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...direct
provided_by*
String		The value in this node property represents the knowledge provider that create...direct
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...direct
full_name0..1
LabelType		a long-form human readable name for a thingdirect
synonym*
LabelType		Alternate human-readable names for a thingdirect
license0..1
String		direct
rights0..1
String		direct
format0..1
String		direct
creation_date0..1
Date		date on which an entity was createddirect
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
GenomeAnnotationversiondomainDataset
GenomeAssemblyversiondomainDataset
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:Dataset
nativebican:Dataset
exactIAO:0000100, dctypes:Dataset, schema:dataset, dcid:Dataset
+

LinkML Source

+ +

Direct

+
+
name: dataset
+definition_uri: https://w3id.org/biolink/vocab/Dataset
+description: an item that refers to a collection of data from a data source.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- IAO:0000100
+- dctypes:Dataset
+- schema:dataset
+- dcid:Dataset
+is_a: information content entity
+slots:
+- id
+- iri
+- category
+- type
+- name
+- description
+- has attribute
+- deprecated
+- provided by
+- xref
+- full name
+- synonym
+- license
+- rights
+- format
+- creation date
+class_uri: biolink:Dataset
+
+
+
+

Induced

+
+
name: dataset
+definition_uri: https://w3id.org/biolink/vocab/Dataset
+description: an item that refers to a collection of data from a data source.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- IAO:0000100
+- dctypes:Dataset
+- schema:dataset
+- dcid:Dataset
+is_a: information content entity
+attributes:
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: dataset
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: dataset
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: dataset
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: dataset
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: dataset
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: dataset
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: dataset
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: dataset
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: dataset
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: dataset
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: dataset
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: dataset
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+  license:
+    name: license
+    definition_uri: https://w3id.org/biolink/vocab/license
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - dct:license
+    narrow_mappings:
+    - WIKIDATA_PROPERTY:P275
+    rank: 1000
+    is_a: node property
+    domain: information content entity
+    slot_uri: biolink:license
+    alias: license
+    owner: dataset
+    domain_of:
+    - information content entity
+    - dataset
+    range: string
+  rights:
+    name: rights
+    definition_uri: https://w3id.org/biolink/vocab/rights
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - dct:rights
+    rank: 1000
+    is_a: node property
+    domain: information content entity
+    slot_uri: biolink:rights
+    alias: rights
+    owner: dataset
+    domain_of:
+    - information content entity
+    - dataset
+    range: string
+  format:
+    name: format
+    definition_uri: https://w3id.org/biolink/vocab/format
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - dct:format
+    - WIKIDATA_PROPERTY:P2701
+    rank: 1000
+    is_a: node property
+    domain: information content entity
+    slot_uri: biolink:format
+    alias: format
+    owner: dataset
+    domain_of:
+    - information content entity
+    - dataset
+    range: string
+  creation date:
+    name: creation date
+    definition_uri: https://w3id.org/biolink/vocab/creation_date
+    description: date on which an entity was created. This can be applied to nodes
+      or edges
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - publication date
+    exact_mappings:
+    - dct:createdOn
+    - WIKIDATA_PROPERTY:P577
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:creation_date
+    alias: creation_date
+    owner: dataset
+    domain_of:
+    - information content entity
+    - dataset
+    range: date
+class_uri: biolink:Dataset
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/Date/index.html b/Date/index.html new file mode 100644 index 00000000..563a7200 --- /dev/null +++ b/Date/index.html @@ -0,0 +1,617 @@ + + + + + + + + + + + + + + + + + + + Type: Date - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
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+ +
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+ + +
+ +
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+ + + + + +
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+ + + +
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+ + + +
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+ + + +
+
+ + + + + + + +

Type: Date

+

a date (year, month and day) in an idealized calendar

+

URI: xsd:date

+
    +
  • +

    base: XSDDate

    +
    • +
  • +

    uri: xsd:date

    +
    • +
  • +

    repr: str

    +
    • +
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfxsd:date
nativebican:date
exactschema:Date
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/DateOrDatetime/index.html b/DateOrDatetime/index.html new file mode 100644 index 00000000..b2680bf5 --- /dev/null +++ b/DateOrDatetime/index.html @@ -0,0 +1,613 @@ + + + + + + + + + + + + + + + + + + + Type: DateOrDatetime - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
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+ +
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+ + + + + + + +

Type: DateOrDatetime

+

Either a date or a datetime

+

URI: linkml:DateOrDatetime

+
    +
  • +

    base: str

    +
    • +
  • +

    uri: linkml:DateOrDatetime

    +
    • +
  • +

    repr: str

    +
    • +
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selflinkml:DateOrDatetime
nativebican:date_or_datetime
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/Datetime/index.html b/Datetime/index.html new file mode 100644 index 00000000..7efad986 --- /dev/null +++ b/Datetime/index.html @@ -0,0 +1,617 @@ + + + + + + + + + + + + + + + + + + + Type: Datetime - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
+
+ + + +
+
+
+ + + + + +
+
+
+ + + +
+
+
+ + + +
+
+
+ + + +
+
+ + + + + + + +

Type: Datetime

+

The combination of a date and time

+

URI: xsd:dateTime

+
    +
  • +

    base: XSDDateTime

    +
    • +
  • +

    uri: xsd:dateTime

    +
    • +
  • +

    repr: str

    +
    • +
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfxsd:dateTime
nativebican:datetime
exactschema:DateTime
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/Decimal/index.html b/Decimal/index.html new file mode 100644 index 00000000..4b287282 --- /dev/null +++ b/Decimal/index.html @@ -0,0 +1,614 @@ + + + + + + + + + + + + + + + + + + + Type: Decimal - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
+
+ + + +
+
+
+ + + + + +
+
+
+ + + +
+
+
+ + + +
+
+
+ + + +
+
+ + + + + + + +

Type: Decimal

+

A real number with arbitrary precision that conforms to the xsd:decimal specification

+

URI: xsd:decimal

+
    +
  • +

    base: Decimal

    +
    • +
  • +

    uri: xsd:decimal

    +
    • +
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfxsd:decimal
nativebican:decimal
broadschema:Number
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/DigestType/index.html b/DigestType/index.html new file mode 100644 index 00000000..b33679f4 --- /dev/null +++ b/DigestType/index.html @@ -0,0 +1,665 @@ + + + + + + + + + + + + + + + + + + + Enum: DigestType - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
+
+ + + +
+
+
+ + + + + +
+
+
+ + + +
+
+
+ + + +
+
+
+ + + +
+
+ + + + + + + +

Enum: DigestType

+

URI: DigestType

+

Permissible Values

+ + + + + + + + + + + + + + + + + + + + + + + + + +
ValueMeaningDescription
spdx:checksumAlgorithm_sha1spdx:checksumAlgorithm_sha1
spdx:checksumAlgorithm_md5spdx:checksumAlgorithm_md5
spdx:checksumAlgorithm_sha256spdx:checksumAlgorithm_sha256
+

Slots

+ + + + + + + + + + + + + +
NameDescription
checksum_algorithmThe type of cryptographic hash function used to calculate the checksum value
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

LinkML Source

+
+ +
name: DigestType
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+rank: 1000
+permissible_values:
+  spdx:checksumAlgorithm_sha1:
+    text: spdx:checksumAlgorithm_sha1
+    meaning: spdx:checksumAlgorithm_sha1
+    title: SHA1
+  spdx:checksumAlgorithm_md5:
+    text: spdx:checksumAlgorithm_md5
+    meaning: spdx:checksumAlgorithm_md5
+    title: MD5
+  spdx:checksumAlgorithm_sha256:
+    text: spdx:checksumAlgorithm_sha256
+    meaning: spdx:checksumAlgorithm_sha256
+    title: SHA256
+
+
+ +
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/DigitalAsset/index.html b/DigitalAsset/index.html new file mode 100644 index 00000000..0043c37a --- /dev/null +++ b/DigitalAsset/index.html @@ -0,0 +1,1248 @@ + + + + + + + + + +Class: DigitalAsset - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: DigitalAsset

+

URI: bican:DigitalAsset

+
classDiagram + class DigitalAsset + click DigitalAsset href "../DigitalAsset" + ProvEntity <|-- DigitalAsset + click ProvEntity href "../ProvEntity" + Dataset <|-- DigitalAsset + click Dataset href "../Dataset" + + DigitalAsset : category + + DigitalAsset : content_url + + DigitalAsset : creation_date + + DigitalAsset : data_type + + DigitalAsset : deprecated + + DigitalAsset : description + + DigitalAsset : digest + + DigitalAsset : format + + DigitalAsset : full_name + + DigitalAsset : has_attribute + + + + + DigitalAsset --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + DigitalAsset : id + + DigitalAsset : iri + + DigitalAsset : license + + DigitalAsset : name + + DigitalAsset : provided_by + + DigitalAsset : rights + + DigitalAsset : synonym + + DigitalAsset : type + + DigitalAsset : was_derived_from + + + + + DigitalAsset --> "0..1" LibraryPool : was_derived_from + click LibraryPool href "../LibraryPool" + + + DigitalAsset : was_generated_by + + DigitalAsset : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
was_derived_from0..1
LibraryPool		direct
digest0..1
String		direct
content_url0..1
String		direct
data_type0..1
String		The type of data in the filedirect
was_generated_by0..1
String		ProvEntity
id1
String		A unique identifier for an entityInformationContentEntity, NamedThing, Dataset, Entity
iri0..1
IriType		An IRI for an entityInformationContentEntity, NamedThing, Dataset, Entity
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizedInformationContentEntity, NamedThing, Dataset, Entity
type*
String		InformationContentEntity, NamedThing, Dataset, Entity
name0..1
LabelType		A human-readable name for an attribute or entityInformationContentEntity, NamedThing, Dataset, Entity
description0..1
NarrativeText		a human-readable description of an entityInformationContentEntity, NamedThing, Dataset, Entity
has_attribute*
Attribute		connects any entity to an attributeInformationContentEntity, NamedThing, Dataset, Entity
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...InformationContentEntity, NamedThing, Dataset, Entity
provided_by*
String		The value in this node property represents the knowledge provider that create...InformationContentEntity, NamedThing, Dataset
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...InformationContentEntity, NamedThing, Dataset
full_name0..1
LabelType		a long-form human readable name for a thingInformationContentEntity, NamedThing, Dataset
synonym*
LabelType		Alternate human-readable names for a thingInformationContentEntity, NamedThing, Dataset
license0..1
String		InformationContentEntity, Dataset
rights0..1
String		InformationContentEntity, Dataset
format0..1
String		InformationContentEntity, Dataset
creation_date0..1
Date		date on which an entity was createdInformationContentEntity, Dataset
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:DigitalAsset
nativebican:DigitalAsset
+

LinkML Source

+ +

Direct

+
+
name: DigitalAsset
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: dataset
+mixins:
+- ProvEntity
+slots:
+- was_derived_from
+- digest
+- content_url
+slot_usage:
+  was_derived_from:
+    name: was_derived_from
+    range: LibraryPool
+  digest:
+    name: digest
+  content_url:
+    name: content_url
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  data_type:
+    name: data_type
+    description: The type of data in the file
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    domain_of:
+    - DigitalAsset
+
+
+
+

Induced

+
+
name: DigitalAsset
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: dataset
+mixins:
+- ProvEntity
+slot_usage:
+  was_derived_from:
+    name: was_derived_from
+    range: LibraryPool
+  digest:
+    name: digest
+  content_url:
+    name: content_url
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  data_type:
+    name: data_type
+    description: The type of data in the file
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: data_type
+    owner: DigitalAsset
+    domain_of:
+    - DigitalAsset
+    range: string
+  was_derived_from:
+    name: was_derived_from
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: was_derived_from
+    owner: DigitalAsset
+    domain_of:
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DigitalAsset
+    - ProvEntity
+    range: LibraryPool
+  digest:
+    name: digest
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: digest
+    owner: DigitalAsset
+    domain_of:
+    - DigitalAsset
+    range: string
+  content_url:
+    name: content_url
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: content_url
+    owner: DigitalAsset
+    domain_of:
+    - DigitalAsset
+    range: string
+  was_generated_by:
+    name: was_generated_by
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: was_generated_by
+    owner: DigitalAsset
+    domain_of:
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryPool
+    - DissectionRoiPolygon
+    - ProvEntity
+    range: string
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: DigitalAsset
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: DigitalAsset
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: DigitalAsset
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+    pattern: ^bican:[A-Z][A-Za-z]+$
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: DigitalAsset
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: DigitalAsset
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - Donor
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DissectionRoiPolygon
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: DigitalAsset
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: DigitalAsset
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: DigitalAsset
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: DigitalAsset
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: DigitalAsset
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: DigitalAsset
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: DigitalAsset
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+  license:
+    name: license
+    definition_uri: https://w3id.org/biolink/vocab/license
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - dct:license
+    narrow_mappings:
+    - WIKIDATA_PROPERTY:P275
+    rank: 1000
+    is_a: node property
+    domain: information content entity
+    slot_uri: biolink:license
+    alias: license
+    owner: DigitalAsset
+    domain_of:
+    - information content entity
+    - dataset
+    range: string
+  rights:
+    name: rights
+    definition_uri: https://w3id.org/biolink/vocab/rights
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - dct:rights
+    rank: 1000
+    is_a: node property
+    domain: information content entity
+    slot_uri: biolink:rights
+    alias: rights
+    owner: DigitalAsset
+    domain_of:
+    - information content entity
+    - dataset
+    range: string
+  format:
+    name: format
+    definition_uri: https://w3id.org/biolink/vocab/format
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - dct:format
+    - WIKIDATA_PROPERTY:P2701
+    rank: 1000
+    is_a: node property
+    domain: information content entity
+    slot_uri: biolink:format
+    alias: format
+    owner: DigitalAsset
+    domain_of:
+    - information content entity
+    - dataset
+    range: string
+  creation date:
+    name: creation date
+    definition_uri: https://w3id.org/biolink/vocab/creation_date
+    description: date on which an entity was created. This can be applied to nodes
+      or edges
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - publication date
+    exact_mappings:
+    - dct:createdOn
+    - WIKIDATA_PROPERTY:P577
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:creation_date
+    alias: creation_date
+    owner: DigitalAsset
+    domain_of:
+    - information content entity
+    - dataset
+    range: date
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/DissectionRoiDelineation/index.html b/DissectionRoiDelineation/index.html new file mode 100644 index 00000000..255a90aa --- /dev/null +++ b/DissectionRoiDelineation/index.html @@ -0,0 +1,1085 @@ + + + + + + + + + +Class: DissectionRoiDelineation - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
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+ +
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+

Class: DissectionRoiDelineation

+

The process of outlining a region of interest on a brain slab image to guide the dissection and generation of a tissue sample.

+

URI: bican:DissectionRoiDelineation

+
classDiagram + class DissectionRoiDelineation + click DissectionRoiDelineation href "../DissectionRoiDelineation" + ProvActivity <|-- DissectionRoiDelineation + click ProvActivity href "../ProvActivity" + Procedure <|-- DissectionRoiDelineation + click Procedure href "../Procedure" + + DissectionRoiDelineation : category + + DissectionRoiDelineation : deprecated + + DissectionRoiDelineation : description + + DissectionRoiDelineation : full_name + + DissectionRoiDelineation : has_attribute + + + + + DissectionRoiDelineation --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + DissectionRoiDelineation : id + + DissectionRoiDelineation : iri + + DissectionRoiDelineation : name + + DissectionRoiDelineation : provided_by + + DissectionRoiDelineation : synonym + + DissectionRoiDelineation : type + + DissectionRoiDelineation : used + + + + + DissectionRoiDelineation --> "0..1" BrainSlab : used + click BrainSlab href "../BrainSlab" + + + DissectionRoiDelineation : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
used0..1
BrainSlab		The brain slab that was annotated by the delineation processdirect
id1
String		A unique identifier for an entityProcedure, NamedThing, Entity
iri0..1
IriType		An IRI for an entityProcedure, NamedThing, Entity
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizedProcedure, NamedThing, Entity
type*
String		Procedure, NamedThing, Entity
name0..1
LabelType		A human-readable name for an attribute or entityProcedure, NamedThing, Entity
description0..1
NarrativeText		a human-readable description of an entityProcedure, NamedThing, Entity
has_attribute*
Attribute		connects any entity to an attributeProcedure, NamedThing, Entity
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...Procedure, NamedThing, Entity
provided_by*
String		The value in this node property represents the knowledge provider that create...Procedure, NamedThing
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...Procedure, NamedThing
full_name0..1
LabelType		a long-form human readable name for a thingProcedure, NamedThing
synonym*
LabelType		Alternate human-readable names for a thingProcedure, NamedThing
+

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
DissectionRoiPolygonwas_generated_byrangeDissectionRoiDelineation
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:DissectionRoiDelineation
nativebican:DissectionRoiDelineation
+

LinkML Source

+ +

Direct

+
+
name: DissectionRoiDelineation
+description: The process of outlining a region of interest on a brain slab image to
+  guide the dissection and generation of a tissue sample.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slots:
+- used
+slot_usage:
+  used:
+    name: used
+    description: The brain slab that was annotated by the delineation process.
+    range: BrainSlab
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+
+
+
+

Induced

+
+
name: DissectionRoiDelineation
+description: The process of outlining a region of interest on a brain slab image to
+  guide the dissection and generation of a tissue sample.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slot_usage:
+  used:
+    name: used
+    description: The brain slab that was annotated by the delineation process.
+    range: BrainSlab
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  used:
+    name: used
+    description: The brain slab that was annotated by the delineation process.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: used
+    owner: DissectionRoiDelineation
+    domain_of:
+    - DissectionRoiDelineation
+    - TissueDissection
+    - CellDissociation
+    - CellEnrichment
+    - EnrichedCellSampleSplitting
+    - CellBarcoding
+    - CdnaAmplification
+    - LibraryConstruction
+    - LibraryPooling
+    - ProvActivity
+    range: BrainSlab
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: DissectionRoiDelineation
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: DissectionRoiDelineation
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: DissectionRoiDelineation
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+    pattern: ^bican:[A-Z][A-Za-z]+$
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: DissectionRoiDelineation
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: DissectionRoiDelineation
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - Donor
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DissectionRoiPolygon
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: DissectionRoiDelineation
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: DissectionRoiDelineation
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: DissectionRoiDelineation
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: DissectionRoiDelineation
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: DissectionRoiDelineation
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: DissectionRoiDelineation
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: DissectionRoiDelineation
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/DissectionRoiPolygon/index.html b/DissectionRoiPolygon/index.html new file mode 100644 index 00000000..8643774c --- /dev/null +++ b/DissectionRoiPolygon/index.html @@ -0,0 +1,1018 @@ + + + + + + + + + +Class: DissectionRoiPolygon - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: DissectionRoiPolygon

+

A polygon annotated on a brain slab image delineating a region of interest (ROI) for a tissue sample dissectioning.

+

URI: bican:DissectionRoiPolygon

+
classDiagram + class DissectionRoiPolygon + click DissectionRoiPolygon href "../DissectionRoiPolygon" + ProvEntity <|-- DissectionRoiPolygon + click ProvEntity href "../ProvEntity" + Entity <|-- DissectionRoiPolygon + click Entity href "../Entity" + + DissectionRoiPolygon : annotates + + + + + DissectionRoiPolygon --> "0..1" BrainSlab : annotates + click BrainSlab href "../BrainSlab" + + + DissectionRoiPolygon : category + + DissectionRoiPolygon : deprecated + + DissectionRoiPolygon : description + + DissectionRoiPolygon : has_attribute + + + + + DissectionRoiPolygon --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + DissectionRoiPolygon : id + + DissectionRoiPolygon : iri + + DissectionRoiPolygon : name + + DissectionRoiPolygon : type + + DissectionRoiPolygon : was_derived_from + + DissectionRoiPolygon : was_generated_by + + + + + DissectionRoiPolygon --> "0..1" DissectionRoiDelineation : was_generated_by + click DissectionRoiDelineation href "../DissectionRoiDelineation" + + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
was_generated_by0..1
DissectionRoiDelineation		The delineation process from which the dissection ROI polygon was generated b...direct
name0..1
LabelType		Name of a polygon annotated on a brain slab image delineating a region of int...direct
annotates0..1
BrainSlab		The brain slab that was annotated by the delineation processdirect
was_derived_from0..1
String		ProvEntity
id1
String		A unique identifier for an entityEntity
iri0..1
IriType		An IRI for an entityEntity
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizedEntity
type*
String		Entity
description0..1
NarrativeText		a human-readable description of an entityEntity
has_attribute*
Attribute		connects any entity to an attributeEntity
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...Entity
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
TissueSampledissection_was_guided_byrangeDissectionRoiPolygon
TissueDissectionwas_guided_byrangeDissectionRoiPolygon
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:DissectionRoiPolygon
nativebican:DissectionRoiPolygon
exactNIMP:Specimen%20Dissected%20ROI
+

LinkML Source

+ +

Direct

+
+
name: DissectionRoiPolygon
+description: A polygon annotated on a brain slab image delineating a region of interest
+  (ROI) for a tissue sample dissectioning.
+in_subset:
+- bican
+- tissue_specimen
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Specimen%20Dissected%20ROI
+is_a: entity
+mixins:
+- ProvEntity
+slots:
+- was_generated_by
+- name
+slot_usage:
+  was_generated_by:
+    name: was_generated_by
+    description: The delineation process from which the dissection ROI polygon was
+      generated by.
+    range: DissectionRoiDelineation
+  name:
+    name: name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: local_name
+    description: Name of a polygon annotated on a brain slab image delineating a region
+      of interest (ROI) for a tissue sample dissectioning.
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  annotates:
+    name: annotates
+    description: The brain slab that was annotated by the delineation process.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:has_parent
+    rank: 1000
+    domain_of:
+    - DissectionRoiPolygon
+    range: BrainSlab
+
+
+
+

Induced

+
+
name: DissectionRoiPolygon
+description: A polygon annotated on a brain slab image delineating a region of interest
+  (ROI) for a tissue sample dissectioning.
+in_subset:
+- bican
+- tissue_specimen
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Specimen%20Dissected%20ROI
+is_a: entity
+mixins:
+- ProvEntity
+slot_usage:
+  was_generated_by:
+    name: was_generated_by
+    description: The delineation process from which the dissection ROI polygon was
+      generated by.
+    range: DissectionRoiDelineation
+  name:
+    name: name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: local_name
+    description: Name of a polygon annotated on a brain slab image delineating a region
+      of interest (ROI) for a tissue sample dissectioning.
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  annotates:
+    name: annotates
+    description: The brain slab that was annotated by the delineation process.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:has_parent
+    rank: 1000
+    alias: annotates
+    owner: DissectionRoiPolygon
+    domain_of:
+    - DissectionRoiPolygon
+    range: BrainSlab
+  was_generated_by:
+    name: was_generated_by
+    description: The delineation process from which the dissection ROI polygon was
+      generated by.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: was_generated_by
+    owner: DissectionRoiPolygon
+    domain_of:
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryPool
+    - DissectionRoiPolygon
+    - ProvEntity
+    range: DissectionRoiDelineation
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: local_name
+    description: Name of a polygon annotated on a brain slab image delineating a region
+      of interest (ROI) for a tissue sample dissectioning.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: DissectionRoiPolygon
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - Donor
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DissectionRoiPolygon
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  was_derived_from:
+    name: was_derived_from
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: was_derived_from
+    owner: DissectionRoiPolygon
+    domain_of:
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DigitalAsset
+    - ProvEntity
+    range: string
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: DissectionRoiPolygon
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: DissectionRoiPolygon
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: DissectionRoiPolygon
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+    pattern: ^bican:[A-Z][A-Za-z]+$
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: DissectionRoiPolygon
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: DissectionRoiPolygon
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: DissectionRoiPolygon
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: DissectionRoiPolygon
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/DissociatedCellSample/index.html b/DissociatedCellSample/index.html new file mode 100644 index 00000000..c6626ba9 --- /dev/null +++ b/DissociatedCellSample/index.html @@ -0,0 +1,1316 @@ + + + + + + + + + +Class: DissociatedCellSample - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: DissociatedCellSample

+

A collection of dissociated cells or nuclei derived from dissociation of a tissue sample.

+

URI: bican:DissociatedCellSample

+
classDiagram + class DissociatedCellSample + click DissociatedCellSample href "../DissociatedCellSample" + ProvEntity <|-- DissociatedCellSample + click ProvEntity href "../ProvEntity" + MaterialSample <|-- DissociatedCellSample + click MaterialSample href "../MaterialSample" + + DissociatedCellSample : category + + DissociatedCellSample : cell_prep_type + + + + + DissociatedCellSample --> "0..1" DissociatedCellSampleCellPrepType : cell_prep_type + click DissociatedCellSampleCellPrepType href "../DissociatedCellSampleCellPrepType" + + + DissociatedCellSample : cell_source_oligo_name + + + + + DissociatedCellSample --> "0..1" DissociatedCellSampleCellLabelBarcode : cell_source_oligo_name + click DissociatedCellSampleCellLabelBarcode href "../DissociatedCellSampleCellLabelBarcode" + + + DissociatedCellSample : deprecated + + DissociatedCellSample : description + + DissociatedCellSample : full_name + + DissociatedCellSample : has_attribute + + + + + DissociatedCellSample --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + DissociatedCellSample : id + + DissociatedCellSample : iri + + DissociatedCellSample : name + + DissociatedCellSample : provided_by + + DissociatedCellSample : synonym + + DissociatedCellSample : type + + DissociatedCellSample : was_derived_from + + + + + DissociatedCellSample --> "*" TissueSample : was_derived_from + click TissueSample href "../TissueSample" + + + DissociatedCellSample : was_generated_by + + + + + DissociatedCellSample --> "0..1" CellDissociation : was_generated_by + click CellDissociation href "../CellDissociation" + + + DissociatedCellSample : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
was_generated_by0..1
CellDissociation		The cell dissociation process from which the dissociated cell sample was gene...direct
was_derived_from*
TissueSample		The input tissue sample(s) from which dissociated cell sample was derived fro...direct
name0..1
LabelType		Name of a collection of dissociated cells or nuclei derived from dissociation...direct
cell_prep_type0..1
DissociatedCellSampleCellPrepType		The type of cell preparationdirect
cell_source_oligo_name0..1
DissociatedCellSampleCellLabelBarcode		Name of cell source oligo used in cell plexingdirect
id1
String		A unique identifier for an entityNamedThing, MaterialSample, PhysicalEntity, Entity
iri0..1
IriType		An IRI for an entityNamedThing, MaterialSample, PhysicalEntity, Entity
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizedNamedThing, MaterialSample, PhysicalEntity, Entity
type*
String		NamedThing, MaterialSample, PhysicalEntity, Entity
description0..1
NarrativeText		a human-readable description of an entityNamedThing, MaterialSample, PhysicalEntity, Entity
has_attribute*
Attribute		connects any entity to an attributeNamedThing, MaterialSample, PhysicalEntity, Entity
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...NamedThing, MaterialSample, PhysicalEntity, Entity
provided_by*
String		The value in this node property represents the knowledge provider that create...NamedThing, MaterialSample, PhysicalEntity
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...NamedThing, MaterialSample, PhysicalEntity
full_name0..1
LabelType		a long-form human readable name for a thingNamedThing, MaterialSample, PhysicalEntity
synonym*
LabelType		Alternate human-readable names for a thingNamedThing, MaterialSample, PhysicalEntity
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
EnrichedCellSamplewas_derived_fromexactly_one_of[range]DissociatedCellSample
BarcodedCellSamplewas_derived_fromexactly_one_of[range]DissociatedCellSample
CellEnrichmentusedrangeDissociatedCellSample
CellBarcodingusedexactly_one_of[range]DissociatedCellSample
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:DissociatedCellSample
nativebican:DissociatedCellSample
exactNIMP:Dissociated%20Cell%20Sample
+

LinkML Source

+ +

Direct

+
+
name: DissociatedCellSample
+description: A collection of dissociated cells or nuclei derived from dissociation
+  of a tissue sample.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Dissociated%20Cell%20Sample
+is_a: material sample
+mixins:
+- ProvEntity
+slots:
+- was_generated_by
+- was_derived_from
+- name
+slot_usage:
+  was_generated_by:
+    name: was_generated_by
+    description: The cell dissociation process from which the dissociated cell sample
+      was generated by.
+    range: CellDissociation
+  was_derived_from:
+    name: was_derived_from
+    description: The input tissue sample(s) from which dissociated cell sample was
+      derived from.
+    exact_mappings:
+    - NIMP:has_parent
+    range: TissueSample
+    multivalued: true
+  name:
+    name: name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: dissociated_cell_sample_local_name
+    description: Name of a collection of dissociated cells or nuclei derived from
+      dissociation of a tissue sample.
+    exact_mappings:
+    - NIMP:PD-RQRWHS40
+    slot_uri: bican:65e2c7da-9eb4-45b2-8ccb-d69ef9785ee2
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  cell_prep_type:
+    name: cell_prep_type
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: dissociated_cell_sample_cell_prep_type
+    description: 'The type of cell preparation. For example: Cells, Nuclei. This is
+      a property of dissociated_cell_sample.'
+    in_subset:
+    - analysis
+    - tracking
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-RELLGO26
+    rank: 1000
+    slot_uri: bican:baae4ac3-f959-4594-b943-3a82ec19bd34
+    alias: dissociated cell sample cell prep type
+    domain_of:
+    - DissociatedCellSample
+    range: dissociated_cell_sample_cell_prep_type
+  cell_source_oligo_name:
+    name: cell_source_oligo_name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: dissociated_cell_sample_cell_label_barcode
+    description: Name of cell source oligo used in cell plexing.  The oligo molecularly
+      tags all the cells in the dissociated cell sample and allows separate dissociated
+      cell samples to be combined downstream in the barcoded cell sample.  The oligo
+      name is associated with a sequence in a lookup table.  This sequence will be
+      needed during alignment to associate reads with the parent source dissociated
+      cell sample.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-CFCFPS27
+    rank: 1000
+    slot_uri: bican:184abbaf-baff-4b5f-b51e-dd38de6006af
+    alias: dissociated cell oligo tag name
+    domain_of:
+    - DissociatedCellSample
+    - EnrichedCellSample
+    range: dissociated_cell_sample_cell_label_barcode
+
+
+
+

Induced

+
+
name: DissociatedCellSample
+description: A collection of dissociated cells or nuclei derived from dissociation
+  of a tissue sample.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Dissociated%20Cell%20Sample
+is_a: material sample
+mixins:
+- ProvEntity
+slot_usage:
+  was_generated_by:
+    name: was_generated_by
+    description: The cell dissociation process from which the dissociated cell sample
+      was generated by.
+    range: CellDissociation
+  was_derived_from:
+    name: was_derived_from
+    description: The input tissue sample(s) from which dissociated cell sample was
+      derived from.
+    exact_mappings:
+    - NIMP:has_parent
+    range: TissueSample
+    multivalued: true
+  name:
+    name: name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: dissociated_cell_sample_local_name
+    description: Name of a collection of dissociated cells or nuclei derived from
+      dissociation of a tissue sample.
+    exact_mappings:
+    - NIMP:PD-RQRWHS40
+    slot_uri: bican:65e2c7da-9eb4-45b2-8ccb-d69ef9785ee2
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  cell_prep_type:
+    name: cell_prep_type
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: dissociated_cell_sample_cell_prep_type
+    description: 'The type of cell preparation. For example: Cells, Nuclei. This is
+      a property of dissociated_cell_sample.'
+    in_subset:
+    - analysis
+    - tracking
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-RELLGO26
+    rank: 1000
+    slot_uri: bican:baae4ac3-f959-4594-b943-3a82ec19bd34
+    alias: dissociated cell sample cell prep type
+    owner: DissociatedCellSample
+    domain_of:
+    - DissociatedCellSample
+    range: dissociated_cell_sample_cell_prep_type
+  cell_source_oligo_name:
+    name: cell_source_oligo_name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: dissociated_cell_sample_cell_label_barcode
+    description: Name of cell source oligo used in cell plexing.  The oligo molecularly
+      tags all the cells in the dissociated cell sample and allows separate dissociated
+      cell samples to be combined downstream in the barcoded cell sample.  The oligo
+      name is associated with a sequence in a lookup table.  This sequence will be
+      needed during alignment to associate reads with the parent source dissociated
+      cell sample.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-CFCFPS27
+    rank: 1000
+    slot_uri: bican:184abbaf-baff-4b5f-b51e-dd38de6006af
+    alias: dissociated cell oligo tag name
+    owner: DissociatedCellSample
+    domain_of:
+    - DissociatedCellSample
+    - EnrichedCellSample
+    range: dissociated_cell_sample_cell_label_barcode
+  was_generated_by:
+    name: was_generated_by
+    description: The cell dissociation process from which the dissociated cell sample
+      was generated by.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: was_generated_by
+    owner: DissociatedCellSample
+    domain_of:
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryPool
+    - DissectionRoiPolygon
+    - ProvEntity
+    range: CellDissociation
+  was_derived_from:
+    name: was_derived_from
+    description: The input tissue sample(s) from which dissociated cell sample was
+      derived from.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:has_parent
+    rank: 1000
+    alias: was_derived_from
+    owner: DissociatedCellSample
+    domain_of:
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DigitalAsset
+    - ProvEntity
+    range: TissueSample
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: dissociated_cell_sample_local_name
+    description: Name of a collection of dissociated cells or nuclei derived from
+      dissociation of a tissue sample.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - NIMP:PD-RQRWHS40
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: bican:65e2c7da-9eb4-45b2-8ccb-d69ef9785ee2
+    alias: name
+    owner: DissociatedCellSample
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - Donor
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DissectionRoiPolygon
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: DissociatedCellSample
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: DissociatedCellSample
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: DissociatedCellSample
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+    pattern: ^bican:[A-Z][A-Za-z]+$
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: DissociatedCellSample
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: DissociatedCellSample
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: DissociatedCellSample
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: DissociatedCellSample
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: DissociatedCellSample
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: DissociatedCellSample
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: DissociatedCellSample
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: DissociatedCellSample
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/DissociatedCellSampleCellLabelBarcode/index.html b/DissociatedCellSampleCellLabelBarcode/index.html new file mode 100644 index 00000000..02c373b5 --- /dev/null +++ b/DissociatedCellSampleCellLabelBarcode/index.html @@ -0,0 +1,868 @@ + + + + + + + + + + + + + + + + + + + Enum: DissociatedCellSampleCellLabelBarcode - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
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+
+ + + + + + + +

Enum: DissociatedCellSampleCellLabelBarcode

+

URI: DissociatedCellSampleCellLabelBarcode

+

Permissible Values

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ValueMeaningDescription
CMO301NIMP:PD-CFCFPS2710x Cell Plex oligo tag for multiplexing tissue sources into a single 10x loa...
CMO302NIMP:PD-CFCFPS2710x Cell Plex oligo tag for multiplexing tissue sources into a single 10x loa...
CMO303NIMP:PD-CFCFPS2710x Cell Plex oligo tag for multiplexing tissue sources into a single 10x loa...
CMO304NIMP:PD-CFCFPS2710x Cell Plex oligo tag for multiplexing tissue sources into a single 10x loa...
CMO305NIMP:PD-CFCFPS2710x Cell Plex oligo tag for multiplexing tissue sources into a single 10x loa...
CMO306NIMP:PD-CFCFPS2710x Cell Plex oligo tag for multiplexing tissue sources into a single 10x loa...
CMO307NIMP:PD-CFCFPS2710x Cell Plex oligo tag for multiplexing tissue sources into a single 10x loa...
CMO308NIMP:PD-CFCFPS2710x Cell Plex oligo tag for multiplexing tissue sources into a single 10x loa...
CMO309NIMP:PD-CFCFPS2710x Cell Plex oligo tag for multiplexing tissue sources into a single 10x loa...
CMO310NIMP:PD-CFCFPS2710x Cell Plex oligo tag for multiplexing tissue sources into a single 10x loa...
CMO311NIMP:PD-CFCFPS2710x Cell Plex oligo tag for multiplexing tissue sources into a single 10x loa...
CMO312NIMP:PD-CFCFPS2710x Cell Plex oligo tag for multiplexing tissue sources into a single 10x loa...
2nt-001NIMP:PD-CFCFPS27Used in conjunction with Histone antibody to capture and tag separate subcomp...
2nt-002NIMP:PD-CFCFPS27Used in conjunction with Histone antibody to capture and tag separate subcomp...
2nt-003NIMP:PD-CFCFPS27Used in conjunction with Histone antibody to capture and tag separate subcomp...
2nt-004NIMP:PD-CFCFPS27Used in conjunction with Histone antibody to capture and tag separate subcomp...
3nt-001NIMP:PD-CFCFPS27Used in conjunction with Histone antibody to capture and tag separate subcomp...
3nt-002NIMP:PD-CFCFPS27Used in conjunction with Histone antibody to capture and tag separate subcomp...
3nt-003NIMP:PD-CFCFPS27Used in conjunction with Histone antibody to capture and tag separate subcomp...
3nt-004NIMP:PD-CFCFPS27Used in conjunction with Histone antibody to capture and tag separate subcomp...
3nt-005NIMP:PD-CFCFPS27Used in conjunction with Histone antibody to capture and tag separate subcomp...
3nt-006NIMP:PD-CFCFPS27Used in conjunction with Histone antibody to capture and tag separate subcomp...
+

Slots

+ + + + + + + + + + + + + +
NameDescription
cell_source_oligo_nameName of cell source oligo used in cell plexing
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

LinkML Source

+
+ +
name: dissociated_cell_sample_cell_label_barcode
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+rank: 1000
+permissible_values:
+  CMO301:
+    text: CMO301
+    description: 10x Cell Plex oligo tag for multiplexing tissue sources into a single
+      10x load.
+    meaning: NIMP:PD-CFCFPS27
+  CMO302:
+    text: CMO302
+    description: 10x Cell Plex oligo tag for multiplexing tissue sources into a single
+      10x load.
+    meaning: NIMP:PD-CFCFPS27
+  CMO303:
+    text: CMO303
+    description: 10x Cell Plex oligo tag for multiplexing tissue sources into a single
+      10x load.
+    meaning: NIMP:PD-CFCFPS27
+  CMO304:
+    text: CMO304
+    description: 10x Cell Plex oligo tag for multiplexing tissue sources into a single
+      10x load.
+    meaning: NIMP:PD-CFCFPS27
+  CMO305:
+    text: CMO305
+    description: 10x Cell Plex oligo tag for multiplexing tissue sources into a single
+      10x load.
+    meaning: NIMP:PD-CFCFPS27
+  CMO306:
+    text: CMO306
+    description: 10x Cell Plex oligo tag for multiplexing tissue sources into a single
+      10x load.
+    meaning: NIMP:PD-CFCFPS27
+  CMO307:
+    text: CMO307
+    description: 10x Cell Plex oligo tag for multiplexing tissue sources into a single
+      10x load.
+    meaning: NIMP:PD-CFCFPS27
+  CMO308:
+    text: CMO308
+    description: 10x Cell Plex oligo tag for multiplexing tissue sources into a single
+      10x load.
+    meaning: NIMP:PD-CFCFPS27
+  CMO309:
+    text: CMO309
+    description: 10x Cell Plex oligo tag for multiplexing tissue sources into a single
+      10x load.
+    meaning: NIMP:PD-CFCFPS27
+  CMO310:
+    text: CMO310
+    description: 10x Cell Plex oligo tag for multiplexing tissue sources into a single
+      10x load.
+    meaning: NIMP:PD-CFCFPS27
+  CMO311:
+    text: CMO311
+    description: 10x Cell Plex oligo tag for multiplexing tissue sources into a single
+      10x load.
+    meaning: NIMP:PD-CFCFPS27
+  CMO312:
+    text: CMO312
+    description: 10x Cell Plex oligo tag for multiplexing tissue sources into a single
+      10x load.
+    meaning: NIMP:PD-CFCFPS27
+  2nt-001:
+    text: 2nt-001
+    description: Used in conjunction with Histone antibody to capture and tag separate
+      subcomponents of the epigenome. Allows for pooling of enriched cell samples
+      into a single 10x load.
+    meaning: NIMP:PD-CFCFPS27
+  2nt-002:
+    text: 2nt-002
+    description: Used in conjunction with Histone antibody to capture and tag separate
+      subcomponents of the epigenome. Allows for pooling of enriched cell samples
+      into a single 10x load.
+    meaning: NIMP:PD-CFCFPS27
+  2nt-003:
+    text: 2nt-003
+    description: Used in conjunction with Histone antibody to capture and tag separate
+      subcomponents of the epigenome. Allows for pooling of enriched cell samples
+      into a single 10x load.
+    meaning: NIMP:PD-CFCFPS27
+  2nt-004:
+    text: 2nt-004
+    description: Used in conjunction with Histone antibody to capture and tag separate
+      subcomponents of the epigenome. Allows for pooling of enriched cell samples
+      into a single 10x load.
+    meaning: NIMP:PD-CFCFPS27
+  3nt-001:
+    text: 3nt-001
+    description: Used in conjunction with Histone antibody to capture and tag separate
+      subcomponents of the epigenome. Allows for pooling of enriched cell samples
+      into a single 10x load.
+    meaning: NIMP:PD-CFCFPS27
+  3nt-002:
+    text: 3nt-002
+    description: Used in conjunction with Histone antibody to capture and tag separate
+      subcomponents of the epigenome. Allows for pooling of enriched cell samples
+      into a single 10x load.
+    meaning: NIMP:PD-CFCFPS27
+  3nt-003:
+    text: 3nt-003
+    description: Used in conjunction with Histone antibody to capture and tag separate
+      subcomponents of the epigenome. Allows for pooling of enriched cell samples
+      into a single 10x load.
+    meaning: NIMP:PD-CFCFPS27
+  3nt-004:
+    text: 3nt-004
+    description: Used in conjunction with Histone antibody to capture and tag separate
+      subcomponents of the epigenome. Allows for pooling of enriched cell samples
+      into a single 10x load.
+    meaning: NIMP:PD-CFCFPS27
+  3nt-005:
+    text: 3nt-005
+    description: Used in conjunction with Histone antibody to capture and tag separate
+      subcomponents of the epigenome. Allows for pooling of enriched cell samples
+      into a single 10x load.
+    meaning: NIMP:PD-CFCFPS27
+  3nt-006:
+    text: 3nt-006
+    description: Used in conjunction with Histone antibody to capture and tag separate
+      subcomponents of the epigenome. Allows for pooling of enriched cell samples
+      into a single 10x load.
+    meaning: NIMP:PD-CFCFPS27
+
+
+ +
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/DissociatedCellSampleCellPrepType/index.html b/DissociatedCellSampleCellPrepType/index.html new file mode 100644 index 00000000..252be974 --- /dev/null +++ b/DissociatedCellSampleCellPrepType/index.html @@ -0,0 +1,656 @@ + + + + + + + + + + + + + + + + + + + Enum: DissociatedCellSampleCellPrepType - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
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+ + +
+ +
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+ + + + + +
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+ + + +
+
+ + + + + + + +

Enum: DissociatedCellSampleCellPrepType

+

URI: DissociatedCellSampleCellPrepType

+

Permissible Values

+ + + + + + + + + + + + + + + + + + + + +
ValueMeaningDescription
NucleiNIMP:PD-RELLGO26isolated nuclei
CellsNIMP:PD-RELLGO26isolated whole cells
+

Slots

+ + + + + + + + + + + + + +
NameDescription
cell_prep_typeThe type of cell preparation
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

LinkML Source

+
+ +
name: dissociated_cell_sample_cell_prep_type
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+rank: 1000
+permissible_values:
+  Nuclei:
+    text: Nuclei
+    description: isolated nuclei
+    meaning: NIMP:PD-RELLGO26
+  Cells:
+    text: Cells
+    description: isolated whole cells
+    meaning: NIMP:PD-RELLGO26
+
+
+ +
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/Donor/index.html b/Donor/index.html new file mode 100644 index 00000000..270119ab --- /dev/null +++ b/Donor/index.html @@ -0,0 +1,1472 @@ + + + + + + + + + +Class: Donor - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
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+ +
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+ +
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+ +
+
+
+
+
+

Class: Donor

+

A person or organism that is the source of a biological sample for scientific study. Many biological samples are generated from a single donor.

+

URI: bican:Donor

+
classDiagram + class Donor + click Donor href "../Donor" + ThingWithTaxon <|-- Donor + click ThingWithTaxon href "../ThingWithTaxon" + ProvEntity <|-- Donor + click ProvEntity href "../ProvEntity" + PhysicalEntity <|-- Donor + click PhysicalEntity href "../PhysicalEntity" + + Donor : age_at_death_description + + Donor : age_at_death_reference_point + + + + + Donor --> "0..1" age_at_death_reference_point : age_at_death_reference_point + click age_at_death_reference_point href "../age_at_death_reference_point" + + + Donor : age_at_death_unit + + + + + Donor --> "0..1" age_at_death_unit : age_at_death_unit + click age_at_death_unit href "../age_at_death_unit" + + + Donor : age_at_death_value + + Donor : biological_sex + + + + + Donor --> "0..1" Sex : biological_sex + click Sex href "../Sex" + + + Donor : category + + Donor : deprecated + + Donor : description + + Donor : full_name + + Donor : has_attribute + + + + + Donor --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + Donor : id + + Donor : in_taxon + + + + + Donor --> "*" OrganismTaxon : in_taxon + click OrganismTaxon href "../OrganismTaxon" + + + Donor : in_taxon_label + + Donor : iri + + Donor : name + + Donor : provided_by + + Donor : species + + Donor : synonym + + Donor : type + + Donor : was_derived_from + + Donor : was_generated_by + + Donor : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
name0..1
LabelType		Name of person or organism that is the source of a biological sample for scie...direct
biological_sex0..1
Sex		Biological sex of donor at birthdirect
age_at_death_description0..1
String		Text description of the age of death following typical scientific convention ...direct
age_at_death_reference_point0..1
age_at_death_reference_point		The reference point for an age interval; for example, birth or conceptiondirect
age_at_death_unit0..1
age_at_death_unit		The unit used for representing the donor age from the reference pointdirect
age_at_death_value0..1
Float		The value representing the donor age from the reference pointdirect
species0..1
String		Species of donordirect
in_taxon*
OrganismTaxon		connects an entity to its taxonomic classificationThingWithTaxon
in_taxon_label0..1
LabelType		The human readable scientific name for the taxon of the entityThingWithTaxon
was_derived_from0..1
String		ProvEntity
was_generated_by0..1
String		ProvEntity
id1
String		A unique identifier for an entityNamedThing, Entity, PhysicalEntity
iri0..1
IriType		An IRI for an entityNamedThing, Entity, PhysicalEntity
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizedNamedThing, Entity, PhysicalEntity
type*
String		NamedThing, Entity, PhysicalEntity
description0..1
NarrativeText		a human-readable description of an entityNamedThing, Entity, PhysicalEntity
has_attribute*
Attribute		connects any entity to an attributeNamedThing, Entity, PhysicalEntity
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...NamedThing, Entity, PhysicalEntity
provided_by*
String		The value in this node property represents the knowledge provider that create...NamedThing, PhysicalEntity
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...NamedThing, PhysicalEntity
full_name0..1
LabelType		a long-form human readable name for a thingNamedThing, PhysicalEntity
synonym*
LabelType		Alternate human-readable names for a thingNamedThing, PhysicalEntity
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
BrainSlabwas_derived_fromany_of[range]Donor
TissueSamplewas_derived_fromrangeDonor
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:Donor
nativebican:Donor
exactNIMP:Donor
+

LinkML Source

+ +

Direct

+
+
name: Donor
+description: A person or organism that is the source of a biological sample for scientific
+  study.  Many biological samples are generated from a single donor.
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Donor
+is_a: physical entity
+mixins:
+- thing with taxon
+- ProvEntity
+slots:
+- name
+slot_usage:
+  name:
+    name: name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: donor_local_id
+    description: Name of person or organism that is the source of a biological sample
+      for scientific study.  Many biological samples are generated from a single donor.
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  biological_sex:
+    name: biological_sex
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: sex
+    description: Biological sex of donor at birth
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-LXUBTM45
+    rank: 1000
+    slot_uri: bican:632d3d3f-f85b-4efc-a1ab-010fe417ae81
+    domain_of:
+    - Donor
+    range: sex
+  age_at_death_description:
+    name: age_at_death_description
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: age_at_death_description
+    description: 'Text description of the age of death following typical scientific
+      convention for the species or developmental stage. For example: P56, E11.5'
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-ZJZJLE33
+    rank: 1000
+    slot_uri: bican:0630a265-4a63-48f4-8853-66b929002306
+    domain_of:
+    - Donor
+  age_at_death_reference_point:
+    name: age_at_death_reference_point
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: age_at_death_reference_point
+    description: The reference point for an age interval; for example, birth or conception.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-RARAGG39
+    rank: 1000
+    slot_uri: bican:3bed1f94-9d82-4ed7-afdf-79d896b24dbb
+    domain_of:
+    - Donor
+    range: age_at_death_reference_point
+  age_at_death_unit:
+    name: age_at_death_unit
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: age_at_death_unit
+    description: The unit used for representing the donor age from the reference point.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-AVAVEV39
+    rank: 1000
+    slot_uri: bican:b5436e99-f0a7-4c30-825d-56b88ee2ac1d
+    domain_of:
+    - Donor
+    range: age_at_death_unit
+  age_at_death_value:
+    name: age_at_death_value
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: age_at_death
+    description: The value representing the donor age from the reference point.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-FTFTCP24
+    rank: 1000
+    slot_uri: bican:57e24d3c-c9c7-4ef3-9809-a35802d563ec
+    domain_of:
+    - Donor
+    range: float
+  species:
+    name: species
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: donor_species
+    description: Species of donor.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    slot_uri: bican:6837cb02-6bd7-4fb8-838c-9062ead96ba4
+    alias: donor_species
+    domain_of:
+    - Donor
+
+
+
+

Induced

+
+
name: Donor
+description: A person or organism that is the source of a biological sample for scientific
+  study.  Many biological samples are generated from a single donor.
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Donor
+is_a: physical entity
+mixins:
+- thing with taxon
+- ProvEntity
+slot_usage:
+  name:
+    name: name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: donor_local_id
+    description: Name of person or organism that is the source of a biological sample
+      for scientific study.  Many biological samples are generated from a single donor.
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  biological_sex:
+    name: biological_sex
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: sex
+    description: Biological sex of donor at birth
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-LXUBTM45
+    rank: 1000
+    slot_uri: bican:632d3d3f-f85b-4efc-a1ab-010fe417ae81
+    alias: biological_sex
+    owner: Donor
+    domain_of:
+    - Donor
+    range: sex
+  age_at_death_description:
+    name: age_at_death_description
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: age_at_death_description
+    description: 'Text description of the age of death following typical scientific
+      convention for the species or developmental stage. For example: P56, E11.5'
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-ZJZJLE33
+    rank: 1000
+    slot_uri: bican:0630a265-4a63-48f4-8853-66b929002306
+    alias: age_at_death_description
+    owner: Donor
+    domain_of:
+    - Donor
+    range: string
+  age_at_death_reference_point:
+    name: age_at_death_reference_point
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: age_at_death_reference_point
+    description: The reference point for an age interval; for example, birth or conception.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-RARAGG39
+    rank: 1000
+    slot_uri: bican:3bed1f94-9d82-4ed7-afdf-79d896b24dbb
+    alias: age_at_death_reference_point
+    owner: Donor
+    domain_of:
+    - Donor
+    range: age_at_death_reference_point
+  age_at_death_unit:
+    name: age_at_death_unit
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: age_at_death_unit
+    description: The unit used for representing the donor age from the reference point.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-AVAVEV39
+    rank: 1000
+    slot_uri: bican:b5436e99-f0a7-4c30-825d-56b88ee2ac1d
+    alias: age_at_death_unit
+    owner: Donor
+    domain_of:
+    - Donor
+    range: age_at_death_unit
+  age_at_death_value:
+    name: age_at_death_value
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: age_at_death
+    description: The value representing the donor age from the reference point.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-FTFTCP24
+    rank: 1000
+    slot_uri: bican:57e24d3c-c9c7-4ef3-9809-a35802d563ec
+    alias: age_at_death_value
+    owner: Donor
+    domain_of:
+    - Donor
+    range: float
+  species:
+    name: species
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: donor_species
+    description: Species of donor.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    slot_uri: bican:6837cb02-6bd7-4fb8-838c-9062ead96ba4
+    alias: donor_species
+    owner: Donor
+    domain_of:
+    - Donor
+    range: string
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: donor_local_id
+    description: Name of person or organism that is the source of a biological sample
+      for scientific study.  Many biological samples are generated from a single donor.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: Donor
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - Donor
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DissectionRoiPolygon
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  in taxon:
+    name: in taxon
+    definition_uri: https://w3id.org/biolink/vocab/in_taxon
+    annotations:
+      canonical_predicate:
+        tag: canonical_predicate
+        value: true
+    description: connects an entity to its taxonomic classification. Only certain
+      kinds of entities can be taxonomically classified; see 'thing with taxon'
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - instance of
+    - is organism source of gene product
+    - organism has gene
+    - gene found in organism
+    - gene product has organism source
+    exact_mappings:
+    - RO:0002162
+    - WIKIDATA_PROPERTY:P703
+    narrow_mappings:
+    - RO:0002160
+    rank: 1000
+    is_a: related to at instance level
+    domain: thing with taxon
+    slot_uri: biolink:in_taxon
+    inherited: true
+    alias: in_taxon
+    owner: Donor
+    domain_of:
+    - thing with taxon
+    - biological entity
+    - gene
+    - genome
+    range: organism taxon
+    multivalued: true
+  in taxon label:
+    name: in taxon label
+    definition_uri: https://w3id.org/biolink/vocab/in_taxon_label
+    annotations:
+      denormalized:
+        tag: denormalized
+        value: true
+    description: The human readable scientific name for the taxon of the entity.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P225
+    rank: 1000
+    is_a: node property
+    domain: thing with taxon
+    slot_uri: biolink:in_taxon_label
+    alias: in_taxon_label
+    owner: Donor
+    domain_of:
+    - thing with taxon
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  was_derived_from:
+    name: was_derived_from
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: was_derived_from
+    owner: Donor
+    domain_of:
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DigitalAsset
+    - ProvEntity
+    range: string
+  was_generated_by:
+    name: was_generated_by
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: was_generated_by
+    owner: Donor
+    domain_of:
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryPool
+    - DissectionRoiPolygon
+    - ProvEntity
+    range: string
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: Donor
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: Donor
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: Donor
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+    pattern: ^bican:[A-Z][A-Za-z]+$
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: Donor
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: Donor
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: Donor
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: Donor
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: Donor
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: Donor
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: Donor
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: Donor
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/Double/index.html b/Double/index.html new file mode 100644 index 00000000..5fe212f3 --- /dev/null +++ b/Double/index.html @@ -0,0 +1,614 @@ + + + + + + + + + + + + + + + + + + + Type: Double - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
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+ +
+ + + + + + +
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+ +
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Type: Double

+

A real number that conforms to the xsd:double specification

+

URI: xsd:double

+
    +
  • +

    base: float

    +
    • +
  • +

    uri: xsd:double

    +
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+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfxsd:double
nativebican:double
closeschema:Float
+ + + + + + + + + + + + + +
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+ + + + + +
+ +
+ + + +
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+ + + + + + + + + + \ No newline at end of file diff --git a/EnrichedCellSample/index.html b/EnrichedCellSample/index.html new file mode 100644 index 00000000..21e847aa --- /dev/null +++ b/EnrichedCellSample/index.html @@ -0,0 +1,1343 @@ + + + + + + + + + +Class: EnrichedCellSample - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
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+

Class: EnrichedCellSample

+

A collection of enriched cells or nuclei after enrichment process, usually via fluorescence-activated cell sorting (FACS) using the enrichment plan, is applied to dissociated cell sample.

+

URI: bican:EnrichedCellSample

+
classDiagram + class EnrichedCellSample + click EnrichedCellSample href "../EnrichedCellSample" + ProvEntity <|-- EnrichedCellSample + click ProvEntity href "../ProvEntity" + MaterialSample <|-- EnrichedCellSample + click MaterialSample href "../MaterialSample" + + EnrichedCellSample : category + + EnrichedCellSample : cell_source_oligo_name + + EnrichedCellSample : deprecated + + EnrichedCellSample : description + + EnrichedCellSample : enrichment_population + + EnrichedCellSample : full_name + + EnrichedCellSample : has_attribute + + + + + EnrichedCellSample --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + EnrichedCellSample : histone_modification_marker + + EnrichedCellSample : id + + EnrichedCellSample : iri + + EnrichedCellSample : name + + EnrichedCellSample : provided_by + + EnrichedCellSample : synonym + + EnrichedCellSample : type + + EnrichedCellSample : was_derived_from + + EnrichedCellSample : was_generated_by + + EnrichedCellSample : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
was_generated_by0..1
String or 
CellEnrichment or 
EnrichedCellSampleSplitting		The cell enrichment or sample splitting process from which the enriched cell ...direct
was_derived_from*
String or 
DissociatedCellSample or 
EnrichedCellSample		The dissociated or enriched cell sample(s) from which the enriched cell sampl...direct
name0..1
LabelType		Name of collection of enriched cells or nuclei after enrichment process (usua...direct
enrichment_population0..1
String		Actual percentage of cells as a result of using set of fluorescent marker lab...direct
cell_source_oligo_name0..1
String		Name of cell source oligo used in cell plexingdirect
histone_modification_marker0..1
String		Histone modification marker antibodies (eg H3K27ac, H3K27me3, H3K9me3) used i...direct
id1
String		A unique identifier for an entityNamedThing, MaterialSample, PhysicalEntity, Entity
iri0..1
IriType		An IRI for an entityNamedThing, MaterialSample, PhysicalEntity, Entity
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizedNamedThing, MaterialSample, PhysicalEntity, Entity
type*
String		NamedThing, MaterialSample, PhysicalEntity, Entity
description0..1
NarrativeText		a human-readable description of an entityNamedThing, MaterialSample, PhysicalEntity, Entity
has_attribute*
Attribute		connects any entity to an attributeNamedThing, MaterialSample, PhysicalEntity, Entity
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...NamedThing, MaterialSample, PhysicalEntity, Entity
provided_by*
String		The value in this node property represents the knowledge provider that create...NamedThing, MaterialSample, PhysicalEntity
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...NamedThing, MaterialSample, PhysicalEntity
full_name0..1
LabelType		a long-form human readable name for a thingNamedThing, MaterialSample, PhysicalEntity
synonym*
LabelType		Alternate human-readable names for a thingNamedThing, MaterialSample, PhysicalEntity
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
EnrichedCellSamplewas_derived_fromexactly_one_of[range]EnrichedCellSample
BarcodedCellSamplewas_derived_fromexactly_one_of[range]EnrichedCellSample
EnrichedCellSampleSplittingusedrangeEnrichedCellSample
CellBarcodingusedexactly_one_of[range]EnrichedCellSample
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:EnrichedCellSample
nativebican:EnrichedCellSample
exactNIMP:Enriched%20Cell%20Sample
+

LinkML Source

+ +

Direct

+
+
name: EnrichedCellSample
+description: A collection of enriched cells or nuclei after enrichment process, usually
+  via fluorescence-activated cell sorting (FACS) using the enrichment plan, is applied
+  to dissociated cell sample.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Enriched%20Cell%20Sample
+is_a: material sample
+mixins:
+- ProvEntity
+slots:
+- was_generated_by
+- was_derived_from
+- name
+slot_usage:
+  was_generated_by:
+    name: was_generated_by
+    description: The cell enrichment or sample splitting process from which the enriched
+      cell sample was generated by.
+    any_of:
+    - range: CellEnrichment
+    - range: EnrichedCellSampleSplitting
+  was_derived_from:
+    name: was_derived_from
+    description: The dissociated or enriched cell sample(s) from which the enriched
+      cell sample was derived from.
+    exact_mappings:
+    - NIMP:has_parent
+    multivalued: true
+    exactly_one_of:
+    - range: DissociatedCellSample
+    - range: EnrichedCellSample
+  name:
+    name: name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: enriched_cell_sample_local_name
+    description: Name of collection of enriched cells or nuclei after enrichment process
+      (usually via FACS using the Enrichment Plan) applied to dissociated_cell_sample.
+    exact_mappings:
+    - NIMP:PD-BERWTM41
+    slot_uri: bican:bb3fc701-23a7-45c1-890d-7471730e0ec1
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  enrichment_population:
+    name: enrichment_population
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: enrichment_population
+    description: Actual percentage of cells as a result of using set of fluorescent
+      marker label(s) to enrich dissociated_cell_sample with desired mix of cell populations.  This
+      plan can also be used to describe 'No FACS' where no enrichment was performed.  This
+      is a property of enriched_cell_prep_container.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-TZTZPI37
+    rank: 1000
+    slot_uri: bican:875f1c70-f5aa-45e3-94b9-5e482f6c4830
+    alias: enrichment population
+    domain_of:
+    - EnrichedCellSample
+    range: string
+  cell_source_oligo_name:
+    name: cell_source_oligo_name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: enriched_cell_sample_cell_label_barcode
+    description: Name of cell source oligo used in cell plexing.  The oligo molecularly
+      tags all the cells in the enriched cell sample and allows separate enriched
+      cell samples to be combined downstream in the barcoded cell sample.  The oligo
+      name is associated with a sequence in a lookup table.  This sequence will be
+      needed during alignment to associate reads with the parent source enriched cell
+      sample.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-CFCFPS27
+    domain_of:
+    - DissociatedCellSample
+    - EnrichedCellSample
+  histone_modification_marker:
+    name: histone_modification_marker
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: histone_modification_marker
+    description: Histone modification marker antibodies (eg H3K27ac, H3K27me3, H3K9me3)
+      used in conjunction with an Enriched Cell Source Barcode in order to combine
+      multiple Enriched Cell Populations before Barcoded Cell Sample step for 10xMultiome
+      method. Each of the Histone antibodies captures an essential part of the epigenome.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-ESESLW44
+    rank: 1000
+    domain_of:
+    - EnrichedCellSample
+
+
+
+

Induced

+
+
name: EnrichedCellSample
+description: A collection of enriched cells or nuclei after enrichment process, usually
+  via fluorescence-activated cell sorting (FACS) using the enrichment plan, is applied
+  to dissociated cell sample.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Enriched%20Cell%20Sample
+is_a: material sample
+mixins:
+- ProvEntity
+slot_usage:
+  was_generated_by:
+    name: was_generated_by
+    description: The cell enrichment or sample splitting process from which the enriched
+      cell sample was generated by.
+    any_of:
+    - range: CellEnrichment
+    - range: EnrichedCellSampleSplitting
+  was_derived_from:
+    name: was_derived_from
+    description: The dissociated or enriched cell sample(s) from which the enriched
+      cell sample was derived from.
+    exact_mappings:
+    - NIMP:has_parent
+    multivalued: true
+    exactly_one_of:
+    - range: DissociatedCellSample
+    - range: EnrichedCellSample
+  name:
+    name: name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: enriched_cell_sample_local_name
+    description: Name of collection of enriched cells or nuclei after enrichment process
+      (usually via FACS using the Enrichment Plan) applied to dissociated_cell_sample.
+    exact_mappings:
+    - NIMP:PD-BERWTM41
+    slot_uri: bican:bb3fc701-23a7-45c1-890d-7471730e0ec1
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  enrichment_population:
+    name: enrichment_population
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: enrichment_population
+    description: Actual percentage of cells as a result of using set of fluorescent
+      marker label(s) to enrich dissociated_cell_sample with desired mix of cell populations.  This
+      plan can also be used to describe 'No FACS' where no enrichment was performed.  This
+      is a property of enriched_cell_prep_container.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-TZTZPI37
+    rank: 1000
+    slot_uri: bican:875f1c70-f5aa-45e3-94b9-5e482f6c4830
+    alias: enrichment population
+    owner: EnrichedCellSample
+    domain_of:
+    - EnrichedCellSample
+    range: string
+  cell_source_oligo_name:
+    name: cell_source_oligo_name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: enriched_cell_sample_cell_label_barcode
+    description: Name of cell source oligo used in cell plexing.  The oligo molecularly
+      tags all the cells in the enriched cell sample and allows separate enriched
+      cell samples to be combined downstream in the barcoded cell sample.  The oligo
+      name is associated with a sequence in a lookup table.  This sequence will be
+      needed during alignment to associate reads with the parent source enriched cell
+      sample.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-CFCFPS27
+    alias: cell_source_oligo_name
+    owner: EnrichedCellSample
+    domain_of:
+    - DissociatedCellSample
+    - EnrichedCellSample
+    range: string
+  histone_modification_marker:
+    name: histone_modification_marker
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: histone_modification_marker
+    description: Histone modification marker antibodies (eg H3K27ac, H3K27me3, H3K9me3)
+      used in conjunction with an Enriched Cell Source Barcode in order to combine
+      multiple Enriched Cell Populations before Barcoded Cell Sample step for 10xMultiome
+      method. Each of the Histone antibodies captures an essential part of the epigenome.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-ESESLW44
+    rank: 1000
+    alias: histone_modification_marker
+    owner: EnrichedCellSample
+    domain_of:
+    - EnrichedCellSample
+    range: string
+  was_generated_by:
+    name: was_generated_by
+    description: The cell enrichment or sample splitting process from which the enriched
+      cell sample was generated by.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: was_generated_by
+    owner: EnrichedCellSample
+    domain_of:
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryPool
+    - DissectionRoiPolygon
+    - ProvEntity
+    range: string
+    any_of:
+    - range: CellEnrichment
+    - range: EnrichedCellSampleSplitting
+  was_derived_from:
+    name: was_derived_from
+    description: The dissociated or enriched cell sample(s) from which the enriched
+      cell sample was derived from.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:has_parent
+    rank: 1000
+    alias: was_derived_from
+    owner: EnrichedCellSample
+    domain_of:
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DigitalAsset
+    - ProvEntity
+    range: string
+    multivalued: true
+    exactly_one_of:
+    - range: DissociatedCellSample
+    - range: EnrichedCellSample
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: enriched_cell_sample_local_name
+    description: Name of collection of enriched cells or nuclei after enrichment process
+      (usually via FACS using the Enrichment Plan) applied to dissociated_cell_sample.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - NIMP:PD-BERWTM41
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: bican:bb3fc701-23a7-45c1-890d-7471730e0ec1
+    alias: name
+    owner: EnrichedCellSample
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - Donor
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DissectionRoiPolygon
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: EnrichedCellSample
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: EnrichedCellSample
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: EnrichedCellSample
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+    pattern: ^bican:[A-Z][A-Za-z]+$
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: EnrichedCellSample
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: EnrichedCellSample
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: EnrichedCellSample
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: EnrichedCellSample
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: EnrichedCellSample
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: EnrichedCellSample
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: EnrichedCellSample
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: EnrichedCellSample
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/EnrichedCellSampleSplitting/index.html b/EnrichedCellSampleSplitting/index.html new file mode 100644 index 00000000..38507be2 --- /dev/null +++ b/EnrichedCellSampleSplitting/index.html @@ -0,0 +1,1090 @@ + + + + + + + + + +Class: EnrichedCellSampleSplitting - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
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+ +
+
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+
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+ +
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+ +
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+

Class: EnrichedCellSampleSplitting

+

The process of splitting an enriched cell sample into several portions. Each portion may be used by the same or different groups for different scientific studies.

+

URI: bican:EnrichedCellSampleSplitting

+
classDiagram + class EnrichedCellSampleSplitting + click EnrichedCellSampleSplitting href "../EnrichedCellSampleSplitting" + ProvActivity <|-- EnrichedCellSampleSplitting + click ProvActivity href "../ProvActivity" + Procedure <|-- EnrichedCellSampleSplitting + click Procedure href "../Procedure" + + EnrichedCellSampleSplitting : category + + EnrichedCellSampleSplitting : deprecated + + EnrichedCellSampleSplitting : description + + EnrichedCellSampleSplitting : full_name + + EnrichedCellSampleSplitting : has_attribute + + + + + EnrichedCellSampleSplitting --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + EnrichedCellSampleSplitting : id + + EnrichedCellSampleSplitting : iri + + EnrichedCellSampleSplitting : name + + EnrichedCellSampleSplitting : provided_by + + EnrichedCellSampleSplitting : synonym + + EnrichedCellSampleSplitting : type + + EnrichedCellSampleSplitting : used + + + + + EnrichedCellSampleSplitting --> "0..1" EnrichedCellSample : used + click EnrichedCellSample href "../EnrichedCellSample" + + + EnrichedCellSampleSplitting : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
used0..1
EnrichedCellSample		The enrichment cell sample splitting process from which the enriched cell sam...direct
id1
String		A unique identifier for an entityProcedure, NamedThing, Entity
iri0..1
IriType		An IRI for an entityProcedure, NamedThing, Entity
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizedProcedure, NamedThing, Entity
type*
String		Procedure, NamedThing, Entity
name0..1
LabelType		A human-readable name for an attribute or entityProcedure, NamedThing, Entity
description0..1
NarrativeText		a human-readable description of an entityProcedure, NamedThing, Entity
has_attribute*
Attribute		connects any entity to an attributeProcedure, NamedThing, Entity
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...Procedure, NamedThing, Entity
provided_by*
String		The value in this node property represents the knowledge provider that create...Procedure, NamedThing
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...Procedure, NamedThing
full_name0..1
LabelType		a long-form human readable name for a thingProcedure, NamedThing
synonym*
LabelType		Alternate human-readable names for a thingProcedure, NamedThing
+

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
EnrichedCellSamplewas_generated_byany_of[range]EnrichedCellSampleSplitting
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:EnrichedCellSampleSplitting
nativebican:EnrichedCellSampleSplitting
+

LinkML Source

+ +

Direct

+
+
name: EnrichedCellSampleSplitting
+description: The process of splitting an enriched cell sample into several portions.
+  Each portion may be used by the same or different groups for different scientific
+  studies.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slots:
+- used
+slot_usage:
+  used:
+    name: used
+    description: The enrichment cell sample splitting process from which the enriched
+      cell sample was generated by.
+    range: EnrichedCellSample
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+
+
+
+

Induced

+
+
name: EnrichedCellSampleSplitting
+description: The process of splitting an enriched cell sample into several portions.
+  Each portion may be used by the same or different groups for different scientific
+  studies.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slot_usage:
+  used:
+    name: used
+    description: The enrichment cell sample splitting process from which the enriched
+      cell sample was generated by.
+    range: EnrichedCellSample
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  used:
+    name: used
+    description: The enrichment cell sample splitting process from which the enriched
+      cell sample was generated by.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: used
+    owner: EnrichedCellSampleSplitting
+    domain_of:
+    - DissectionRoiDelineation
+    - TissueDissection
+    - CellDissociation
+    - CellEnrichment
+    - EnrichedCellSampleSplitting
+    - CellBarcoding
+    - CdnaAmplification
+    - LibraryConstruction
+    - LibraryPooling
+    - ProvActivity
+    range: EnrichedCellSample
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: EnrichedCellSampleSplitting
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: EnrichedCellSampleSplitting
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: EnrichedCellSampleSplitting
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+    pattern: ^bican:[A-Z][A-Za-z]+$
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: EnrichedCellSampleSplitting
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: EnrichedCellSampleSplitting
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - Donor
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DissectionRoiPolygon
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: EnrichedCellSampleSplitting
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: EnrichedCellSampleSplitting
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: EnrichedCellSampleSplitting
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: EnrichedCellSampleSplitting
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: EnrichedCellSampleSplitting
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: EnrichedCellSampleSplitting
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: EnrichedCellSampleSplitting
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/Entity/index.html b/Entity/index.html new file mode 100644 index 00000000..9e8b808c --- /dev/null +++ b/Entity/index.html @@ -0,0 +1,1386 @@ + + + + + + + + + +Class: Entity - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
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+ +
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+ +
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+ +
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+

Class: Entity

+

Root Biolink Model class for all things and informational relationships, real or imagined.

+
    +
  • NOTE: this is an abstract class and should not be instantiated directly
    • +
+

URI: biolink:Entity

+
classDiagram + class Entity + click Entity href "../Entity" + Entity <|-- NamedThing + click NamedThing href "../NamedThing" + Entity <|-- Checksum + click Checksum href "../Checksum" + + Entity : category + + Entity : deprecated + + Entity : description + + Entity : has_attribute + + + + + Entity --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + Entity : id + + Entity : iri + + Entity : name + + Entity : type + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
id1
String		A unique identifier for an entitydirect
iri0..1
IriType		An IRI for an entitydirect
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizeddirect
type*
String		direct
name0..1
LabelType		A human-readable name for an attribute or entitydirect
description0..1
NarrativeText		a human-readable description of an entitydirect
has_attribute*
Attribute		connects any entity to an attributedirect
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...direct
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
GeneAnnotationiddomainEntity
GeneAnnotationcategorydomainEntity
GeneAnnotationtypedomainEntity
GeneAnnotationnamedomainEntity
GeneAnnotationhas_attributedomainEntity
GenomeAnnotationiddomainEntity
GenomeAnnotationcategorydomainEntity
GenomeAnnotationtypedomainEntity
GenomeAnnotationnamedomainEntity
GenomeAnnotationhas_attributedomainEntity
GenomeAssemblyiddomainEntity
GenomeAssemblycategorydomainEntity
GenomeAssemblytypedomainEntity
GenomeAssemblynamedomainEntity
GenomeAssemblyhas_attributedomainEntity
OntologyClassiddomainEntity
AttributeiddomainEntity
AttributecategorydomainEntity
AttributetypedomainEntity
Attributehas_attributedomainEntity
AttributenamedomainEntity
EntityiddomainEntity
EntitycategorydomainEntity
EntitytypedomainEntity
EntitynamedomainEntity
Entityhas_attributedomainEntity
NamedThingiddomainEntity
NamedThingcategorydomainEntity
NamedThingtypedomainEntity
NamedThingnamedomainEntity
NamedThinghas_attributedomainEntity
TaxonomicRankiddomainEntity
OrganismTaxoniddomainEntity
OrganismTaxoncategorydomainEntity
OrganismTaxontypedomainEntity
OrganismTaxonnamedomainEntity
OrganismTaxonhas_attributedomainEntity
InformationContentEntityiddomainEntity
InformationContentEntitycategorydomainEntity
InformationContentEntitytypedomainEntity
InformationContentEntitynamedomainEntity
InformationContentEntityhas_attributedomainEntity
DatasetiddomainEntity
DatasetcategorydomainEntity
DatasettypedomainEntity
DatasetnamedomainEntity
Datasethas_attributedomainEntity
PhysicalEntityiddomainEntity
PhysicalEntitycategorydomainEntity
PhysicalEntitytypedomainEntity
PhysicalEntitynamedomainEntity
PhysicalEntityhas_attributedomainEntity
ActivityiddomainEntity
ActivitycategorydomainEntity
ActivitytypedomainEntity
ActivitynamedomainEntity
Activityhas_attributedomainEntity
ProcedureiddomainEntity
ProcedurecategorydomainEntity
ProceduretypedomainEntity
ProcedurenamedomainEntity
Procedurehas_attributedomainEntity
MaterialSampleiddomainEntity
MaterialSamplecategorydomainEntity
MaterialSampletypedomainEntity
MaterialSamplenamedomainEntity
MaterialSamplehas_attributedomainEntity
BiologicalEntityiddomainEntity
BiologicalEntitycategorydomainEntity
BiologicalEntitytypedomainEntity
BiologicalEntitynamedomainEntity
BiologicalEntityhas_attributedomainEntity
MacromolecularMachineMixinnamedomainEntity
GeneOrGeneProductnamedomainEntity
GeneiddomainEntity
GenecategorydomainEntity
GenetypedomainEntity
GenenamedomainEntity
Genehas_attributedomainEntity
GenomeiddomainEntity
GenomecategorydomainEntity
GenometypedomainEntity
GenomenamedomainEntity
Genomehas_attributedomainEntity
ChecksumiddomainEntity
ChecksumcategorydomainEntity
ChecksumtypedomainEntity
ChecksumnamedomainEntity
Checksumhas_attributedomainEntity
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:Entity
nativebican:Entity
+

LinkML Source

+ +

Direct

+
+
name: entity
+definition_uri: https://w3id.org/biolink/vocab/Entity
+description: Root Biolink Model class for all things and informational relationships,
+  real or imagined.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+abstract: true
+slots:
+- id
+- iri
+- category
+- type
+- name
+- description
+- has attribute
+- deprecated
+class_uri: biolink:Entity
+
+
+
+

Induced

+
+
name: entity
+definition_uri: https://w3id.org/biolink/vocab/Entity
+description: Root Biolink Model class for all things and informational relationships,
+  real or imagined.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+abstract: true
+attributes:
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: entity
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: entity
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: entity
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: entity
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: entity
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: entity
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: entity
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: entity
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+class_uri: biolink:Entity
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/Float/index.html b/Float/index.html new file mode 100644 index 00000000..5c3adfd2 --- /dev/null +++ b/Float/index.html @@ -0,0 +1,614 @@ + + + + + + + + + + + + + + + + + + + Type: Float - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
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Type: Float

+

A real number that conforms to the xsd:float specification

+

URI: xsd:float

+
    +
  • +

    base: float

    +
    • +
  • +

    uri: xsd:float

    +
    • +
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfxsd:float
nativebican:float
exactschema:Float
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/FrequencyValue/index.html b/FrequencyValue/index.html new file mode 100644 index 00000000..88fb8552 --- /dev/null +++ b/FrequencyValue/index.html @@ -0,0 +1,612 @@ + + + + + + + + + + + + + + + + + + + Type: FrequencyValue - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
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+
+
+ + + +
+
+
+ + + +
+
+
+ + + +
+
+ + + + + + + +

Type: FrequencyValue

+

URI: UO:0000105

+ +

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfUO:0000105
nativebican:frequency_value
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/Gene/index.html b/Gene/index.html new file mode 100644 index 00000000..02dba611 --- /dev/null +++ b/Gene/index.html @@ -0,0 +1,1309 @@ + + + + + + + + + +Class: Gene - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
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+ +
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+ +
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+ +
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+
+

Class: Gene

+

A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions.

+

URI: biolink:Gene

+
classDiagram + class Gene + click Gene href "../Gene" + GeneOrGeneProduct <|-- Gene + click GeneOrGeneProduct href "../GeneOrGeneProduct" + GenomicEntity <|-- Gene + click GenomicEntity href "../GenomicEntity" + ChemicalEntityOrGeneOrGeneProduct <|-- Gene + click ChemicalEntityOrGeneOrGeneProduct href "../ChemicalEntityOrGeneOrGeneProduct" + PhysicalEssence <|-- Gene + click PhysicalEssence href "../PhysicalEssence" + OntologyClass <|-- Gene + click OntologyClass href "../OntologyClass" + BiologicalEntity <|-- Gene + click BiologicalEntity href "../BiologicalEntity" + + + Gene <|-- GeneAnnotation + click GeneAnnotation href "../GeneAnnotation" + + + Gene : category + + Gene : deprecated + + Gene : description + + Gene : full_name + + Gene : has_attribute + + + + + Gene --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + Gene : has_biological_sequence + + Gene : id + + Gene : in_taxon + + + + + Gene --> "*" OrganismTaxon : in_taxon + click OrganismTaxon href "../OrganismTaxon" + + + Gene : in_taxon_label + + Gene : iri + + Gene : name + + Gene : provided_by + + Gene : symbol + + Gene : synonym + + Gene : type + + Gene : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
id1
String		A unique identifier for an entitydirect
iri0..1
IriType		An IRI for an entitydirect
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizeddirect
type*
String		direct
name0..1
LabelType		A human-readable name for an attribute or entitydirect
description0..1
NarrativeText		a human-readable description of an entitydirect
has_attribute*
Attribute		connects any entity to an attributedirect
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...direct
provided_by*
String		The value in this node property represents the knowledge provider that create...direct
full_name0..1
LabelType		a long-form human readable name for a thingdirect
synonym*
LabelType		Alternate human-readable names for a thingdirect
in_taxon*
OrganismTaxon		connects an entity to its taxonomic classificationdirect
in_taxon_label0..1
LabelType		The human readable scientific name for the taxon of the entitydirect
symbol0..1
String		Symbol for a particular thingdirect
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...direct
has_biological_sequence0..1
BiologicalSequence		connects a genomic feature to its sequencedirect
+

Identifier and Mapping Information

+

Valid ID Prefixes

+

Instances of this class should have identifiers with one of the following prefixes:

+
    +
  • +

    NCBIGene

    +
    • +
  • +

    ENSEMBL

    +
    • +
  • +

    HGNC

    +
    • +
  • +

    MGI

    +
    • +
  • +

    ZFIN

    +
    • +
  • +

    dictyBase

    +
    • +
  • +

    WB

    +
    • +
  • +

    WormBase

    +
    • +
  • +

    FB

    +
    • +
  • +

    RGD

    +
    • +
  • +

    SGD

    +
    • +
  • +

    PomBase

    +
    • +
  • +

    OMIM

    +
    • +
  • +

    KEGG.GENES

    +
    • +
  • +

    UMLS

    +
    • +
  • +

    Xenbase

    +
    • +
  • +

    AspGD

    +
    • +
  • +

    PHARMGKB.GENE

    +
    • +
+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:Gene
nativebican:Gene
exactSO:0000704, SIO:010035, WIKIDATA:Q7187, dcid:Gene
narrowbioschemas:gene
broadNCIT:C45822
+

LinkML Source

+ +

Direct

+
+
name: gene
+id_prefixes:
+- NCBIGene
+- ENSEMBL
+- HGNC
+- MGI
+- ZFIN
+- dictyBase
+- WB
+- WormBase
+- FB
+- RGD
+- SGD
+- PomBase
+- OMIM
+- KEGG.GENES
+- UMLS
+- Xenbase
+- AspGD
+- PHARMGKB.GENE
+definition_uri: https://w3id.org/biolink/vocab/Gene
+description: A region (or regions) that includes all of the sequence elements necessary
+  to encode a functional transcript. A gene locus may include regulatory regions,
+  transcribed regions and/or other functional sequence regions.
+in_subset:
+- translator_minimal
+- model_organism_database
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- SO:0000704
+- SIO:010035
+- WIKIDATA:Q7187
+- dcid:Gene
+narrow_mappings:
+- bioschemas:gene
+broad_mappings:
+- NCIT:C45822
+is_a: biological entity
+mixins:
+- gene or gene product
+- genomic entity
+- chemical entity or gene or gene product
+- physical essence
+- ontology class
+slots:
+- id
+- iri
+- category
+- type
+- name
+- description
+- has attribute
+- deprecated
+- provided by
+- full name
+- synonym
+- in taxon
+- in taxon label
+- symbol
+- xref
+- has biological sequence
+class_uri: biolink:Gene
+
+
+
+

Induced

+
+
name: gene
+id_prefixes:
+- NCBIGene
+- ENSEMBL
+- HGNC
+- MGI
+- ZFIN
+- dictyBase
+- WB
+- WormBase
+- FB
+- RGD
+- SGD
+- PomBase
+- OMIM
+- KEGG.GENES
+- UMLS
+- Xenbase
+- AspGD
+- PHARMGKB.GENE
+definition_uri: https://w3id.org/biolink/vocab/Gene
+description: A region (or regions) that includes all of the sequence elements necessary
+  to encode a functional transcript. A gene locus may include regulatory regions,
+  transcribed regions and/or other functional sequence regions.
+in_subset:
+- translator_minimal
+- model_organism_database
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- SO:0000704
+- SIO:010035
+- WIKIDATA:Q7187
+- dcid:Gene
+narrow_mappings:
+- bioschemas:gene
+broad_mappings:
+- NCIT:C45822
+is_a: biological entity
+mixins:
+- gene or gene product
+- genomic entity
+- chemical entity or gene or gene product
+- physical essence
+- ontology class
+attributes:
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: gene
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: gene
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: gene
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: gene
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: gene
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: gene
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: gene
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: gene
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: gene
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: gene
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: gene
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+  in taxon:
+    name: in taxon
+    definition_uri: https://w3id.org/biolink/vocab/in_taxon
+    annotations:
+      canonical_predicate:
+        tag: canonical_predicate
+        value: true
+    description: connects an entity to its taxonomic classification. Only certain
+      kinds of entities can be taxonomically classified; see 'thing with taxon'
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - instance of
+    - is organism source of gene product
+    - organism has gene
+    - gene found in organism
+    - gene product has organism source
+    exact_mappings:
+    - RO:0002162
+    - WIKIDATA_PROPERTY:P703
+    narrow_mappings:
+    - RO:0002160
+    rank: 1000
+    is_a: related to at instance level
+    domain: thing with taxon
+    slot_uri: biolink:in_taxon
+    inherited: true
+    alias: in_taxon
+    owner: gene
+    domain_of:
+    - thing with taxon
+    - biological entity
+    - gene
+    - genome
+    range: organism taxon
+    multivalued: true
+  in taxon label:
+    name: in taxon label
+    definition_uri: https://w3id.org/biolink/vocab/in_taxon_label
+    annotations:
+      denormalized:
+        tag: denormalized
+        value: true
+    description: The human readable scientific name for the taxon of the entity.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P225
+    rank: 1000
+    is_a: node property
+    domain: thing with taxon
+    slot_uri: biolink:in_taxon_label
+    alias: in_taxon_label
+    owner: gene
+    domain_of:
+    - thing with taxon
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  symbol:
+    name: symbol
+    definition_uri: https://w3id.org/biolink/vocab/symbol
+    description: Symbol for a particular thing
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - AGRKB:symbol
+    - gpi:DB_Object_Symbol
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:symbol
+    alias: symbol
+    owner: gene
+    domain_of:
+    - gene
+    range: string
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: gene
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  has biological sequence:
+    name: has biological sequence
+    definition_uri: https://w3id.org/biolink/vocab/has_biological_sequence
+    description: connects a genomic feature to its sequence
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:has_biological_sequence
+    alias: has_biological_sequence
+    owner: gene
+    domain_of:
+    - genomic entity
+    - gene
+    - genome
+    range: biological sequence
+class_uri: biolink:Gene
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/GeneAnnotation/index.html b/GeneAnnotation/index.html new file mode 100644 index 00000000..b3dfa160 --- /dev/null +++ b/GeneAnnotation/index.html @@ -0,0 +1,1252 @@ + + + + + + + + + +Class: GeneAnnotation - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: GeneAnnotation

+

An annotation describing the location, boundaries, and functions of individual genes within a genome annotation.

+

URI: bican:GeneAnnotation

+
classDiagram + class GeneAnnotation + click GeneAnnotation href "../GeneAnnotation" + Gene <|-- GeneAnnotation + click Gene href "../Gene" + + GeneAnnotation : category + + GeneAnnotation : deprecated + + GeneAnnotation : description + + GeneAnnotation : full_name + + GeneAnnotation : has_attribute + + + + + GeneAnnotation --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + GeneAnnotation : has_biological_sequence + + GeneAnnotation : id + + GeneAnnotation : in_taxon + + + + + GeneAnnotation --> "*" OrganismTaxon : in_taxon + click OrganismTaxon href "../OrganismTaxon" + + + GeneAnnotation : in_taxon_label + + GeneAnnotation : iri + + GeneAnnotation : molecular_type + + GeneAnnotation : name + + GeneAnnotation : provided_by + + GeneAnnotation : referenced_in + + GeneAnnotation : source_id + + GeneAnnotation : symbol + + GeneAnnotation : synonym + + GeneAnnotation : type + + GeneAnnotation : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
molecular_type0..1
String or 
BioType or 
String		direct
source_id0..1
String		The authority specific identifierdirect
referenced_in1
String or 
GenomeAnnotation or 
String		The genome annotation that this gene annotation was referenced fromdirect
id1
String		A unique identifier for an entityEntity, Gene, BiologicalEntity, NamedThing, OntologyClass
iri0..1
IriType		An IRI for an entityBiologicalEntity, NamedThing, Entity, Gene
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizedBiologicalEntity, NamedThing, Entity, Gene
type*
String		BiologicalEntity, NamedThing, Entity, Gene
name0..1
LabelType		A human-readable name for an attribute or entityEntity, Gene, MacromolecularMachineMixin, BiologicalEntity, NamedThing, GeneOrGeneProduct
description0..1
NarrativeText		a human-readable description of an entityBiologicalEntity, NamedThing, Entity, Gene
has_attribute*
Attribute		connects any entity to an attributeBiologicalEntity, NamedThing, Entity, Gene
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...BiologicalEntity, NamedThing, Entity, Gene
provided_by*
String		The value in this node property represents the knowledge provider that create...BiologicalEntity, NamedThing, Gene
full_name0..1
LabelType		a long-form human readable name for a thingBiologicalEntity, NamedThing, Gene
synonym*
LabelType		Alternate human-readable names for a thingBiologicalEntity, NamedThing, Gene
in_taxon*
OrganismTaxon		connects an entity to its taxonomic classificationBiologicalEntity, ThingWithTaxon, Gene
in_taxon_label0..1
LabelType		The human readable scientific name for the taxon of the entityBiologicalEntity, ThingWithTaxon, Gene
symbol0..1
String		Symbol for a particular thingGene
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...BiologicalEntity, NamedThing, Gene
has_biological_sequence0..1
BiologicalSequence		connects a genomic feature to its sequenceGene, GenomicEntity
+

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
AnnotationCollectionannotationsrangeGeneAnnotation
+

Identifier and Mapping Information

+

Valid ID Prefixes

+

Instances of this class should have identifiers with one of the following prefixes:

+
    +
  • +

    ENSEMBL

    +
    • +
  • +

    MGI

    +
    • +
  • +

    NCBIGene

    +
    • +
+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:GeneAnnotation
nativebican:GeneAnnotation
+

LinkML Source

+ +

Direct

+
+
name: gene annotation
+id_prefixes:
+- ENSEMBL
+- MGI
+- NCBIGene
+description: An annotation describing the location, boundaries, and functions of  individual
+  genes within a genome annotation.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: gene
+slots:
+- molecular type
+- source id
+attributes:
+  referenced in:
+    name: referenced in
+    description: The genome annotation that this gene annotation was referenced from.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    domain_of:
+    - gene annotation
+    required: true
+    inlined: true
+    any_of:
+    - range: genome annotation
+    - range: string
+
+
+
+

Induced

+
+
name: gene annotation
+id_prefixes:
+- ENSEMBL
+- MGI
+- NCBIGene
+description: An annotation describing the location, boundaries, and functions of  individual
+  genes within a genome annotation.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: gene
+attributes:
+  referenced in:
+    name: referenced in
+    description: The genome annotation that this gene annotation was referenced from.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    alias: referenced_in
+    owner: gene annotation
+    domain_of:
+    - gene annotation
+    range: string
+    required: true
+    inlined: true
+    any_of:
+    - range: genome annotation
+    - range: string
+  molecular type:
+    name: molecular type
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    alias: molecular_type
+    owner: gene annotation
+    domain_of:
+    - gene annotation
+    range: string
+    any_of:
+    - range: BioType
+    - range: string
+  source id:
+    name: source id
+    description: The authority specific identifier.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    slot_uri: schema:identifier
+    alias: source_id
+    owner: gene annotation
+    domain_of:
+    - gene annotation
+    range: string
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: gene annotation
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: gene annotation
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: gene annotation
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: gene annotation
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: gene annotation
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: gene annotation
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: gene annotation
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: gene annotation
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: gene annotation
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: gene annotation
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: gene annotation
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+  in taxon:
+    name: in taxon
+    definition_uri: https://w3id.org/biolink/vocab/in_taxon
+    annotations:
+      canonical_predicate:
+        tag: canonical_predicate
+        value: true
+    description: connects an entity to its taxonomic classification. Only certain
+      kinds of entities can be taxonomically classified; see 'thing with taxon'
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - instance of
+    - is organism source of gene product
+    - organism has gene
+    - gene found in organism
+    - gene product has organism source
+    exact_mappings:
+    - RO:0002162
+    - WIKIDATA_PROPERTY:P703
+    narrow_mappings:
+    - RO:0002160
+    rank: 1000
+    is_a: related to at instance level
+    domain: thing with taxon
+    slot_uri: biolink:in_taxon
+    inherited: true
+    alias: in_taxon
+    owner: gene annotation
+    domain_of:
+    - thing with taxon
+    - biological entity
+    - gene
+    - genome
+    range: organism taxon
+    multivalued: true
+  in taxon label:
+    name: in taxon label
+    definition_uri: https://w3id.org/biolink/vocab/in_taxon_label
+    annotations:
+      denormalized:
+        tag: denormalized
+        value: true
+    description: The human readable scientific name for the taxon of the entity.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P225
+    rank: 1000
+    is_a: node property
+    domain: thing with taxon
+    slot_uri: biolink:in_taxon_label
+    alias: in_taxon_label
+    owner: gene annotation
+    domain_of:
+    - thing with taxon
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  symbol:
+    name: symbol
+    definition_uri: https://w3id.org/biolink/vocab/symbol
+    description: Symbol for a particular thing
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - AGRKB:symbol
+    - gpi:DB_Object_Symbol
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:symbol
+    alias: symbol
+    owner: gene annotation
+    domain_of:
+    - gene
+    range: string
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: gene annotation
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  has biological sequence:
+    name: has biological sequence
+    definition_uri: https://w3id.org/biolink/vocab/has_biological_sequence
+    description: connects a genomic feature to its sequence
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:has_biological_sequence
+    alias: has_biological_sequence
+    owner: gene annotation
+    domain_of:
+    - genomic entity
+    - gene
+    - genome
+    range: biological sequence
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/GeneOrGeneProduct/index.html b/GeneOrGeneProduct/index.html new file mode 100644 index 00000000..1bb32cb2 --- /dev/null +++ b/GeneOrGeneProduct/index.html @@ -0,0 +1,501 @@ + + + + + + + + + +Class: GeneOrGeneProduct - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
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+ +
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+ +
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+ +
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+

Class: GeneOrGeneProduct

+

A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another

+

URI: biolink:GeneOrGeneProduct

+
classDiagram + class GeneOrGeneProduct + click GeneOrGeneProduct href "../GeneOrGeneProduct" + MacromolecularMachineMixin <|-- GeneOrGeneProduct + click MacromolecularMachineMixin href "../MacromolecularMachineMixin" + + + GeneOrGeneProduct <|-- Gene + click Gene href "../Gene" + + + GeneOrGeneProduct : name + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
name0..1
LabelType		A human-readable name for an attribute or entitydirect
+

Mixin Usage

+ + + + + + + + + + + + + +
mixed intodescription
GeneA region (or regions) that includes all of the sequence elements necessary to...
+

Identifier and Mapping Information

+

Valid ID Prefixes

+

Instances of this class should have identifiers with one of the following prefixes:

+
    +
  • +

    CHEMBL.TARGET

    +
    • +
  • +

    IUPHAR.FAMILY

    +
    • +
+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:GeneOrGeneProduct
nativebican:GeneOrGeneProduct
+

LinkML Source

+ +

Direct

+
+
name: gene or gene product
+id_prefixes:
+- CHEMBL.TARGET
+- IUPHAR.FAMILY
+definition_uri: https://w3id.org/biolink/vocab/GeneOrGeneProduct
+description: A union of gene loci or gene products. Frequently an identifier for one
+  will be used as proxy for another
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: macromolecular machine mixin
+mixin: true
+slots:
+- name
+class_uri: biolink:GeneOrGeneProduct
+
+
+
+

Induced

+
+
name: gene or gene product
+id_prefixes:
+- CHEMBL.TARGET
+- IUPHAR.FAMILY
+definition_uri: https://w3id.org/biolink/vocab/GeneOrGeneProduct
+description: A union of gene loci or gene products. Frequently an identifier for one
+  will be used as proxy for another
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: macromolecular machine mixin
+mixin: true
+attributes:
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: gene or gene product
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+class_uri: biolink:GeneOrGeneProduct
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/Genome/index.html b/Genome/index.html new file mode 100644 index 00000000..26f17160 --- /dev/null +++ b/Genome/index.html @@ -0,0 +1,1156 @@ + + + + + + + + + +Class: Genome - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: Genome

+

A genome is the sum of genetic material within a cell or virion.

+

URI: biolink:Genome

+
classDiagram + class Genome + click Genome href "../Genome" + GenomicEntity <|-- Genome + click GenomicEntity href "../GenomicEntity" + PhysicalEssence <|-- Genome + click PhysicalEssence href "../PhysicalEssence" + OntologyClass <|-- Genome + click OntologyClass href "../OntologyClass" + BiologicalEntity <|-- Genome + click BiologicalEntity href "../BiologicalEntity" + + + Genome <|-- GenomeAnnotation + click GenomeAnnotation href "../GenomeAnnotation" + + + Genome : category + + Genome : deprecated + + Genome : description + + Genome : full_name + + Genome : has_attribute + + + + + Genome --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + Genome : has_biological_sequence + + Genome : id + + Genome : in_taxon + + + + + Genome --> "*" OrganismTaxon : in_taxon + click OrganismTaxon href "../OrganismTaxon" + + + Genome : in_taxon_label + + Genome : iri + + Genome : name + + Genome : provided_by + + Genome : synonym + + Genome : type + + Genome : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
id1
String		A unique identifier for an entitydirect
iri0..1
IriType		An IRI for an entitydirect
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizeddirect
type*
String		direct
name0..1
LabelType		A human-readable name for an attribute or entitydirect
description0..1
NarrativeText		a human-readable description of an entitydirect
has_attribute*
Attribute		connects any entity to an attributedirect
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...direct
provided_by*
String		The value in this node property represents the knowledge provider that create...direct
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...direct
full_name0..1
LabelType		a long-form human readable name for a thingdirect
synonym*
LabelType		Alternate human-readable names for a thingdirect
in_taxon*
OrganismTaxon		connects an entity to its taxonomic classificationdirect
in_taxon_label0..1
LabelType		The human readable scientific name for the taxon of the entitydirect
has_biological_sequence0..1
BiologicalSequence		connects a genomic feature to its sequencedirect
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:Genome
nativebican:Genome
exactSO:0001026, SIO:000984, WIKIDATA:Q7020
closedcid:GenomeAssemblyUnit
+

LinkML Source

+ +

Direct

+
+
name: genome
+definition_uri: https://w3id.org/biolink/vocab/Genome
+description: A genome is the sum of genetic material within a cell or virion.
+in_subset:
+- model_organism_database
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- SO:0001026
+- SIO:000984
+- WIKIDATA:Q7020
+close_mappings:
+- dcid:GenomeAssemblyUnit
+is_a: biological entity
+mixins:
+- genomic entity
+- physical essence
+- ontology class
+slots:
+- id
+- iri
+- category
+- type
+- name
+- description
+- has attribute
+- deprecated
+- provided by
+- xref
+- full name
+- synonym
+- in taxon
+- in taxon label
+- has biological sequence
+class_uri: biolink:Genome
+
+
+
+

Induced

+
+
name: genome
+definition_uri: https://w3id.org/biolink/vocab/Genome
+description: A genome is the sum of genetic material within a cell or virion.
+in_subset:
+- model_organism_database
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- SO:0001026
+- SIO:000984
+- WIKIDATA:Q7020
+close_mappings:
+- dcid:GenomeAssemblyUnit
+is_a: biological entity
+mixins:
+- genomic entity
+- physical essence
+- ontology class
+attributes:
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: genome
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: genome
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: genome
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: genome
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: genome
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: genome
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: genome
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: genome
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: genome
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: genome
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: genome
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: genome
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+  in taxon:
+    name: in taxon
+    definition_uri: https://w3id.org/biolink/vocab/in_taxon
+    annotations:
+      canonical_predicate:
+        tag: canonical_predicate
+        value: true
+    description: connects an entity to its taxonomic classification. Only certain
+      kinds of entities can be taxonomically classified; see 'thing with taxon'
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - instance of
+    - is organism source of gene product
+    - organism has gene
+    - gene found in organism
+    - gene product has organism source
+    exact_mappings:
+    - RO:0002162
+    - WIKIDATA_PROPERTY:P703
+    narrow_mappings:
+    - RO:0002160
+    rank: 1000
+    is_a: related to at instance level
+    domain: thing with taxon
+    slot_uri: biolink:in_taxon
+    inherited: true
+    alias: in_taxon
+    owner: genome
+    domain_of:
+    - thing with taxon
+    - biological entity
+    - gene
+    - genome
+    range: organism taxon
+    multivalued: true
+  in taxon label:
+    name: in taxon label
+    definition_uri: https://w3id.org/biolink/vocab/in_taxon_label
+    annotations:
+      denormalized:
+        tag: denormalized
+        value: true
+    description: The human readable scientific name for the taxon of the entity.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P225
+    rank: 1000
+    is_a: node property
+    domain: thing with taxon
+    slot_uri: biolink:in_taxon_label
+    alias: in_taxon_label
+    owner: genome
+    domain_of:
+    - thing with taxon
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  has biological sequence:
+    name: has biological sequence
+    definition_uri: https://w3id.org/biolink/vocab/has_biological_sequence
+    description: connects a genomic feature to its sequence
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:has_biological_sequence
+    alias: has_biological_sequence
+    owner: genome
+    domain_of:
+    - genomic entity
+    - gene
+    - genome
+    range: biological sequence
+class_uri: biolink:Genome
+
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+ + + + \ No newline at end of file diff --git a/GenomeAnnotation/index.html b/GenomeAnnotation/index.html new file mode 100644 index 00000000..b544ea56 --- /dev/null +++ b/GenomeAnnotation/index.html @@ -0,0 +1,1263 @@ + + + + + + + + + +Class: GenomeAnnotation - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
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Class: GenomeAnnotation

+

Location and nomenclature of genes and all of the coding regions in a genome assembly and the classification of genes and transcripts into types.

+

URI: bican:GenomeAnnotation

+
classDiagram + class GenomeAnnotation + click GenomeAnnotation href "../GenomeAnnotation" + Genome <|-- GenomeAnnotation + click Genome href "../Genome" + + GenomeAnnotation : authority + + + + + GenomeAnnotation --> "0..1" AuthorityType : authority + click AuthorityType href "../AuthorityType" + + + GenomeAnnotation : category + + GenomeAnnotation : content_url + + GenomeAnnotation : deprecated + + GenomeAnnotation : description + + GenomeAnnotation : digest + + GenomeAnnotation : full_name + + GenomeAnnotation : has_attribute + + + + + GenomeAnnotation --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + GenomeAnnotation : has_biological_sequence + + GenomeAnnotation : id + + GenomeAnnotation : in_taxon + + + + + GenomeAnnotation --> "*" OrganismTaxon : in_taxon + click OrganismTaxon href "../OrganismTaxon" + + + GenomeAnnotation : in_taxon_label + + GenomeAnnotation : iri + + GenomeAnnotation : name + + GenomeAnnotation : provided_by + + GenomeAnnotation : reference_assembly + + GenomeAnnotation : synonym + + GenomeAnnotation : type + + GenomeAnnotation : version + + GenomeAnnotation : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
version0..1
String		direct
digest*
String or 
Checksum or 
String		Stores checksum informationdirect
content_url*
String		direct
authority0..1
AuthorityType		The organization responsible for publishing the datadirect
reference_assembly1
String or 
GenomeAssembly or 
String		The reference genome assembly that this genome annotation was created fromdirect
id1
String		A unique identifier for an entityEntity, BiologicalEntity, NamedThing, OntologyClass, Genome
iri0..1
IriType		An IRI for an entityBiologicalEntity, NamedThing, Entity, Genome
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizedBiologicalEntity, NamedThing, Entity, Genome
type*
String		BiologicalEntity, NamedThing, Entity, Genome
name0..1
LabelType		A human-readable name for an attribute or entityBiologicalEntity, NamedThing, Entity, Genome
description0..1
NarrativeText		a human-readable description of an entityBiologicalEntity, NamedThing, Entity, Genome
has_attribute*
Attribute		connects any entity to an attributeBiologicalEntity, NamedThing, Entity, Genome
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...BiologicalEntity, NamedThing, Entity, Genome
provided_by*
String		The value in this node property represents the knowledge provider that create...BiologicalEntity, NamedThing, Genome
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...BiologicalEntity, NamedThing, Genome
full_name0..1
LabelType		a long-form human readable name for a thingBiologicalEntity, NamedThing, Genome
synonym*
LabelType		Alternate human-readable names for a thingBiologicalEntity, NamedThing, Genome
in_taxon*
OrganismTaxon		connects an entity to its taxonomic classificationBiologicalEntity, ThingWithTaxon, Genome
in_taxon_label0..1
LabelType		The human readable scientific name for the taxon of the entityBiologicalEntity, ThingWithTaxon, Genome
has_biological_sequence0..1
BiologicalSequence		connects a genomic feature to its sequenceGenomicEntity, Genome
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
GeneAnnotationreferenced_inany_of[range]GenomeAnnotation
AnnotationCollectiongenome_annotationsrangeGenomeAnnotation
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:GenomeAnnotation
nativebican:GenomeAnnotation
+

LinkML Source

+ +

Direct

+
+
name: genome annotation
+description: Location and nomenclature of genes and all of the coding regions in a
+  genome assembly  and the classification of genes and transcripts into types.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: genome
+slots:
+- version
+- digest
+- content_url
+- authority
+attributes:
+  reference assembly:
+    name: reference assembly
+    description: The reference genome assembly that this genome annotation was created
+      from.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    domain_of:
+    - genome annotation
+    required: true
+    inlined: true
+    any_of:
+    - range: genome assembly
+    - range: string
+
+
+
+

Induced

+
+
name: genome annotation
+description: Location and nomenclature of genes and all of the coding regions in a
+  genome assembly  and the classification of genes and transcripts into types.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: genome
+attributes:
+  reference assembly:
+    name: reference assembly
+    description: The reference genome assembly that this genome annotation was created
+      from.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    alias: reference_assembly
+    owner: genome annotation
+    domain_of:
+    - genome annotation
+    range: string
+    required: true
+    inlined: true
+    any_of:
+    - range: genome assembly
+    - range: string
+  version:
+    name: version
+    definition_uri: https://w3id.org/biolink/vocab/version
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    broad_mappings:
+    - pav:version
+    - owl:versionInfo
+    rank: 1000
+    is_a: node property
+    domain: dataset
+    slot_uri: biolink:version
+    alias: version
+    owner: genome annotation
+    domain_of:
+    - genome annotation
+    - genome assembly
+    range: string
+  digest:
+    name: digest
+    description: Stores checksum information.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    alias: digest
+    owner: genome annotation
+    domain_of:
+    - genome annotation
+    range: string
+    multivalued: true
+    inlined: true
+    inlined_as_list: true
+    any_of:
+    - range: checksum
+    - range: string
+  content_url:
+    name: content_url
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    slot_uri: schema:url
+    alias: content_url
+    owner: genome annotation
+    domain_of:
+    - genome annotation
+    range: string
+    multivalued: true
+  authority:
+    name: authority
+    description: The organization responsible for publishing the data.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    alias: authority
+    owner: genome annotation
+    domain_of:
+    - genome annotation
+    range: AuthorityType
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: genome annotation
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: genome annotation
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: genome annotation
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: genome annotation
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: genome annotation
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: genome annotation
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: genome annotation
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: genome annotation
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: genome annotation
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: genome annotation
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: genome annotation
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: genome annotation
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+  in taxon:
+    name: in taxon
+    definition_uri: https://w3id.org/biolink/vocab/in_taxon
+    annotations:
+      canonical_predicate:
+        tag: canonical_predicate
+        value: true
+    description: connects an entity to its taxonomic classification. Only certain
+      kinds of entities can be taxonomically classified; see 'thing with taxon'
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - instance of
+    - is organism source of gene product
+    - organism has gene
+    - gene found in organism
+    - gene product has organism source
+    exact_mappings:
+    - RO:0002162
+    - WIKIDATA_PROPERTY:P703
+    narrow_mappings:
+    - RO:0002160
+    rank: 1000
+    is_a: related to at instance level
+    domain: thing with taxon
+    slot_uri: biolink:in_taxon
+    inherited: true
+    alias: in_taxon
+    owner: genome annotation
+    domain_of:
+    - thing with taxon
+    - biological entity
+    - gene
+    - genome
+    range: organism taxon
+    multivalued: true
+  in taxon label:
+    name: in taxon label
+    definition_uri: https://w3id.org/biolink/vocab/in_taxon_label
+    annotations:
+      denormalized:
+        tag: denormalized
+        value: true
+    description: The human readable scientific name for the taxon of the entity.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P225
+    rank: 1000
+    is_a: node property
+    domain: thing with taxon
+    slot_uri: biolink:in_taxon_label
+    alias: in_taxon_label
+    owner: genome annotation
+    domain_of:
+    - thing with taxon
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  has biological sequence:
+    name: has biological sequence
+    definition_uri: https://w3id.org/biolink/vocab/has_biological_sequence
+    description: connects a genomic feature to its sequence
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:has_biological_sequence
+    alias: has_biological_sequence
+    owner: genome annotation
+    domain_of:
+    - genomic entity
+    - gene
+    - genome
+    range: biological sequence
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/GenomeAssembly/index.html b/GenomeAssembly/index.html new file mode 100644 index 00000000..0213f470 --- /dev/null +++ b/GenomeAssembly/index.html @@ -0,0 +1,1147 @@ + + + + + + + + + +Class: GenomeAssembly - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: GenomeAssembly

+

Genome assembly to contain version and label information

+

URI: bican:GenomeAssembly

+
classDiagram + class GenomeAssembly + click GenomeAssembly href "../GenomeAssembly" + ThingWithTaxon <|-- GenomeAssembly + click ThingWithTaxon href "../ThingWithTaxon" + NamedThing <|-- GenomeAssembly + click NamedThing href "../NamedThing" + + GenomeAssembly : category + + GenomeAssembly : deprecated + + GenomeAssembly : description + + GenomeAssembly : full_name + + GenomeAssembly : has_attribute + + + + + GenomeAssembly --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + GenomeAssembly : id + + GenomeAssembly : in_taxon + + + + + GenomeAssembly --> "*" OrganismTaxon : in_taxon + click OrganismTaxon href "../OrganismTaxon" + + + GenomeAssembly : in_taxon_label + + GenomeAssembly : iri + + GenomeAssembly : name + + GenomeAssembly : provided_by + + GenomeAssembly : strain + + GenomeAssembly : synonym + + GenomeAssembly : type + + GenomeAssembly : version + + GenomeAssembly : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
version0..1
String		direct
strain0..1
String		The genetic variant or subtype of a species or organismdirect
in_taxon*
OrganismTaxon		connects an entity to its taxonomic classificationThingWithTaxon
in_taxon_label0..1
LabelType		The human readable scientific name for the taxon of the entityThingWithTaxon
id1
String		A unique identifier for an entityNamedThing, Entity
iri0..1
IriType		An IRI for an entityNamedThing, Entity
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizedNamedThing, Entity
type*
String		NamedThing, Entity
name0..1
LabelType		A human-readable name for an attribute or entityNamedThing, Entity
description0..1
NarrativeText		a human-readable description of an entityNamedThing, Entity
has_attribute*
Attribute		connects any entity to an attributeNamedThing, Entity
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...NamedThing, Entity
provided_by*
String		The value in this node property represents the knowledge provider that create...NamedThing
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...NamedThing
full_name0..1
LabelType		a long-form human readable name for a thingNamedThing
synonym*
LabelType		Alternate human-readable names for a thingNamedThing
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
GenomeAnnotationreference_assemblyany_of[range]GenomeAssembly
AnnotationCollectiongenome_assembliesrangeGenomeAssembly
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:GenomeAssembly
nativebican:GenomeAssembly
+

LinkML Source

+ +

Direct

+
+
name: genome assembly
+description: Genome assembly to contain version and label information
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: named thing
+mixins:
+- thing with taxon
+slots:
+- version
+- strain
+
+
+
+

Induced

+
+
name: genome assembly
+description: Genome assembly to contain version and label information
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: named thing
+mixins:
+- thing with taxon
+attributes:
+  version:
+    name: version
+    definition_uri: https://w3id.org/biolink/vocab/version
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    broad_mappings:
+    - pav:version
+    - owl:versionInfo
+    rank: 1000
+    is_a: node property
+    domain: dataset
+    slot_uri: biolink:version
+    alias: version
+    owner: genome assembly
+    domain_of:
+    - genome annotation
+    - genome assembly
+    range: string
+  strain:
+    name: strain
+    description: The genetic variant or subtype of a species or organism.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    alias: strain
+    owner: genome assembly
+    domain_of:
+    - genome assembly
+    range: string
+  in taxon:
+    name: in taxon
+    definition_uri: https://w3id.org/biolink/vocab/in_taxon
+    annotations:
+      canonical_predicate:
+        tag: canonical_predicate
+        value: true
+    description: connects an entity to its taxonomic classification. Only certain
+      kinds of entities can be taxonomically classified; see 'thing with taxon'
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - instance of
+    - is organism source of gene product
+    - organism has gene
+    - gene found in organism
+    - gene product has organism source
+    exact_mappings:
+    - RO:0002162
+    - WIKIDATA_PROPERTY:P703
+    narrow_mappings:
+    - RO:0002160
+    rank: 1000
+    is_a: related to at instance level
+    domain: thing with taxon
+    slot_uri: biolink:in_taxon
+    inherited: true
+    alias: in_taxon
+    owner: genome assembly
+    domain_of:
+    - thing with taxon
+    - biological entity
+    - gene
+    - genome
+    range: organism taxon
+    multivalued: true
+  in taxon label:
+    name: in taxon label
+    definition_uri: https://w3id.org/biolink/vocab/in_taxon_label
+    annotations:
+      denormalized:
+        tag: denormalized
+        value: true
+    description: The human readable scientific name for the taxon of the entity.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P225
+    rank: 1000
+    is_a: node property
+    domain: thing with taxon
+    slot_uri: biolink:in_taxon_label
+    alias: in_taxon_label
+    owner: genome assembly
+    domain_of:
+    - thing with taxon
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: genome assembly
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: genome assembly
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: genome assembly
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: genome assembly
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: genome assembly
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: genome assembly
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: genome assembly
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: genome assembly
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: genome assembly
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: genome assembly
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: genome assembly
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: genome assembly
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/GenomicEntity/index.html b/GenomicEntity/index.html new file mode 100644 index 00000000..fe623000 --- /dev/null +++ b/GenomicEntity/index.html @@ -0,0 +1,447 @@ + + + + + + + + + +Class: GenomicEntity - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: GenomicEntity

+

URI: biolink:GenomicEntity

+
classDiagram + class GenomicEntity + click GenomicEntity href "../GenomicEntity" + GenomicEntity <|-- Gene + click Gene href "../Gene" + GenomicEntity <|-- Genome + click Genome href "../Genome" + + GenomicEntity : has_biological_sequence + + +
+ +

Slots

+ + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
has_biological_sequence0..1
BiologicalSequence		connects a genomic feature to its sequencedirect
+

Mixin Usage

+ + + + + + + + + + + + + + + + + +
mixed intodescription
GeneA region (or regions) that includes all of the sequence elements necessary to...
GenomeA genome is the sum of genetic material within a cell or virion
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:GenomicEntity
nativebican:GenomicEntity
narrowSTY:T028, GENO:0000897
+

LinkML Source

+ +

Direct

+
+
name: genomic entity
+definition_uri: https://w3id.org/biolink/vocab/GenomicEntity
+in_subset:
+- translator_minimal
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+narrow_mappings:
+- STY:T028
+- GENO:0000897
+mixin: true
+slots:
+- has biological sequence
+class_uri: biolink:GenomicEntity
+
+
+
+

Induced

+
+
name: genomic entity
+definition_uri: https://w3id.org/biolink/vocab/GenomicEntity
+in_subset:
+- translator_minimal
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+narrow_mappings:
+- STY:T028
+- GENO:0000897
+mixin: true
+attributes:
+  has biological sequence:
+    name: has biological sequence
+    definition_uri: https://w3id.org/biolink/vocab/has_biological_sequence
+    description: connects a genomic feature to its sequence
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:has_biological_sequence
+    alias: has_biological_sequence
+    owner: genomic entity
+    domain_of:
+    - genomic entity
+    - gene
+    - genome
+    range: biological sequence
+class_uri: biolink:GenomicEntity
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/ImageDataset/index.html b/ImageDataset/index.html new file mode 100644 index 00000000..f1a697af --- /dev/null +++ b/ImageDataset/index.html @@ -0,0 +1,883 @@ + + + + + + + + + +Class: ImageDataset - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: ImageDataset

+

An image dataset is versioned release of a multidimensional regular grid of measurements and metadata required for a morphological representation of an entity such as an anatomical structure (ref: OBI_0003327, RRID:SCR_006266)

+

URI: AnS:ImageDataset

+
classDiagram + class ImageDataset + click ImageDataset href "../ImageDataset" + VersionedNamedThing <|-- ImageDataset + click VersionedNamedThing href "../VersionedNamedThing" + + ImageDataset : category + + ImageDataset : description + + ImageDataset : id + + ImageDataset : name + + ImageDataset : revision_of + + + + + ImageDataset --> "0..1" VersionedNamedThing : revision_of + click VersionedNamedThing href "../VersionedNamedThing" + + + ImageDataset : unit + + + + + ImageDataset --> "0..1" DISTANCEUNIT : unit + click DISTANCEUNIT href "../DISTANCEUNIT" + + + ImageDataset : version + + ImageDataset : x_direction + + + + + ImageDataset --> "0..1" ANATOMICALDIRECTION : x_direction + click ANATOMICALDIRECTION href "../ANATOMICALDIRECTION" + + + ImageDataset : x_resolution + + ImageDataset : x_size + + ImageDataset : y_direction + + + + + ImageDataset --> "0..1" ANATOMICALDIRECTION : y_direction + click ANATOMICALDIRECTION href "../ANATOMICALDIRECTION" + + + ImageDataset : y_resolution + + ImageDataset : y_size + + ImageDataset : z_direction + + + + + ImageDataset --> "0..1" ANATOMICALDIRECTION : z_direction + click ANATOMICALDIRECTION href "../ANATOMICALDIRECTION" + + + ImageDataset : z_resolution + + ImageDataset : z_size + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
x_direction0..1
ANATOMICALDIRECTION		A controlled vocabulary attribute defining the x axis direction in terms of a...direct
y_direction0..1
ANATOMICALDIRECTION		A controlled vocabulary attribute defining the y axis direction in terms of a...direct
z_direction0..1
ANATOMICALDIRECTION		A controlled vocabulary attribute defining the z axis direction in terms of a...direct
x_size0..1
Integer		The number of pixels/voxels (size) along the x axisdirect
y_size0..1
Integer		The number of pixels/voxels (size) along the y axisdirect
z_size0..1
Integer		The number of pixels/voxels (size) along the y axisdirect
x_resolution0..1
Float		The resolution (length / pixel) in along the x axis (numerical value part)direct
y_resolution0..1
Float		The resolution (length / pixel) in along the y axis (numerical value part)direct
z_resolution0..1
Float		The resolution (length / pixel) in along the z axis (numerical value part)direct
unit0..1
DISTANCEUNIT		A controlled vocabulary attribute defining the length unit of the x, y, and z...direct
version1
String		VersionedNamedThing
revision_of0..1
VersionedNamedThing or 
ImageDataset or 
String		VersionedNamedThing
id1
Uriorcurie		NamedThing
name1
String		NamedThing
description1
String		NamedThing
category*
Uriorcurie		NamedThing
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
ImageDatasetrevision_ofany_of[range]ImageDataset
AnatomicalSpacemeasuresany_of[range]ImageDataset
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/my-org/anatomical-structure-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfAnS:ImageDataset
nativeAnS:ImageDataset
+

LinkML Source

+ +

Direct

+
+
name: ImageDataset
+description: 'An image dataset is versioned release of a multidimensional regular
+  grid of measurements  and metadata required for a morphological representation of
+  an entity such as an anatomical  structure (ref: OBI_0003327, RRID:SCR_006266)'
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: VersionedNamedThing
+slot_usage:
+  revision_of:
+    name: revision_of
+    any_of:
+    - range: ImageDataset
+    - range: string
+attributes:
+  x_direction:
+    name: x_direction
+    description: A controlled vocabulary attribute defining the x axis direction in
+      terms of anatomical  direction.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ImageDataset
+    range: ANATOMICAL_DIRECTION
+  y_direction:
+    name: y_direction
+    description: A controlled vocabulary attribute defining the y axis direction in
+      terms of anatomical  direction.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ImageDataset
+    range: ANATOMICAL_DIRECTION
+  z_direction:
+    name: z_direction
+    description: A controlled vocabulary attribute defining the z axis direction in
+      terms of anatomical  direction.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ImageDataset
+    range: ANATOMICAL_DIRECTION
+  x_size:
+    name: x_size
+    description: The number of pixels/voxels (size) along the x axis.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ImageDataset
+    range: integer
+    minimum_value: 1
+  y_size:
+    name: y_size
+    description: The number of pixels/voxels (size) along the y axis.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ImageDataset
+    range: integer
+    minimum_value: 1
+  z_size:
+    name: z_size
+    description: The number of pixels/voxels (size) along the y axis.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ImageDataset
+    range: integer
+    minimum_value: 1
+  x_resolution:
+    name: x_resolution
+    description: The resolution (length / pixel) in along the x axis (numerical value
+      part).
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ImageDataset
+    range: float
+    structured_pattern:
+      syntax: '{PositiveFloat}'
+  y_resolution:
+    name: y_resolution
+    description: The resolution (length / pixel) in along the y axis (numerical value
+      part).
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ImageDataset
+    range: float
+    structured_pattern:
+      syntax: '{PositiveFloat}'
+  z_resolution:
+    name: z_resolution
+    description: The resolution (length / pixel) in along the z axis (numerical value
+      part).
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ImageDataset
+    range: float
+    structured_pattern:
+      syntax: '{PositiveFloat}'
+  unit:
+    name: unit
+    description: A controlled vocabulary attribute defining the length unit of the
+      x, y, and z  resolution values.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ImageDataset
+    range: DISTANCE_UNIT
+
+
+
+

Induced

+
+
name: ImageDataset
+description: 'An image dataset is versioned release of a multidimensional regular
+  grid of measurements  and metadata required for a morphological representation of
+  an entity such as an anatomical  structure (ref: OBI_0003327, RRID:SCR_006266)'
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: VersionedNamedThing
+slot_usage:
+  revision_of:
+    name: revision_of
+    any_of:
+    - range: ImageDataset
+    - range: string
+attributes:
+  x_direction:
+    name: x_direction
+    description: A controlled vocabulary attribute defining the x axis direction in
+      terms of anatomical  direction.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: x_direction
+    owner: ImageDataset
+    domain_of:
+    - ImageDataset
+    range: ANATOMICAL_DIRECTION
+  y_direction:
+    name: y_direction
+    description: A controlled vocabulary attribute defining the y axis direction in
+      terms of anatomical  direction.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: y_direction
+    owner: ImageDataset
+    domain_of:
+    - ImageDataset
+    range: ANATOMICAL_DIRECTION
+  z_direction:
+    name: z_direction
+    description: A controlled vocabulary attribute defining the z axis direction in
+      terms of anatomical  direction.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: z_direction
+    owner: ImageDataset
+    domain_of:
+    - ImageDataset
+    range: ANATOMICAL_DIRECTION
+  x_size:
+    name: x_size
+    description: The number of pixels/voxels (size) along the x axis.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: x_size
+    owner: ImageDataset
+    domain_of:
+    - ImageDataset
+    range: integer
+    minimum_value: 1
+  y_size:
+    name: y_size
+    description: The number of pixels/voxels (size) along the y axis.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: y_size
+    owner: ImageDataset
+    domain_of:
+    - ImageDataset
+    range: integer
+    minimum_value: 1
+  z_size:
+    name: z_size
+    description: The number of pixels/voxels (size) along the y axis.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: z_size
+    owner: ImageDataset
+    domain_of:
+    - ImageDataset
+    range: integer
+    minimum_value: 1
+  x_resolution:
+    name: x_resolution
+    description: The resolution (length / pixel) in along the x axis (numerical value
+      part).
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: x_resolution
+    owner: ImageDataset
+    domain_of:
+    - ImageDataset
+    range: float
+    structured_pattern:
+      syntax: '{PositiveFloat}'
+  y_resolution:
+    name: y_resolution
+    description: The resolution (length / pixel) in along the y axis (numerical value
+      part).
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: y_resolution
+    owner: ImageDataset
+    domain_of:
+    - ImageDataset
+    range: float
+    structured_pattern:
+      syntax: '{PositiveFloat}'
+  z_resolution:
+    name: z_resolution
+    description: The resolution (length / pixel) in along the z axis (numerical value
+      part).
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: z_resolution
+    owner: ImageDataset
+    domain_of:
+    - ImageDataset
+    range: float
+    structured_pattern:
+      syntax: '{PositiveFloat}'
+  unit:
+    name: unit
+    description: A controlled vocabulary attribute defining the length unit of the
+      x, y, and z  resolution values.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: unit
+    owner: ImageDataset
+    domain_of:
+    - ImageDataset
+    range: DISTANCE_UNIT
+  version:
+    name: version
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: version
+    owner: ImageDataset
+    domain_of:
+    - VersionedNamedThing
+    range: string
+    required: true
+  revision_of:
+    name: revision_of
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: revision_of
+    owner: ImageDataset
+    domain_of:
+    - VersionedNamedThing
+    range: VersionedNamedThing
+    any_of:
+    - range: ImageDataset
+    - range: string
+  id:
+    name: id
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    identifier: true
+    alias: id
+    owner: ImageDataset
+    domain_of:
+    - NamedThing
+    range: uriorcurie
+    required: true
+  name:
+    name: name
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: name
+    owner: ImageDataset
+    domain_of:
+    - NamedThing
+    range: string
+    required: true
+  description:
+    name: description
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: description
+    owner: ImageDataset
+    domain_of:
+    - NamedThing
+    range: string
+    required: true
+  category:
+    name: category
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    designates_type: true
+    alias: category
+    owner: ImageDataset
+    domain_of:
+    - NamedThing
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/InformationContentEntity/index.html b/InformationContentEntity/index.html new file mode 100644 index 00000000..24aba054 --- /dev/null +++ b/InformationContentEntity/index.html @@ -0,0 +1,1249 @@ + + + + + + + + + +Class: InformationContentEntity - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: InformationContentEntity

+

a piece of information that typically describes some topic of discourse or is used as support.

+
    +
  • NOTE: this is an abstract class and should not be instantiated directly
    • +
+

URI: biolink:InformationContentEntity

+
classDiagram + class InformationContentEntity + click InformationContentEntity href "../InformationContentEntity" + NamedThing <|-- InformationContentEntity + click NamedThing href "../NamedThing" + + + InformationContentEntity <|-- Dataset + click Dataset href "../Dataset" + + + InformationContentEntity : category + + InformationContentEntity : creation_date + + InformationContentEntity : deprecated + + InformationContentEntity : description + + InformationContentEntity : format + + InformationContentEntity : full_name + + InformationContentEntity : has_attribute + + + + + InformationContentEntity --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + InformationContentEntity : id + + InformationContentEntity : iri + + InformationContentEntity : license + + InformationContentEntity : name + + InformationContentEntity : provided_by + + InformationContentEntity : rights + + InformationContentEntity : synonym + + InformationContentEntity : type + + InformationContentEntity : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
id1
String		A unique identifier for an entitydirect
iri0..1
IriType		An IRI for an entitydirect
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizeddirect
type*
String		direct
name0..1
LabelType		A human-readable name for an attribute or entitydirect
description0..1
NarrativeText		a human-readable description of an entitydirect
has_attribute*
Attribute		connects any entity to an attributedirect
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...direct
provided_by*
String		The value in this node property represents the knowledge provider that create...direct
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...direct
full_name0..1
LabelType		a long-form human readable name for a thingdirect
synonym*
LabelType		Alternate human-readable names for a thingdirect
license0..1
String		direct
rights0..1
String		direct
format0..1
String		direct
creation_date0..1
Date		date on which an entity was createddirect
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
InformationContentEntitylicensedomainInformationContentEntity
InformationContentEntityrightsdomainInformationContentEntity
InformationContentEntityformatdomainInformationContentEntity
DatasetlicensedomainInformationContentEntity
DatasetrightsdomainInformationContentEntity
DatasetformatdomainInformationContentEntity
+

Aliases

+
    +
  • information
    • +
  • information artefact
    • +
  • information entity
    • +
+

Identifier and Mapping Information

+

Valid ID Prefixes

+

Instances of this class should have identifiers with one of the following prefixes:

+
    +
  • doi
    • +
+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:InformationContentEntity
nativebican:InformationContentEntity
exactIAO:0000030
narrowUMLSSG:CONC, STY:T077, STY:T078, STY:T079, STY:T080, STY:T081, STY:T082, STY:T089, STY:T102, STY:T169, STY:T171, STY:T185
+

LinkML Source

+ +

Direct

+
+
name: information content entity
+id_prefixes:
+- doi
+definition_uri: https://w3id.org/biolink/vocab/InformationContentEntity
+description: a piece of information that typically describes some topic of discourse
+  or is used as support.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+aliases:
+- information
+- information artefact
+- information entity
+exact_mappings:
+- IAO:0000030
+narrow_mappings:
+- UMLSSG:CONC
+- STY:T077
+- STY:T078
+- STY:T079
+- STY:T080
+- STY:T081
+- STY:T082
+- STY:T089
+- STY:T102
+- STY:T169
+- STY:T171
+- STY:T185
+is_a: named thing
+abstract: true
+slots:
+- id
+- iri
+- category
+- type
+- name
+- description
+- has attribute
+- deprecated
+- provided by
+- xref
+- full name
+- synonym
+- license
+- rights
+- format
+- creation date
+class_uri: biolink:InformationContentEntity
+
+
+
+

Induced

+
+
name: information content entity
+id_prefixes:
+- doi
+definition_uri: https://w3id.org/biolink/vocab/InformationContentEntity
+description: a piece of information that typically describes some topic of discourse
+  or is used as support.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+aliases:
+- information
+- information artefact
+- information entity
+exact_mappings:
+- IAO:0000030
+narrow_mappings:
+- UMLSSG:CONC
+- STY:T077
+- STY:T078
+- STY:T079
+- STY:T080
+- STY:T081
+- STY:T082
+- STY:T089
+- STY:T102
+- STY:T169
+- STY:T171
+- STY:T185
+is_a: named thing
+abstract: true
+attributes:
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: information content entity
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: information content entity
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: information content entity
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: information content entity
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: information content entity
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: information content entity
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: information content entity
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: information content entity
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: information content entity
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: information content entity
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: information content entity
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: information content entity
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+  license:
+    name: license
+    definition_uri: https://w3id.org/biolink/vocab/license
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - dct:license
+    narrow_mappings:
+    - WIKIDATA_PROPERTY:P275
+    rank: 1000
+    is_a: node property
+    domain: information content entity
+    slot_uri: biolink:license
+    alias: license
+    owner: information content entity
+    domain_of:
+    - information content entity
+    - dataset
+    range: string
+  rights:
+    name: rights
+    definition_uri: https://w3id.org/biolink/vocab/rights
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - dct:rights
+    rank: 1000
+    is_a: node property
+    domain: information content entity
+    slot_uri: biolink:rights
+    alias: rights
+    owner: information content entity
+    domain_of:
+    - information content entity
+    - dataset
+    range: string
+  format:
+    name: format
+    definition_uri: https://w3id.org/biolink/vocab/format
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - dct:format
+    - WIKIDATA_PROPERTY:P2701
+    rank: 1000
+    is_a: node property
+    domain: information content entity
+    slot_uri: biolink:format
+    alias: format
+    owner: information content entity
+    domain_of:
+    - information content entity
+    - dataset
+    range: string
+  creation date:
+    name: creation date
+    definition_uri: https://w3id.org/biolink/vocab/creation_date
+    description: date on which an entity was created. This can be applied to nodes
+      or edges
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - publication date
+    exact_mappings:
+    - dct:createdOn
+    - WIKIDATA_PROPERTY:P577
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:creation_date
+    alias: creation_date
+    owner: information content entity
+    domain_of:
+    - information content entity
+    - dataset
+    range: date
+class_uri: biolink:InformationContentEntity
+
+
+
+
+
+ + +
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+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/Integer/index.html b/Integer/index.html new file mode 100644 index 00000000..a6e4729f --- /dev/null +++ b/Integer/index.html @@ -0,0 +1,614 @@ + + + + + + + + + + + + + + + + + + + Type: Integer - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
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Type: Integer

+

An integer

+

URI: xsd:integer

+
    +
  • +

    base: int

    +
    • +
  • +

    uri: xsd:integer

    +
    • +
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfxsd:integer
nativebican:integer
exactschema:Integer
+ + + + + + + + + + + + + +
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+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/IriType/index.html b/IriType/index.html new file mode 100644 index 00000000..68578548 --- /dev/null +++ b/IriType/index.html @@ -0,0 +1,616 @@ + + + + + + + + + + + + + + + + + + + Type: IriType - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
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Type: IriType

+

An IRI

+

URI: xsd:anyURI

+ +

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfxsd:anyURI
nativebican:iri_type
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/Jsonpath/index.html b/Jsonpath/index.html new file mode 100644 index 00000000..8e3f6d08 --- /dev/null +++ b/Jsonpath/index.html @@ -0,0 +1,613 @@ + + + + + + + + + + + + + + + + + + + Type: Jsonpath - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
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Type: Jsonpath

+

A string encoding a JSON Path. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded in tree form.

+

URI: xsd:string

+ +

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfxsd:string
nativebican:jsonpath
+ + + + + + + + + + + + + +
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+ +
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+ + + + + + + + + + \ No newline at end of file diff --git a/Jsonpointer/index.html b/Jsonpointer/index.html new file mode 100644 index 00000000..49ff4349 --- /dev/null +++ b/Jsonpointer/index.html @@ -0,0 +1,613 @@ + + + + + + + + + + + + + + + + + + + Type: Jsonpointer - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Type: Jsonpointer

+

A string encoding a JSON Pointer. The value of the string MUST conform to JSON Point syntax and SHOULD dereference to a valid object within the current instance document when encoded in tree form.

+

URI: xsd:string

+ +

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfxsd:string
nativebican:jsonpointer
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
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+ + + + + + + + + + \ No newline at end of file diff --git a/LabelType/index.html b/LabelType/index.html new file mode 100644 index 00000000..bc5c0eeb --- /dev/null +++ b/LabelType/index.html @@ -0,0 +1,613 @@ + + + + + + + + + + + + + + + + + + + Type: LabelType - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Type: LabelType

+

A string that provides a human-readable name for an entity

+

URI: xsd:string

+ +

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfxsd:string
nativebican:label_type
+ + + + + + + + + + + + + +
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+ + + + + +
+ +
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+ + + + + + + + + + \ No newline at end of file diff --git a/Library/index.html b/Library/index.html new file mode 100644 index 00000000..8a870928 --- /dev/null +++ b/Library/index.html @@ -0,0 +1,1483 @@ + + + + + + + + + +Class: Library - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
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Class: Library

+

A collection of fragmented and barcode-indexed DNA molecules for sequencing. An index or barcode is typically introduced to enable identification of library origin to allow libraries to be pooled together for sequencing.

+

URI: bican:Library

+
classDiagram + class Library + click Library href "../Library" + ProvEntity <|-- Library + click ProvEntity href "../ProvEntity" + MaterialSample <|-- Library + click MaterialSample href "../MaterialSample" + + Library : average_size_bp + + Library : category + + Library : concentration_nm + + Library : deprecated + + Library : description + + Library : full_name + + Library : has_attribute + + + + + Library --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + Library : id + + Library : iri + + Library : name + + Library : pass_fail_result + + + + + Library --> "0..1" LibraryPrepPassFail : pass_fail_result + click LibraryPrepPassFail href "../LibraryPrepPassFail" + + + Library : provided_by + + Library : quantity_fmol + + Library : quantity_ng + + Library : r1_r2_index + + + + + Library --> "0..1" LibraryR1R2Index : r1_r2_index + click LibraryR1R2Index href "../LibraryR1R2Index" + + + Library : synonym + + Library : type + + Library : was_derived_from + + Library : was_generated_by + + + + + Library --> "0..1" LibraryConstruction : was_generated_by + click LibraryConstruction href "../LibraryConstruction" + + + Library : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
was_generated_by0..1
LibraryConstruction		The library construction process from which the library was generated bydirect
was_derived_from0..1
String or 
BarcodedCellSample or 
AmplifiedCdna		The input barcoded cell sample or amplified cDNA from which the library was d...direct
name0..1
LabelType		Name of a library, which is a collection of fragmented and barcode-indexed DN...direct
average_size_bp0..1
Integer		Average size of the library in terms of base pairsdirect
concentration_nm0..1
Float		Concentration of library in terms of nM (nMol/L)direct
pass_fail_result0..1
LibraryPrepPassFail		Pass or Fail result based on qualitative assessment of library yield and sizedirect
quantity_fmol0..1
Float		Amount of library generated in terms of femtomolesdirect
quantity_ng0..1
Float		Amount of library generated in terms of nanogramsdirect
r1_r2_index0..1
LibraryR1R2Index		Name of the pair of library indexes used for sequencingdirect
id1
String		A unique identifier for an entityNamedThing, MaterialSample, PhysicalEntity, Entity
iri0..1
IriType		An IRI for an entityNamedThing, MaterialSample, PhysicalEntity, Entity
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizedNamedThing, MaterialSample, PhysicalEntity, Entity
type*
String		NamedThing, MaterialSample, PhysicalEntity, Entity
description0..1
NarrativeText		a human-readable description of an entityNamedThing, MaterialSample, PhysicalEntity, Entity
has_attribute*
Attribute		connects any entity to an attributeNamedThing, MaterialSample, PhysicalEntity, Entity
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...NamedThing, MaterialSample, PhysicalEntity, Entity
provided_by*
String		The value in this node property represents the knowledge provider that create...NamedThing, MaterialSample, PhysicalEntity
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...NamedThing, MaterialSample, PhysicalEntity
full_name0..1
LabelType		a long-form human readable name for a thingNamedThing, MaterialSample, PhysicalEntity
synonym*
LabelType		Alternate human-readable names for a thingNamedThing, MaterialSample, PhysicalEntity
+

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
LibraryAliquotwas_derived_fromrangeLibrary
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:Library
nativebican:Library
exactNIMP:Library
+

LinkML Source

+ +

Direct

+
+
name: Library
+description: A collection of fragmented and barcode-indexed DNA molecules for sequencing.
+  An index or barcode is typically introduced to enable identification of library
+  origin to allow libraries to be pooled together for sequencing.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Library
+is_a: material sample
+mixins:
+- ProvEntity
+slots:
+- was_generated_by
+- was_derived_from
+- name
+slot_usage:
+  was_generated_by:
+    name: was_generated_by
+    description: The library construction process from which the library was generated
+      by.
+    range: LibraryConstruction
+  was_derived_from:
+    name: was_derived_from
+    description: The input barcoded cell sample or amplified cDNA from which the library
+      was derived from.
+    exact_mappings:
+    - NIMP:has_parent
+    any_of:
+    - range: BarcodedCellSample
+    - range: AmplifiedCdna
+  name:
+    name: name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_local_name
+    description: Name of a library, which is a collection of fragmented and barcode-indexed
+      DNA molecules for sequencing.  An index or barcode is typically introduced to
+      enable identification of library origin to allow libraries to be pooled together
+      for sequencing.
+    exact_mappings:
+    - NIMP:PD-AJJUCC35
+    slot_uri: bican:f717e254-3630-4342-be7b-4d56376e7afe
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  average_size_bp:
+    name: average_size_bp
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_avg_size_bp
+    description: Average size of the library in terms of base pairs.  This is used
+      to calculate the molarity before pooling and sequencing.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-VJVJLC46
+    rank: 1000
+    slot_uri: bican:f851eba9-56d1-4472-9d0c-d7f8bc33000a
+    alias: library avg size bp
+    domain_of:
+    - Library
+    range: integer
+  concentration_nm:
+    name: concentration_nm
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_concentration_nm
+    description: Concentration of library in terms of nM (nMol/L).  Number of molecules
+      is needed for accurate pooling of the libraries and for generating the number
+      of target reads/cell in sequencing.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-DCDCLD43
+    rank: 1000
+    slot_uri: bican:90805b3f-f380-4f23-b159-e7eaa0c8f052
+    alias: library concentration nm
+    domain_of:
+    - Library
+    range: float
+  pass_fail_result:
+    name: pass_fail_result
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_prep_pass_fail
+    description: Pass or Fail result based on qualitative assessment of library yield
+      and size.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-QHQHQB42
+    slot_uri: bican:6817ede2-7ead-402d-9dbc-131aca627c6c
+    alias: library prep pass-fail
+    domain_of:
+    - AmplifiedCdna
+    - Library
+    range: library_prep_pass_fail
+  quantity_fmol:
+    name: quantity_fmol
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_quantification_fmol
+    description: Amount of library generated in terms of femtomoles
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-JYJYDK42
+    rank: 1000
+    slot_uri: bican:4c09ada7-c116-48bc-8fb1-0dcf5c4b939a
+    alias: library quantification fmol
+    domain_of:
+    - Library
+    range: float
+  quantity_ng:
+    name: quantity_ng
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_quantification_ng
+    description: Amount of library generated in terms of nanograms
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-TNTNXP37
+    slot_uri: bican:318b2d3a-dae7-4c63-bfbb-93862b92f63e
+    alias: library quantification ng
+    domain_of:
+    - AmplifiedCdna
+    - Library
+    range: float
+  r1_r2_index:
+    name: r1_r2_index
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_r1_r2_index
+    description: Name of the pair of library indexes used for sequencing.  Indexes
+      allow libraries to be pooled together for sequencing.  Sequencing output (fastq)
+      are demultiplexed by using the indexes for each library.  The name will be associated
+      with the sequences of i7, i5, and i5as, which are needed by SeqCores for demultiplexing.  The
+      required direction of the sequence (sense or antisense) of the index can differ
+      depending on sequencing instruments.
+    in_subset:
+    - analysis
+    - tracking
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-VLLMWZ60
+    rank: 1000
+    slot_uri: bican:c94b5d8a-e92d-47af-8c0e-ea3b58be4d06
+    alias: R1/R2 index name
+    domain_of:
+    - Library
+    range: library_r1_r2_index
+
+
+
+

Induced

+
+
name: Library
+description: A collection of fragmented and barcode-indexed DNA molecules for sequencing.
+  An index or barcode is typically introduced to enable identification of library
+  origin to allow libraries to be pooled together for sequencing.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Library
+is_a: material sample
+mixins:
+- ProvEntity
+slot_usage:
+  was_generated_by:
+    name: was_generated_by
+    description: The library construction process from which the library was generated
+      by.
+    range: LibraryConstruction
+  was_derived_from:
+    name: was_derived_from
+    description: The input barcoded cell sample or amplified cDNA from which the library
+      was derived from.
+    exact_mappings:
+    - NIMP:has_parent
+    any_of:
+    - range: BarcodedCellSample
+    - range: AmplifiedCdna
+  name:
+    name: name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_local_name
+    description: Name of a library, which is a collection of fragmented and barcode-indexed
+      DNA molecules for sequencing.  An index or barcode is typically introduced to
+      enable identification of library origin to allow libraries to be pooled together
+      for sequencing.
+    exact_mappings:
+    - NIMP:PD-AJJUCC35
+    slot_uri: bican:f717e254-3630-4342-be7b-4d56376e7afe
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  average_size_bp:
+    name: average_size_bp
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_avg_size_bp
+    description: Average size of the library in terms of base pairs.  This is used
+      to calculate the molarity before pooling and sequencing.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-VJVJLC46
+    rank: 1000
+    slot_uri: bican:f851eba9-56d1-4472-9d0c-d7f8bc33000a
+    alias: library avg size bp
+    owner: Library
+    domain_of:
+    - Library
+    range: integer
+  concentration_nm:
+    name: concentration_nm
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_concentration_nm
+    description: Concentration of library in terms of nM (nMol/L).  Number of molecules
+      is needed for accurate pooling of the libraries and for generating the number
+      of target reads/cell in sequencing.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-DCDCLD43
+    rank: 1000
+    slot_uri: bican:90805b3f-f380-4f23-b159-e7eaa0c8f052
+    alias: library concentration nm
+    owner: Library
+    domain_of:
+    - Library
+    range: float
+  pass_fail_result:
+    name: pass_fail_result
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_prep_pass_fail
+    description: Pass or Fail result based on qualitative assessment of library yield
+      and size.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-QHQHQB42
+    slot_uri: bican:6817ede2-7ead-402d-9dbc-131aca627c6c
+    alias: library prep pass-fail
+    owner: Library
+    domain_of:
+    - AmplifiedCdna
+    - Library
+    range: library_prep_pass_fail
+  quantity_fmol:
+    name: quantity_fmol
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_quantification_fmol
+    description: Amount of library generated in terms of femtomoles
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-JYJYDK42
+    rank: 1000
+    slot_uri: bican:4c09ada7-c116-48bc-8fb1-0dcf5c4b939a
+    alias: library quantification fmol
+    owner: Library
+    domain_of:
+    - Library
+    range: float
+  quantity_ng:
+    name: quantity_ng
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_quantification_ng
+    description: Amount of library generated in terms of nanograms
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-TNTNXP37
+    slot_uri: bican:318b2d3a-dae7-4c63-bfbb-93862b92f63e
+    alias: library quantification ng
+    owner: Library
+    domain_of:
+    - AmplifiedCdna
+    - Library
+    range: float
+  r1_r2_index:
+    name: r1_r2_index
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_r1_r2_index
+    description: Name of the pair of library indexes used for sequencing.  Indexes
+      allow libraries to be pooled together for sequencing.  Sequencing output (fastq)
+      are demultiplexed by using the indexes for each library.  The name will be associated
+      with the sequences of i7, i5, and i5as, which are needed by SeqCores for demultiplexing.  The
+      required direction of the sequence (sense or antisense) of the index can differ
+      depending on sequencing instruments.
+    in_subset:
+    - analysis
+    - tracking
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-VLLMWZ60
+    rank: 1000
+    slot_uri: bican:c94b5d8a-e92d-47af-8c0e-ea3b58be4d06
+    alias: R1/R2 index name
+    owner: Library
+    domain_of:
+    - Library
+    range: library_r1_r2_index
+  was_generated_by:
+    name: was_generated_by
+    description: The library construction process from which the library was generated
+      by.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: was_generated_by
+    owner: Library
+    domain_of:
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryPool
+    - DissectionRoiPolygon
+    - ProvEntity
+    range: LibraryConstruction
+  was_derived_from:
+    name: was_derived_from
+    description: The input barcoded cell sample or amplified cDNA from which the library
+      was derived from.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:has_parent
+    rank: 1000
+    alias: was_derived_from
+    owner: Library
+    domain_of:
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DigitalAsset
+    - ProvEntity
+    range: string
+    any_of:
+    - range: BarcodedCellSample
+    - range: AmplifiedCdna
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_local_name
+    description: Name of a library, which is a collection of fragmented and barcode-indexed
+      DNA molecules for sequencing.  An index or barcode is typically introduced to
+      enable identification of library origin to allow libraries to be pooled together
+      for sequencing.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - NIMP:PD-AJJUCC35
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: bican:f717e254-3630-4342-be7b-4d56376e7afe
+    alias: name
+    owner: Library
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - Donor
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DissectionRoiPolygon
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: Library
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: Library
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: Library
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+    pattern: ^bican:[A-Z][A-Za-z]+$
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: Library
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: Library
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: Library
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: Library
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: Library
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: Library
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: Library
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: Library
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/LibraryAliquot/index.html b/LibraryAliquot/index.html new file mode 100644 index 00000000..e34d50b6 --- /dev/null +++ b/LibraryAliquot/index.html @@ -0,0 +1,1178 @@ + + + + + + + + + +Class: LibraryAliquot - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
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+ +
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+ +
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+ +
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+

Class: LibraryAliquot

+

One library in the library pool. Each library aliquot in a library pool will have a unique R1/R2 index to allow for sequencing together then separating the sequencing output by originating library aliquot through the process of demultiplexing. The resulting demultiplexed fastq files will include the library aliquot name. A given library may produce multiple library aliquots, which is done in the case of resequencing. Each library aliquot will produce a set of fastq files.

+

URI: bican:LibraryAliquot

+
classDiagram + class LibraryAliquot + click LibraryAliquot href "../LibraryAliquot" + ProvEntity <|-- LibraryAliquot + click ProvEntity href "../ProvEntity" + MaterialSample <|-- LibraryAliquot + click MaterialSample href "../MaterialSample" + + LibraryAliquot : category + + LibraryAliquot : deprecated + + LibraryAliquot : description + + LibraryAliquot : full_name + + LibraryAliquot : has_attribute + + + + + LibraryAliquot --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + LibraryAliquot : id + + LibraryAliquot : iri + + LibraryAliquot : name + + LibraryAliquot : provided_by + + LibraryAliquot : synonym + + LibraryAliquot : type + + LibraryAliquot : was_derived_from + + + + + LibraryAliquot --> "0..1" Library : was_derived_from + click Library href "../Library" + + + LibraryAliquot : was_generated_by + + LibraryAliquot : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
was_derived_from0..1
Library		The input library from which the library aliquot was derived fromdirect
name0..1
LabelType		One library in the library pooldirect
was_generated_by0..1
String		ProvEntity
id1
String		A unique identifier for an entityNamedThing, MaterialSample, PhysicalEntity, Entity
iri0..1
IriType		An IRI for an entityNamedThing, MaterialSample, PhysicalEntity, Entity
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizedNamedThing, MaterialSample, PhysicalEntity, Entity
type*
String		NamedThing, MaterialSample, PhysicalEntity, Entity
description0..1
NarrativeText		a human-readable description of an entityNamedThing, MaterialSample, PhysicalEntity, Entity
has_attribute*
Attribute		connects any entity to an attributeNamedThing, MaterialSample, PhysicalEntity, Entity
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...NamedThing, MaterialSample, PhysicalEntity, Entity
provided_by*
String		The value in this node property represents the knowledge provider that create...NamedThing, MaterialSample, PhysicalEntity
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...NamedThing, MaterialSample, PhysicalEntity
full_name0..1
LabelType		a long-form human readable name for a thingNamedThing, MaterialSample, PhysicalEntity
synonym*
LabelType		Alternate human-readable names for a thingNamedThing, MaterialSample, PhysicalEntity
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
LibraryPoolwas_derived_fromrangeLibraryAliquot
LibraryPoolingusedrangeLibraryAliquot
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:LibraryAliquot
nativebican:LibraryAliquot
exactNIMP:Library%20Aliquot
+

LinkML Source

+ +

Direct

+
+
name: LibraryAliquot
+description: One library in the library pool. Each library aliquot in a library pool
+  will have a unique R1/R2 index to allow for sequencing together then separating
+  the sequencing output by originating library aliquot through the process of demultiplexing.
+  The resulting demultiplexed fastq files will include the library aliquot name.  A
+  given library may produce multiple library aliquots, which is done in the case of
+  resequencing.  Each library aliquot will produce a set of fastq files.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Library%20Aliquot
+is_a: material sample
+mixins:
+- ProvEntity
+slots:
+- was_derived_from
+- name
+slot_usage:
+  was_derived_from:
+    name: was_derived_from
+    description: The input library from which the library aliquot was derived from.
+    exact_mappings:
+    - NIMP:has_parent
+    range: Library
+  name:
+    name: name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_aliquot_local_name
+    description: One library in the library pool.  Each Library_aliquot_name in a
+      library pool will have a unique R1/R2 index to allow for sequencing together
+      then separating the sequencing output by originating library aliquot through
+      the process of demultiplexing.  The resulting demultiplexed fastq files will
+      include the library_aliquot_name.
+    exact_mappings:
+    - NIMP:PD-XCXCCC35
+    slot_uri: bican:34191bad-d167-4335-8224-ade897d3728e
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+
+
+
+

Induced

+
+
name: LibraryAliquot
+description: One library in the library pool. Each library aliquot in a library pool
+  will have a unique R1/R2 index to allow for sequencing together then separating
+  the sequencing output by originating library aliquot through the process of demultiplexing.
+  The resulting demultiplexed fastq files will include the library aliquot name.  A
+  given library may produce multiple library aliquots, which is done in the case of
+  resequencing.  Each library aliquot will produce a set of fastq files.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Library%20Aliquot
+is_a: material sample
+mixins:
+- ProvEntity
+slot_usage:
+  was_derived_from:
+    name: was_derived_from
+    description: The input library from which the library aliquot was derived from.
+    exact_mappings:
+    - NIMP:has_parent
+    range: Library
+  name:
+    name: name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_aliquot_local_name
+    description: One library in the library pool.  Each Library_aliquot_name in a
+      library pool will have a unique R1/R2 index to allow for sequencing together
+      then separating the sequencing output by originating library aliquot through
+      the process of demultiplexing.  The resulting demultiplexed fastq files will
+      include the library_aliquot_name.
+    exact_mappings:
+    - NIMP:PD-XCXCCC35
+    slot_uri: bican:34191bad-d167-4335-8224-ade897d3728e
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  was_derived_from:
+    name: was_derived_from
+    description: The input library from which the library aliquot was derived from.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:has_parent
+    rank: 1000
+    alias: was_derived_from
+    owner: LibraryAliquot
+    domain_of:
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DigitalAsset
+    - ProvEntity
+    range: Library
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_aliquot_local_name
+    description: One library in the library pool.  Each Library_aliquot_name in a
+      library pool will have a unique R1/R2 index to allow for sequencing together
+      then separating the sequencing output by originating library aliquot through
+      the process of demultiplexing.  The resulting demultiplexed fastq files will
+      include the library_aliquot_name.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - NIMP:PD-XCXCCC35
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: bican:34191bad-d167-4335-8224-ade897d3728e
+    alias: name
+    owner: LibraryAliquot
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - Donor
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DissectionRoiPolygon
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  was_generated_by:
+    name: was_generated_by
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: was_generated_by
+    owner: LibraryAliquot
+    domain_of:
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryPool
+    - DissectionRoiPolygon
+    - ProvEntity
+    range: string
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: LibraryAliquot
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: LibraryAliquot
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: LibraryAliquot
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+    pattern: ^bican:[A-Z][A-Za-z]+$
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: LibraryAliquot
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: LibraryAliquot
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: LibraryAliquot
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: LibraryAliquot
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: LibraryAliquot
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: LibraryAliquot
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: LibraryAliquot
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: LibraryAliquot
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+
+
+
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+
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+ +
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+ + + + \ No newline at end of file diff --git a/LibraryConstruction/index.html b/LibraryConstruction/index.html new file mode 100644 index 00000000..56500512 --- /dev/null +++ b/LibraryConstruction/index.html @@ -0,0 +1,1298 @@ + + + + + + + + + +Class: LibraryConstruction - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
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+

Class: LibraryConstruction

+

The process of constructing a library from input material (such as amplified cDNA or barcoded cell sample) derived from one or more cell samples. cDNA is fragmented into smaller pieces appropriate for sequencing and at the same time a library index barcode is incorporated to enable identification of library origin, allowing libraries to be pooled together for sequencing.

+

URI: bican:LibraryConstruction

+
classDiagram + class LibraryConstruction + click LibraryConstruction href "../LibraryConstruction" + ProvActivity <|-- LibraryConstruction + click ProvActivity href "../ProvActivity" + Procedure <|-- LibraryConstruction + click Procedure href "../Procedure" + + LibraryConstruction : category + + LibraryConstruction : deprecated + + LibraryConstruction : description + + LibraryConstruction : full_name + + LibraryConstruction : has_attribute + + + + + LibraryConstruction --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + LibraryConstruction : id + + LibraryConstruction : input_quantity_ng + + LibraryConstruction : iri + + LibraryConstruction : method + + + + + LibraryConstruction --> "0..1" LibraryTechnique : method + click LibraryTechnique href "../LibraryTechnique" + + + LibraryConstruction : name + + LibraryConstruction : process_date + + LibraryConstruction : provided_by + + LibraryConstruction : set + + LibraryConstruction : synonym + + LibraryConstruction : type + + LibraryConstruction : used + + LibraryConstruction : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
used0..1
String or 
BarcodedCellSample or 
AmplifiedCdna		The input barcoded cell sample or amplified cDNA from which the library was d...direct
method0..1
LibraryTechnique		Standardized nomenclature to describe the specific library method useddirect
process_date0..1
Date		Date of library constructiondirect
input_quantity_ng0..1
Float		Amount of cDNA going into library construction in nanogramsdirect
set0..1
String		Library set, containing multiple library_names that were processed at the sam...direct
id1
String		A unique identifier for an entityProcedure, NamedThing, Entity
iri0..1
IriType		An IRI for an entityProcedure, NamedThing, Entity
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizedProcedure, NamedThing, Entity
type*
String		Procedure, NamedThing, Entity
name0..1
LabelType		A human-readable name for an attribute or entityProcedure, NamedThing, Entity
description0..1
NarrativeText		a human-readable description of an entityProcedure, NamedThing, Entity
has_attribute*
Attribute		connects any entity to an attributeProcedure, NamedThing, Entity
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...Procedure, NamedThing, Entity
provided_by*
String		The value in this node property represents the knowledge provider that create...Procedure, NamedThing
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...Procedure, NamedThing
full_name0..1
LabelType		a long-form human readable name for a thingProcedure, NamedThing
synonym*
LabelType		Alternate human-readable names for a thingProcedure, NamedThing
+

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
Librarywas_generated_byrangeLibraryConstruction
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:LibraryConstruction
nativebican:LibraryConstruction
+

LinkML Source

+ +

Direct

+
+
name: LibraryConstruction
+description: The process of constructing a library from input material (such as amplified
+  cDNA or barcoded cell sample) derived from one or more cell samples.  cDNA is fragmented
+  into smaller pieces appropriate for sequencing and at the same time a library index
+  barcode is incorporated to enable identification of library origin, allowing libraries
+  to be pooled together for sequencing.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slots:
+- used
+slot_usage:
+  used:
+    name: used
+    description: The input barcoded cell sample or amplified cDNA from which the library
+      was derived from.
+    any_of:
+    - range: BarcodedCellSample
+    - range: AmplifiedCdna
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  method:
+    name: method
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_technique
+    description: Standardized nomenclature to describe the specific library method
+      used.  This specifies the alignment method required for the library.  For example,
+      10xV3.1 (for RNASeq single assay), 10xMult-GEX (for RNASeq multiome assay),
+      and 10xMult-ATAC (for ATACSeq multiome assay).
+    in_subset:
+    - analysis
+    - tracking
+    - alignment
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-AJAJCN35
+    slot_uri: bican:7b60d59e-fdd7-4b27-a2d4-cae9b69103a6
+    alias: library method
+    domain_of:
+    - CellBarcoding
+    - LibraryConstruction
+    range: library_technique
+  process_date:
+    name: process_date
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_preparation_date
+    description: Date of library construction.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-JCJCNM35
+    slot_uri: bican:9c2f575d-1b64-451d-894f-656861afe07a
+    alias: library creation date
+    domain_of:
+    - CellDissociation
+    - CellEnrichment
+    - CellBarcoding
+    - CdnaAmplification
+    - LibraryConstruction
+    - LibraryPooling
+    range: date
+  input_quantity_ng:
+    name: input_quantity_ng
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_input_ng
+    description: Amount of cDNA going into library construction in nanograms.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-AFAFXP37
+    rank: 1000
+    slot_uri: bican:e4d31d97-722d-4771-a0e4-e6062190f2c1
+    alias: library input ng
+    domain_of:
+    - LibraryConstruction
+    range: float
+  set:
+    name: set
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_prep_set
+    description: Library set, containing multiple library_names that were processed
+      at the same time.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-PCPCVR50
+    slot_uri: bican:b124ffa9-9134-4a61-a30d-bb191b2fc7fa
+    alias: library prep set
+    domain_of:
+    - CdnaAmplification
+    - LibraryConstruction
+    range: string
+
+
+
+

Induced

+
+
name: LibraryConstruction
+description: The process of constructing a library from input material (such as amplified
+  cDNA or barcoded cell sample) derived from one or more cell samples.  cDNA is fragmented
+  into smaller pieces appropriate for sequencing and at the same time a library index
+  barcode is incorporated to enable identification of library origin, allowing libraries
+  to be pooled together for sequencing.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slot_usage:
+  used:
+    name: used
+    description: The input barcoded cell sample or amplified cDNA from which the library
+      was derived from.
+    any_of:
+    - range: BarcodedCellSample
+    - range: AmplifiedCdna
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  method:
+    name: method
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_technique
+    description: Standardized nomenclature to describe the specific library method
+      used.  This specifies the alignment method required for the library.  For example,
+      10xV3.1 (for RNASeq single assay), 10xMult-GEX (for RNASeq multiome assay),
+      and 10xMult-ATAC (for ATACSeq multiome assay).
+    in_subset:
+    - analysis
+    - tracking
+    - alignment
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-AJAJCN35
+    slot_uri: bican:7b60d59e-fdd7-4b27-a2d4-cae9b69103a6
+    alias: library method
+    owner: LibraryConstruction
+    domain_of:
+    - CellBarcoding
+    - LibraryConstruction
+    range: library_technique
+  process_date:
+    name: process_date
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_preparation_date
+    description: Date of library construction.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-JCJCNM35
+    slot_uri: bican:9c2f575d-1b64-451d-894f-656861afe07a
+    alias: library creation date
+    owner: LibraryConstruction
+    domain_of:
+    - CellDissociation
+    - CellEnrichment
+    - CellBarcoding
+    - CdnaAmplification
+    - LibraryConstruction
+    - LibraryPooling
+    range: date
+  input_quantity_ng:
+    name: input_quantity_ng
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_input_ng
+    description: Amount of cDNA going into library construction in nanograms.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-AFAFXP37
+    rank: 1000
+    slot_uri: bican:e4d31d97-722d-4771-a0e4-e6062190f2c1
+    alias: library input ng
+    owner: LibraryConstruction
+    domain_of:
+    - LibraryConstruction
+    range: float
+  set:
+    name: set
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_prep_set
+    description: Library set, containing multiple library_names that were processed
+      at the same time.
+    in_subset:
+    - analysis
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-PCPCVR50
+    slot_uri: bican:b124ffa9-9134-4a61-a30d-bb191b2fc7fa
+    alias: library prep set
+    owner: LibraryConstruction
+    domain_of:
+    - CdnaAmplification
+    - LibraryConstruction
+    range: string
+  used:
+    name: used
+    description: The input barcoded cell sample or amplified cDNA from which the library
+      was derived from.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: used
+    owner: LibraryConstruction
+    domain_of:
+    - DissectionRoiDelineation
+    - TissueDissection
+    - CellDissociation
+    - CellEnrichment
+    - EnrichedCellSampleSplitting
+    - CellBarcoding
+    - CdnaAmplification
+    - LibraryConstruction
+    - LibraryPooling
+    - ProvActivity
+    range: string
+    any_of:
+    - range: BarcodedCellSample
+    - range: AmplifiedCdna
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: LibraryConstruction
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: LibraryConstruction
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: LibraryConstruction
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+    pattern: ^bican:[A-Z][A-Za-z]+$
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: LibraryConstruction
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: LibraryConstruction
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - Donor
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DissectionRoiPolygon
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: LibraryConstruction
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: LibraryConstruction
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: LibraryConstruction
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: LibraryConstruction
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: LibraryConstruction
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: LibraryConstruction
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: LibraryConstruction
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+
+
+
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+
+ + +
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+ +
+
+
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+ + + + \ No newline at end of file diff --git a/LibraryGeneration/index.html b/LibraryGeneration/index.html new file mode 100644 index 00000000..e9d9286b --- /dev/null +++ b/LibraryGeneration/index.html @@ -0,0 +1,662 @@ + + + + + + + + + + + + + + + + + + + Subset: LibraryGeneration - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
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+ +
+ + + + + + +
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Subset: LibraryGeneration

+

A subset of classes that are associated with library generation.

+

URI: LibraryGeneration

+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Classes in subset

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ClassDescription
AmplifiedCdnaA collection of cDNA molecules derived and amplified from an input barcoded c...
BarcodedCellSampleA collection of molecularly barcoded cells
CdnaAmplificationThe process of creating a collection of cDNA molecules derived and amplified ...
CellBarcodingThe process of adding a molecular barcode to individual cells in a sample
CellDissociationThe process of generating dissociated cells from an input tissue sample
CellEnrichmentThe process of enriching a dissociated cell sample by including or excluding ...
DissectionRoiDelineationThe process of outlining a region of interest on a brain slab image to guide ...
DissociatedCellSampleA collection of dissociated cells or nuclei derived from dissociation of a ti...
EnrichedCellSampleA collection of enriched cells or nuclei after enrichment process, usually vi...
EnrichedCellSampleSplittingThe process of splitting an enriched cell sample into several portions
LibraryA collection of fragmented and barcode-indexed DNA molecules for sequencing
LibraryAliquotOne library in the library pool
LibraryConstructionThe process of constructing a library from input material (such as amplified ...
LibraryPoolA library pool is made up of library aliquots from multiple libraries
LibraryPoolingThe process of constructing of a libray pool by combining library aliquots fr...
TissueDissectionThe process of dissecting a tissue sample from a brain slab guided by a disse...
TissueSampleThe final intact piece of tissue before cell or nuclei prep
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+ + + + + + + + + + \ No newline at end of file diff --git a/LibraryPool/index.html b/LibraryPool/index.html new file mode 100644 index 00000000..e44bae5c --- /dev/null +++ b/LibraryPool/index.html @@ -0,0 +1,1242 @@ + + + + + + + + + +Class: LibraryPool - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
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+

Class: LibraryPool

+

A library pool is made up of library aliquots from multiple libraries. Each library aliquot in a library pool will have a unique R1/R2 index to allow for sequencing together then separating the sequencing output by originating library aliquot through the process of demultiplexing.

+

URI: bican:LibraryPool

+
classDiagram + class LibraryPool + click LibraryPool href "../LibraryPool" + ProvEntity <|-- LibraryPool + click ProvEntity href "../ProvEntity" + MaterialSample <|-- LibraryPool + click MaterialSample href "../MaterialSample" + + LibraryPool : category + + LibraryPool : deprecated + + LibraryPool : description + + LibraryPool : full_name + + LibraryPool : has_attribute + + + + + LibraryPool --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + LibraryPool : id + + LibraryPool : iri + + LibraryPool : local_tube_id + + LibraryPool : name + + LibraryPool : provided_by + + LibraryPool : synonym + + LibraryPool : type + + LibraryPool : was_derived_from + + + + + LibraryPool --> "*" LibraryAliquot : was_derived_from + click LibraryAliquot href "../LibraryAliquot" + + + LibraryPool : was_generated_by + + + + + LibraryPool --> "0..1" LibraryPooling : was_generated_by + click LibraryPooling href "../LibraryPooling" + + + LibraryPool : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
was_generated_by0..1
LibraryPooling		The pooling process from which the library pool was generated bydirect
was_derived_from*
LibraryAliquot		The input aliquot(s) from which the library pool was derived fromdirect
name0..1
LabelType		Library lab's library pool namedirect
local_tube_id0..1
String		Library Pool Tube local namedirect
id1
String		A unique identifier for an entityNamedThing, MaterialSample, PhysicalEntity, Entity
iri0..1
IriType		An IRI for an entityNamedThing, MaterialSample, PhysicalEntity, Entity
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizedNamedThing, MaterialSample, PhysicalEntity, Entity
type*
String		NamedThing, MaterialSample, PhysicalEntity, Entity
description0..1
NarrativeText		a human-readable description of an entityNamedThing, MaterialSample, PhysicalEntity, Entity
has_attribute*
Attribute		connects any entity to an attributeNamedThing, MaterialSample, PhysicalEntity, Entity
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...NamedThing, MaterialSample, PhysicalEntity, Entity
provided_by*
String		The value in this node property represents the knowledge provider that create...NamedThing, MaterialSample, PhysicalEntity
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...NamedThing, MaterialSample, PhysicalEntity
full_name0..1
LabelType		a long-form human readable name for a thingNamedThing, MaterialSample, PhysicalEntity
synonym*
LabelType		Alternate human-readable names for a thingNamedThing, MaterialSample, PhysicalEntity
+

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
DigitalAssetwas_derived_fromrangeLibraryPool
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:LibraryPool
nativebican:LibraryPool
exactNIMP:Library%20Pool
+

LinkML Source

+ +

Direct

+
+
name: LibraryPool
+description: A library pool is made up of library aliquots from multiple libraries.
+  Each library aliquot in a library pool will have a unique R1/R2 index to allow for
+  sequencing together then separating the sequencing output by originating library
+  aliquot through the process of demultiplexing.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Library%20Pool
+is_a: material sample
+mixins:
+- ProvEntity
+slots:
+- was_generated_by
+- was_derived_from
+- name
+slot_usage:
+  was_generated_by:
+    name: was_generated_by
+    description: The pooling process from which the library pool was generated by.
+    range: LibraryPooling
+  was_derived_from:
+    name: was_derived_from
+    description: The input aliquot(s) from which the library pool was derived from.
+    exact_mappings:
+    - NIMP:has_parent
+    range: LibraryAliquot
+    multivalued: true
+  name:
+    name: name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_pool_local_name
+    description: Library lab's library pool name.  For some labs this may be the same
+      as "Libray pool tube local name".   Other labs distinguish between the local
+      tube label of the library pool and the library pool name provided to SeqCore
+      for tracking.  Local Pool Name is used to communicate sequencing status between
+      SeqCore and Library Labs.
+    exact_mappings:
+    - NIMP:PD-KKIAPA48
+    slot_uri: bican:29e0578b-6427-4c93-b29b-bde27fbadeec
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  local_tube_id:
+    name: local_tube_id
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_pool_local_tube_id
+    description: Library Pool Tube local name.  Label of the tube containing the library
+      pool, which is made up of multiple library_aliquots.  This is a Library Lab
+      local tube name, before the pool is aliquoted to the Seq Core provided tube
+      'Library Pool Tube Name'.
+    in_subset:
+    - analysis
+    - tracking
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-WNYWPA48
+    rank: 1000
+    slot_uri: bican:f1fdea98-7849-4def-a62f-a04cbbf98922
+    alias: library_pool_tube_internal_label
+    domain_of:
+    - LibraryPool
+    range: string
+
+
+
+

Induced

+
+
name: LibraryPool
+description: A library pool is made up of library aliquots from multiple libraries.
+  Each library aliquot in a library pool will have a unique R1/R2 index to allow for
+  sequencing together then separating the sequencing output by originating library
+  aliquot through the process of demultiplexing.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Library%20Pool
+is_a: material sample
+mixins:
+- ProvEntity
+slot_usage:
+  was_generated_by:
+    name: was_generated_by
+    description: The pooling process from which the library pool was generated by.
+    range: LibraryPooling
+  was_derived_from:
+    name: was_derived_from
+    description: The input aliquot(s) from which the library pool was derived from.
+    exact_mappings:
+    - NIMP:has_parent
+    range: LibraryAliquot
+    multivalued: true
+  name:
+    name: name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_pool_local_name
+    description: Library lab's library pool name.  For some labs this may be the same
+      as "Libray pool tube local name".   Other labs distinguish between the local
+      tube label of the library pool and the library pool name provided to SeqCore
+      for tracking.  Local Pool Name is used to communicate sequencing status between
+      SeqCore and Library Labs.
+    exact_mappings:
+    - NIMP:PD-KKIAPA48
+    slot_uri: bican:29e0578b-6427-4c93-b29b-bde27fbadeec
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  local_tube_id:
+    name: local_tube_id
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_pool_local_tube_id
+    description: Library Pool Tube local name.  Label of the tube containing the library
+      pool, which is made up of multiple library_aliquots.  This is a Library Lab
+      local tube name, before the pool is aliquoted to the Seq Core provided tube
+      'Library Pool Tube Name'.
+    in_subset:
+    - analysis
+    - tracking
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-WNYWPA48
+    rank: 1000
+    slot_uri: bican:f1fdea98-7849-4def-a62f-a04cbbf98922
+    alias: library_pool_tube_internal_label
+    owner: LibraryPool
+    domain_of:
+    - LibraryPool
+    range: string
+  was_generated_by:
+    name: was_generated_by
+    description: The pooling process from which the library pool was generated by.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: was_generated_by
+    owner: LibraryPool
+    domain_of:
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryPool
+    - DissectionRoiPolygon
+    - ProvEntity
+    range: LibraryPooling
+  was_derived_from:
+    name: was_derived_from
+    description: The input aliquot(s) from which the library pool was derived from.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:has_parent
+    rank: 1000
+    alias: was_derived_from
+    owner: LibraryPool
+    domain_of:
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DigitalAsset
+    - ProvEntity
+    range: LibraryAliquot
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_pool_local_name
+    description: Library lab's library pool name.  For some labs this may be the same
+      as "Libray pool tube local name".   Other labs distinguish between the local
+      tube label of the library pool and the library pool name provided to SeqCore
+      for tracking.  Local Pool Name is used to communicate sequencing status between
+      SeqCore and Library Labs.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - NIMP:PD-KKIAPA48
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: bican:29e0578b-6427-4c93-b29b-bde27fbadeec
+    alias: name
+    owner: LibraryPool
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - Donor
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DissectionRoiPolygon
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: LibraryPool
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: LibraryPool
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: LibraryPool
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+    pattern: ^bican:[A-Z][A-Za-z]+$
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: LibraryPool
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: LibraryPool
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: LibraryPool
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: LibraryPool
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: LibraryPool
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: LibraryPool
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: LibraryPool
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: LibraryPool
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/LibraryPooling/index.html b/LibraryPooling/index.html new file mode 100644 index 00000000..c89a1c06 --- /dev/null +++ b/LibraryPooling/index.html @@ -0,0 +1,1138 @@ + + + + + + + + + +Class: LibraryPooling - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
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+ +
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+

Class: LibraryPooling

+

The process of constructing of a libray pool by combining library aliquots from a set of input libraries. Each library aliquot in a library pool will have a unique R1/R2 index to allow for sequencing together then separating the sequencing output by originating library aliquot through the process of demultiplexing.

+

URI: bican:LibraryPooling

+
classDiagram + class LibraryPooling + click LibraryPooling href "../LibraryPooling" + ProvActivity <|-- LibraryPooling + click ProvActivity href "../ProvActivity" + Procedure <|-- LibraryPooling + click Procedure href "../Procedure" + + LibraryPooling : category + + LibraryPooling : deprecated + + LibraryPooling : description + + LibraryPooling : full_name + + LibraryPooling : has_attribute + + + + + LibraryPooling --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + LibraryPooling : id + + LibraryPooling : iri + + LibraryPooling : name + + LibraryPooling : process_date + + LibraryPooling : provided_by + + LibraryPooling : synonym + + LibraryPooling : type + + LibraryPooling : used + + + + + LibraryPooling --> "*" LibraryAliquot : used + click LibraryAliquot href "../LibraryAliquot" + + + LibraryPooling : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
used*
LibraryAliquot		The input aliquot(s) from which the library pool was derived fromdirect
process_date0..1
String		Date of library pooling processdirect
id1
String		A unique identifier for an entityProcedure, NamedThing, Entity
iri0..1
IriType		An IRI for an entityProcedure, NamedThing, Entity
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizedProcedure, NamedThing, Entity
type*
String		Procedure, NamedThing, Entity
name0..1
LabelType		A human-readable name for an attribute or entityProcedure, NamedThing, Entity
description0..1
NarrativeText		a human-readable description of an entityProcedure, NamedThing, Entity
has_attribute*
Attribute		connects any entity to an attributeProcedure, NamedThing, Entity
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...Procedure, NamedThing, Entity
provided_by*
String		The value in this node property represents the knowledge provider that create...Procedure, NamedThing
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...Procedure, NamedThing
full_name0..1
LabelType		a long-form human readable name for a thingProcedure, NamedThing
synonym*
LabelType		Alternate human-readable names for a thingProcedure, NamedThing
+

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
LibraryPoolwas_generated_byrangeLibraryPooling
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:LibraryPooling
nativebican:LibraryPooling
+

LinkML Source

+ +

Direct

+
+
name: LibraryPooling
+description: The process of constructing of a libray pool by combining library aliquots
+  from a set of input libraries. Each library aliquot in a library pool will have
+  a unique R1/R2 index to allow for sequencing together then separating the sequencing
+  output by originating library aliquot through the process of demultiplexing.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slots:
+- used
+slot_usage:
+  used:
+    name: used
+    description: The input aliquot(s) from which the library pool was derived from.
+    range: LibraryAliquot
+    multivalued: true
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  process_date:
+    name: process_date
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_pool_preparation_date
+    description: Date of library pooling process.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-XUXUNM35
+    domain_of:
+    - CellDissociation
+    - CellEnrichment
+    - CellBarcoding
+    - CdnaAmplification
+    - LibraryConstruction
+    - LibraryPooling
+
+
+
+

Induced

+
+
name: LibraryPooling
+description: The process of constructing of a libray pool by combining library aliquots
+  from a set of input libraries. Each library aliquot in a library pool will have
+  a unique R1/R2 index to allow for sequencing together then separating the sequencing
+  output by originating library aliquot through the process of demultiplexing.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slot_usage:
+  used:
+    name: used
+    description: The input aliquot(s) from which the library pool was derived from.
+    range: LibraryAliquot
+    multivalued: true
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  process_date:
+    name: process_date
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: library_pool_preparation_date
+    description: Date of library pooling process.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:PD-XUXUNM35
+    alias: process_date
+    owner: LibraryPooling
+    domain_of:
+    - CellDissociation
+    - CellEnrichment
+    - CellBarcoding
+    - CdnaAmplification
+    - LibraryConstruction
+    - LibraryPooling
+    range: string
+  used:
+    name: used
+    description: The input aliquot(s) from which the library pool was derived from.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: used
+    owner: LibraryPooling
+    domain_of:
+    - DissectionRoiDelineation
+    - TissueDissection
+    - CellDissociation
+    - CellEnrichment
+    - EnrichedCellSampleSplitting
+    - CellBarcoding
+    - CdnaAmplification
+    - LibraryConstruction
+    - LibraryPooling
+    - ProvActivity
+    range: LibraryAliquot
+    multivalued: true
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: LibraryPooling
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: LibraryPooling
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: LibraryPooling
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+    pattern: ^bican:[A-Z][A-Za-z]+$
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: LibraryPooling
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: LibraryPooling
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - Donor
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DissectionRoiPolygon
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: LibraryPooling
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: LibraryPooling
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: LibraryPooling
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: LibraryPooling
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: LibraryPooling
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: LibraryPooling
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: LibraryPooling
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/LibraryPrepPassFail/index.html b/LibraryPrepPassFail/index.html new file mode 100644 index 00000000..638caab7 --- /dev/null +++ b/LibraryPrepPassFail/index.html @@ -0,0 +1,650 @@ + + + + + + + + + + + + + + + + + + + Enum: LibraryPrepPassFail - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
+
+ + + +
+
+
+ + + + + +
+
+
+ + + +
+
+
+ + + +
+
+
+ + + +
+
+ + + + + + + +

Enum: LibraryPrepPassFail

+

URI: LibraryPrepPassFail

+

Permissible Values

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ValueMeaningDescription
PassNIMP:PD-QHQHQB42Library Prep passed the QA/QC
FailNIMP:PD-QHQHQB42Library Prep failed the QA/QC
Low QCNIMP:PD-QHQHQB42Library Prep low passed the QA/QC
Not evaluatedNIMP:PD-QHQHQB42Library Prep not evaluated for QA/QC
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

LinkML Source

+
+ +
name: library_prep_pass_fail
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+rank: 1000
+permissible_values:
+  Pass:
+    text: Pass
+    description: Library Prep passed the QA/QC
+    meaning: NIMP:PD-QHQHQB42
+  Fail:
+    text: Fail
+    description: Library Prep failed the QA/QC
+    meaning: NIMP:PD-QHQHQB42
+  Low QC:
+    text: Low QC
+    description: Library Prep low passed the QA/QC
+    meaning: NIMP:PD-QHQHQB42
+  Not evaluated:
+    text: Not evaluated
+    description: Library Prep not evaluated for QA/QC
+    meaning: NIMP:PD-QHQHQB42
+
+
+ +
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/LibraryR1R2Index/index.html b/LibraryR1R2Index/index.html new file mode 100644 index 00000000..5b68f48c --- /dev/null +++ b/LibraryR1R2Index/index.html @@ -0,0 +1,5165 @@ + + + + + + + + + + + + + + + + + + + Enum: LibraryR1R2Index - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
+
+ + + +
+
+
+ + + + + +
+
+
+ + + +
+
+
+ + + +
+
+
+ + + +
+
+ + + + + + + +

Enum: LibraryR1R2Index

+

URI: LibraryR1R2Index

+

Permissible Values

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + +
ValueMeaningDescription
SI-TT-A1NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-A2NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-A3NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-A4NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-A5NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-A6NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-A7NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-A8NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-A9NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-A10NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-A11NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-A12NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-B1NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-B2NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-B3NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-B4NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-B5NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-B6NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-B7NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-B8NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-B9NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-B10NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-B11NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-B12NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-C1NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-C2NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-C3NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-C4NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-C5NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-C6NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-C7NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-C8NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-C9NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-C10NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-C11NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-C12NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-D1NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-D2NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-D3NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-D4NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-D5NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-D6NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-D7NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-D8NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-D9NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-D10NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-D11NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-D12NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-E1NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-E2NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-E3NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-E4NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-E5NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-E6NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-E7NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-E8NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-E9NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-E10NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-E11NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-E12NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-F1NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-F2NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-F3NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-F4NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-F5NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-F6NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-F7NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-F8NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-F9NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-F10NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-F11NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-F12NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-G1NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-G2NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-G3NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-G4NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-G5NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-G6NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-G7NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-G8NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-G9NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-G10NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-G11NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-G12NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-H1NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-H2NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-H3NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-H4NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-H5NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-H6NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-H7NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-H8NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-H9NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-H10NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-H11NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-TT-H12NIMP:PD-VLLMWZ6010x Dual Index TT Set A
SI-NN-A1NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-A2NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-A3NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-A4NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-A5NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-A6NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-A7NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-A8NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-A9NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-A10NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-A11NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-A12NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-B1NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-B2NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-B3NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-B4NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-B5NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-B6NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-B7NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-B8NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-B9NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-B10NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-B11NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-B12NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-C1NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-C2NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-C3NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-C4NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-C5NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-C6NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-C7NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-C8NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-C9NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-C10NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-C11NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-C12NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-D1NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-D2NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-D3NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-D4NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-D5NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-D6NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-D7NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-D8NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-D9NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-D10NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-D11NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-D12NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-E1NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-E2NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-E3NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-E4NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-E5NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-E6NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-E7NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-E8NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-E9NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-E10NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-E11NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-E12NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-F1NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-F2NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-F3NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-F4NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-F5NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-F6NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-F7NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-F8NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-F9NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-F10NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-F11NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-F12NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-G1NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-G2NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-G3NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-G4NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-G5NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-G6NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-G7NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-G8NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-G9NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-G10NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-G11NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-G12NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-H1NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-H2NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-H3NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-H4NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-H5NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-H6NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-H7NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-H8NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-H9NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-H10NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-H11NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NN-H12NIMP:PD-VLLMWZ6010x Dual Index NN Set A
SI-NA-A1NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-B1NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-C1NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-D1NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-E1NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-F1NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-G1NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-H1NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-A2NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-B2NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-C2NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-D2NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-E2NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-F2NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-G2NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-H2NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-A3NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-B3NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-C3NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-D3NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-E3NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-F3NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-G3NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-H3NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-A4NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-B4NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-C4NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-D4NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-E4NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-F4NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-G4NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-H4NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-A5NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-B5NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-C5NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-D5NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-E5NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-F5NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-G5NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-H5NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-A6NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-B6NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-C6NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-D6NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-E6NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-F6NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-G6NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-H6NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-A7NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-B7NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-C7NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-D7NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-E7NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-F7NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-G7NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-H7NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-A8NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-B8NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-C8NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-D8NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-E8NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-F8NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-G8NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-H8NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-A9NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-B9NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-C9NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-D9NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-E9NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-F9NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-G9NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-H9NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-A10NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-B10NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-C10NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-D10NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-E10NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-F10NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-G10NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-H10NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-A11NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-B11NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-C11NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-D11NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-E11NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-F11NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-G11NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-H11NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-A12NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-B12NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-C12NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-D12NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-E12NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-F12NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-G12NIMP:PD-VLLMWZ6010x Single Index N Set A
SI-NA-H12NIMP:PD-VLLMWZ6010x Single Index N Set A
SetB-A1NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-A10NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-A11NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-A12NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-A13NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-A14NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-A15NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-A16NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-A17NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-A18NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-A19NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-A2NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-A20NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-A21NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-A22NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-A23NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-A24NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-A3NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-A4NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-A5NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-A6NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-A7NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-A8NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-A9NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-B1NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-B10NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-B11NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-B12NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-B13NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-B14NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-B15NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-B16NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-B17NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-B18NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-B19NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-B2NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-B20NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-B21NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-B22NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-B23NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-B24NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-B3NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-B4NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-B5NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-B6NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-B7NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-B8NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-B9NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-C1NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-C10NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-C11NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-C12NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-C13NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-C14NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-C15NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-C16NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-C17NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-C18NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-C19NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-C2NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-C20NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-C21NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-C22NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-C23NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-C24NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-C3NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-C4NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-C5NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-C6NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-C7NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-C8NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-C9NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-D1NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-D10NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-D11NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-D12NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-D13NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-D14NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-D15NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-D16NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-D17NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-D18NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-D19NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-D2NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-D20NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-D21NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-D22NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-D23NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-D24NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-D3NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-D4NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-D5NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-D6NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-D7NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-D8NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-D9NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-E1NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-E10NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-E11NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-E12NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-E13NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-E14NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-E15NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-E16NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-E17NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-E18NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-E19NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-E2NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-E20NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-E21NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-E22NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-E23NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-E24NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-E3NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-E4NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-E5NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-E6NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-E7NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-E8NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-E9NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-F1NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-F10NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-F11NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-F12NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-F13NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-F14NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-F15NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-F16NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-F17NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-F18NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-F19NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-F2NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-F20NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-F21NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-F22NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-F23NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-F24NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-F3NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-F4NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-F5NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-F6NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-F7NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-F8NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-F9NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-G1NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-G10NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-G11NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-G12NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-G13NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-G14NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-G15NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-G16NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-G17NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-G18NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-G19NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-G2NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-G20NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-G21NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-G22NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-G23NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-G24NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-G3NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-G4NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-G5NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-G6NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-G7NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-G8NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-G9NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-H1NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-H10NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-H11NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-H12NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-H13NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-H14NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-H15NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-H16NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-H17NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-H18NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-H19NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-H2NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-H20NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-H21NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-H22NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-H23NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-H24NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-H3NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-H4NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-H5NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-H6NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-H7NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-H8NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-H9NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-I1NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-I10NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-I11NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-I12NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-I13NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-I14NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-I15NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-I16NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-I17NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-I18NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-I19NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-I2NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-I20NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-I21NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-I22NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-I23NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-I24NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-I3NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-I4NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-I5NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-I6NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-I7NIMP:PD-VLLMWZ60NeryLab 384_SetB
SetB-I8NIMP:PD-VLLMWZ60NeryLab 384_SetB/#
+

Slots

+ + + + + + + + + + + + + +
NameDescription
r1_r2_indexName of the pair of library indexes used for sequencing
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

LinkML Source

+
+ +
name: library_r1_r2_index
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+rank: 1000
+permissible_values:
+  SI-TT-A1:
+    text: SI-TT-A1
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-A2:
+    text: SI-TT-A2
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-A3:
+    text: SI-TT-A3
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-A4:
+    text: SI-TT-A4
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-A5:
+    text: SI-TT-A5
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-A6:
+    text: SI-TT-A6
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-A7:
+    text: SI-TT-A7
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-A8:
+    text: SI-TT-A8
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-A9:
+    text: SI-TT-A9
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-A10:
+    text: SI-TT-A10
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-A11:
+    text: SI-TT-A11
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-A12:
+    text: SI-TT-A12
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-B1:
+    text: SI-TT-B1
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-B2:
+    text: SI-TT-B2
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-B3:
+    text: SI-TT-B3
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-B4:
+    text: SI-TT-B4
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-B5:
+    text: SI-TT-B5
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-B6:
+    text: SI-TT-B6
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-B7:
+    text: SI-TT-B7
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-B8:
+    text: SI-TT-B8
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-B9:
+    text: SI-TT-B9
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-B10:
+    text: SI-TT-B10
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-B11:
+    text: SI-TT-B11
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-B12:
+    text: SI-TT-B12
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-C1:
+    text: SI-TT-C1
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-C2:
+    text: SI-TT-C2
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-C3:
+    text: SI-TT-C3
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-C4:
+    text: SI-TT-C4
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-C5:
+    text: SI-TT-C5
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-C6:
+    text: SI-TT-C6
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-C7:
+    text: SI-TT-C7
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-C8:
+    text: SI-TT-C8
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-C9:
+    text: SI-TT-C9
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-C10:
+    text: SI-TT-C10
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-C11:
+    text: SI-TT-C11
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-C12:
+    text: SI-TT-C12
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-D1:
+    text: SI-TT-D1
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-D2:
+    text: SI-TT-D2
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-D3:
+    text: SI-TT-D3
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-D4:
+    text: SI-TT-D4
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-D5:
+    text: SI-TT-D5
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-D6:
+    text: SI-TT-D6
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-D7:
+    text: SI-TT-D7
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-D8:
+    text: SI-TT-D8
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-D9:
+    text: SI-TT-D9
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-D10:
+    text: SI-TT-D10
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-D11:
+    text: SI-TT-D11
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-D12:
+    text: SI-TT-D12
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-E1:
+    text: SI-TT-E1
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-E2:
+    text: SI-TT-E2
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-E3:
+    text: SI-TT-E3
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-E4:
+    text: SI-TT-E4
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-E5:
+    text: SI-TT-E5
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-E6:
+    text: SI-TT-E6
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-E7:
+    text: SI-TT-E7
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-E8:
+    text: SI-TT-E8
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-E9:
+    text: SI-TT-E9
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-E10:
+    text: SI-TT-E10
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-E11:
+    text: SI-TT-E11
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-E12:
+    text: SI-TT-E12
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-F1:
+    text: SI-TT-F1
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-F2:
+    text: SI-TT-F2
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-F3:
+    text: SI-TT-F3
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-F4:
+    text: SI-TT-F4
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-F5:
+    text: SI-TT-F5
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-F6:
+    text: SI-TT-F6
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-F7:
+    text: SI-TT-F7
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-F8:
+    text: SI-TT-F8
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-F9:
+    text: SI-TT-F9
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-F10:
+    text: SI-TT-F10
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-F11:
+    text: SI-TT-F11
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-F12:
+    text: SI-TT-F12
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-G1:
+    text: SI-TT-G1
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-G2:
+    text: SI-TT-G2
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-G3:
+    text: SI-TT-G3
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-G4:
+    text: SI-TT-G4
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-G5:
+    text: SI-TT-G5
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-G6:
+    text: SI-TT-G6
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-G7:
+    text: SI-TT-G7
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-G8:
+    text: SI-TT-G8
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-G9:
+    text: SI-TT-G9
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-G10:
+    text: SI-TT-G10
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-G11:
+    text: SI-TT-G11
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-G12:
+    text: SI-TT-G12
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-H1:
+    text: SI-TT-H1
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-H2:
+    text: SI-TT-H2
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-H3:
+    text: SI-TT-H3
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-H4:
+    text: SI-TT-H4
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-H5:
+    text: SI-TT-H5
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-H6:
+    text: SI-TT-H6
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-H7:
+    text: SI-TT-H7
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-H8:
+    text: SI-TT-H8
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-H9:
+    text: SI-TT-H9
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-H10:
+    text: SI-TT-H10
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-H11:
+    text: SI-TT-H11
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-TT-H12:
+    text: SI-TT-H12
+    description: 10x Dual Index TT Set A. Used with 10xV3.1, 10xV3.1_HT, and 10xMultiome;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-A1:
+    text: SI-NN-A1
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-A2:
+    text: SI-NN-A2
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-A3:
+    text: SI-NN-A3
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-A4:
+    text: SI-NN-A4
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-A5:
+    text: SI-NN-A5
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-A6:
+    text: SI-NN-A6
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-A7:
+    text: SI-NN-A7
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-A8:
+    text: SI-NN-A8
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-A9:
+    text: SI-NN-A9
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-A10:
+    text: SI-NN-A10
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-A11:
+    text: SI-NN-A11
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-A12:
+    text: SI-NN-A12
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-B1:
+    text: SI-NN-B1
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-B2:
+    text: SI-NN-B2
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-B3:
+    text: SI-NN-B3
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-B4:
+    text: SI-NN-B4
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-B5:
+    text: SI-NN-B5
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-B6:
+    text: SI-NN-B6
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-B7:
+    text: SI-NN-B7
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-B8:
+    text: SI-NN-B8
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-B9:
+    text: SI-NN-B9
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-B10:
+    text: SI-NN-B10
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-B11:
+    text: SI-NN-B11
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-B12:
+    text: SI-NN-B12
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-C1:
+    text: SI-NN-C1
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-C2:
+    text: SI-NN-C2
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-C3:
+    text: SI-NN-C3
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-C4:
+    text: SI-NN-C4
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-C5:
+    text: SI-NN-C5
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-C6:
+    text: SI-NN-C6
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-C7:
+    text: SI-NN-C7
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-C8:
+    text: SI-NN-C8
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-C9:
+    text: SI-NN-C9
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-C10:
+    text: SI-NN-C10
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-C11:
+    text: SI-NN-C11
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-C12:
+    text: SI-NN-C12
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-D1:
+    text: SI-NN-D1
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-D2:
+    text: SI-NN-D2
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-D3:
+    text: SI-NN-D3
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-D4:
+    text: SI-NN-D4
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-D5:
+    text: SI-NN-D5
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-D6:
+    text: SI-NN-D6
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-D7:
+    text: SI-NN-D7
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-D8:
+    text: SI-NN-D8
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-D9:
+    text: SI-NN-D9
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-D10:
+    text: SI-NN-D10
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-D11:
+    text: SI-NN-D11
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-D12:
+    text: SI-NN-D12
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-E1:
+    text: SI-NN-E1
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-E2:
+    text: SI-NN-E2
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-E3:
+    text: SI-NN-E3
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-E4:
+    text: SI-NN-E4
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-E5:
+    text: SI-NN-E5
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-E6:
+    text: SI-NN-E6
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-E7:
+    text: SI-NN-E7
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-E8:
+    text: SI-NN-E8
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-E9:
+    text: SI-NN-E9
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-E10:
+    text: SI-NN-E10
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-E11:
+    text: SI-NN-E11
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-E12:
+    text: SI-NN-E12
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-F1:
+    text: SI-NN-F1
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-F2:
+    text: SI-NN-F2
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-F3:
+    text: SI-NN-F3
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-F4:
+    text: SI-NN-F4
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-F5:
+    text: SI-NN-F5
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-F6:
+    text: SI-NN-F6
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-F7:
+    text: SI-NN-F7
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-F8:
+    text: SI-NN-F8
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-F9:
+    text: SI-NN-F9
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-F10:
+    text: SI-NN-F10
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-F11:
+    text: SI-NN-F11
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-F12:
+    text: SI-NN-F12
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-G1:
+    text: SI-NN-G1
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-G2:
+    text: SI-NN-G2
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-G3:
+    text: SI-NN-G3
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-G4:
+    text: SI-NN-G4
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-G5:
+    text: SI-NN-G5
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-G6:
+    text: SI-NN-G6
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-G7:
+    text: SI-NN-G7
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-G8:
+    text: SI-NN-G8
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-G9:
+    text: SI-NN-G9
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-G10:
+    text: SI-NN-G10
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-G11:
+    text: SI-NN-G11
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-G12:
+    text: SI-NN-G12
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-H1:
+    text: SI-NN-H1
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-H2:
+    text: SI-NN-H2
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-H3:
+    text: SI-NN-H3
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-H4:
+    text: SI-NN-H4
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-H5:
+    text: SI-NN-H5
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-H6:
+    text: SI-NN-H6
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-H7:
+    text: SI-NN-H7
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-H8:
+    text: SI-NN-H8
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-H9:
+    text: SI-NN-H9
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-H10:
+    text: SI-NN-H10
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-H11:
+    text: SI-NN-H11
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NN-H12:
+    text: SI-NN-H12
+    description: 10x Dual Index NN Set A. Used with 10xV3.1_CellPlex;GEX and 10xV3.1-HT_CellPlex;GEX
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-A1:
+    text: SI-NA-A1
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-B1:
+    text: SI-NA-B1
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-C1:
+    text: SI-NA-C1
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-D1:
+    text: SI-NA-D1
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-E1:
+    text: SI-NA-E1
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-F1:
+    text: SI-NA-F1
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-G1:
+    text: SI-NA-G1
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-H1:
+    text: SI-NA-H1
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-A2:
+    text: SI-NA-A2
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-B2:
+    text: SI-NA-B2
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-C2:
+    text: SI-NA-C2
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-D2:
+    text: SI-NA-D2
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-E2:
+    text: SI-NA-E2
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-F2:
+    text: SI-NA-F2
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-G2:
+    text: SI-NA-G2
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-H2:
+    text: SI-NA-H2
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-A3:
+    text: SI-NA-A3
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-B3:
+    text: SI-NA-B3
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-C3:
+    text: SI-NA-C3
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-D3:
+    text: SI-NA-D3
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-E3:
+    text: SI-NA-E3
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-F3:
+    text: SI-NA-F3
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-G3:
+    text: SI-NA-G3
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-H3:
+    text: SI-NA-H3
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-A4:
+    text: SI-NA-A4
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-B4:
+    text: SI-NA-B4
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-C4:
+    text: SI-NA-C4
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-D4:
+    text: SI-NA-D4
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-E4:
+    text: SI-NA-E4
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-F4:
+    text: SI-NA-F4
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-G4:
+    text: SI-NA-G4
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-H4:
+    text: SI-NA-H4
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-A5:
+    text: SI-NA-A5
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-B5:
+    text: SI-NA-B5
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-C5:
+    text: SI-NA-C5
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-D5:
+    text: SI-NA-D5
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-E5:
+    text: SI-NA-E5
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-F5:
+    text: SI-NA-F5
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-G5:
+    text: SI-NA-G5
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-H5:
+    text: SI-NA-H5
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-A6:
+    text: SI-NA-A6
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-B6:
+    text: SI-NA-B6
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-C6:
+    text: SI-NA-C6
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-D6:
+    text: SI-NA-D6
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-E6:
+    text: SI-NA-E6
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-F6:
+    text: SI-NA-F6
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-G6:
+    text: SI-NA-G6
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-H6:
+    text: SI-NA-H6
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-A7:
+    text: SI-NA-A7
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-B7:
+    text: SI-NA-B7
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-C7:
+    text: SI-NA-C7
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-D7:
+    text: SI-NA-D7
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-E7:
+    text: SI-NA-E7
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-F7:
+    text: SI-NA-F7
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-G7:
+    text: SI-NA-G7
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-H7:
+    text: SI-NA-H7
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-A8:
+    text: SI-NA-A8
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-B8:
+    text: SI-NA-B8
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-C8:
+    text: SI-NA-C8
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-D8:
+    text: SI-NA-D8
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-E8:
+    text: SI-NA-E8
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-F8:
+    text: SI-NA-F8
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-G8:
+    text: SI-NA-G8
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-H8:
+    text: SI-NA-H8
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-A9:
+    text: SI-NA-A9
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-B9:
+    text: SI-NA-B9
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-C9:
+    text: SI-NA-C9
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-D9:
+    text: SI-NA-D9
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-E9:
+    text: SI-NA-E9
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-F9:
+    text: SI-NA-F9
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-G9:
+    text: SI-NA-G9
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-H9:
+    text: SI-NA-H9
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-A10:
+    text: SI-NA-A10
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-B10:
+    text: SI-NA-B10
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-C10:
+    text: SI-NA-C10
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-D10:
+    text: SI-NA-D10
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-E10:
+    text: SI-NA-E10
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-F10:
+    text: SI-NA-F10
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-G10:
+    text: SI-NA-G10
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-H10:
+    text: SI-NA-H10
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-A11:
+    text: SI-NA-A11
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-B11:
+    text: SI-NA-B11
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-C11:
+    text: SI-NA-C11
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-D11:
+    text: SI-NA-D11
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-E11:
+    text: SI-NA-E11
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-F11:
+    text: SI-NA-F11
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-G11:
+    text: SI-NA-G11
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-H11:
+    text: SI-NA-H11
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-A12:
+    text: SI-NA-A12
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-B12:
+    text: SI-NA-B12
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-C12:
+    text: SI-NA-C12
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-D12:
+    text: SI-NA-D12
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-E12:
+    text: SI-NA-E12
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-F12:
+    text: SI-NA-F12
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-G12:
+    text: SI-NA-G12
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SI-NA-H12:
+    text: SI-NA-H12
+    description: 10x Single Index N Set A. Used with 10xATAC_v2.0 and 10xMultiome;ATAC
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-A1:
+    text: SetB-A1
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-A10:
+    text: SetB-A10
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-A11:
+    text: SetB-A11
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-A12:
+    text: SetB-A12
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-A13:
+    text: SetB-A13
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-A14:
+    text: SetB-A14
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-A15:
+    text: SetB-A15
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-A16:
+    text: SetB-A16
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-A17:
+    text: SetB-A17
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-A18:
+    text: SetB-A18
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-A19:
+    text: SetB-A19
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-A2:
+    text: SetB-A2
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-A20:
+    text: SetB-A20
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-A21:
+    text: SetB-A21
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-A22:
+    text: SetB-A22
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-A23:
+    text: SetB-A23
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-A24:
+    text: SetB-A24
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-A3:
+    text: SetB-A3
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-A4:
+    text: SetB-A4
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-A5:
+    text: SetB-A5
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-A6:
+    text: SetB-A6
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-A7:
+    text: SetB-A7
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-A8:
+    text: SetB-A8
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-A9:
+    text: SetB-A9
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-B1:
+    text: SetB-B1
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-B10:
+    text: SetB-B10
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-B11:
+    text: SetB-B11
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-B12:
+    text: SetB-B12
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-B13:
+    text: SetB-B13
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-B14:
+    text: SetB-B14
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-B15:
+    text: SetB-B15
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-B16:
+    text: SetB-B16
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-B17:
+    text: SetB-B17
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-B18:
+    text: SetB-B18
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-B19:
+    text: SetB-B19
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-B2:
+    text: SetB-B2
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-B20:
+    text: SetB-B20
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-B21:
+    text: SetB-B21
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-B22:
+    text: SetB-B22
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-B23:
+    text: SetB-B23
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-B24:
+    text: SetB-B24
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-B3:
+    text: SetB-B3
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-B4:
+    text: SetB-B4
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-B5:
+    text: SetB-B5
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-B6:
+    text: SetB-B6
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-B7:
+    text: SetB-B7
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-B8:
+    text: SetB-B8
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-B9:
+    text: SetB-B9
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-C1:
+    text: SetB-C1
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-C10:
+    text: SetB-C10
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-C11:
+    text: SetB-C11
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-C12:
+    text: SetB-C12
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-C13:
+    text: SetB-C13
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-C14:
+    text: SetB-C14
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-C15:
+    text: SetB-C15
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-C16:
+    text: SetB-C16
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-C17:
+    text: SetB-C17
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-C18:
+    text: SetB-C18
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-C19:
+    text: SetB-C19
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-C2:
+    text: SetB-C2
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-C20:
+    text: SetB-C20
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-C21:
+    text: SetB-C21
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-C22:
+    text: SetB-C22
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-C23:
+    text: SetB-C23
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-C24:
+    text: SetB-C24
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-C3:
+    text: SetB-C3
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-C4:
+    text: SetB-C4
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-C5:
+    text: SetB-C5
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-C6:
+    text: SetB-C6
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-C7:
+    text: SetB-C7
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-C8:
+    text: SetB-C8
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-C9:
+    text: SetB-C9
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-D1:
+    text: SetB-D1
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-D10:
+    text: SetB-D10
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-D11:
+    text: SetB-D11
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-D12:
+    text: SetB-D12
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-D13:
+    text: SetB-D13
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-D14:
+    text: SetB-D14
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-D15:
+    text: SetB-D15
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-D16:
+    text: SetB-D16
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-D17:
+    text: SetB-D17
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-D18:
+    text: SetB-D18
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-D19:
+    text: SetB-D19
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-D2:
+    text: SetB-D2
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-D20:
+    text: SetB-D20
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-D21:
+    text: SetB-D21
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-D22:
+    text: SetB-D22
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-D23:
+    text: SetB-D23
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-D24:
+    text: SetB-D24
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-D3:
+    text: SetB-D3
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-D4:
+    text: SetB-D4
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-D5:
+    text: SetB-D5
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-D6:
+    text: SetB-D6
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-D7:
+    text: SetB-D7
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-D8:
+    text: SetB-D8
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-D9:
+    text: SetB-D9
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-E1:
+    text: SetB-E1
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-E10:
+    text: SetB-E10
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-E11:
+    text: SetB-E11
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-E12:
+    text: SetB-E12
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-E13:
+    text: SetB-E13
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-E14:
+    text: SetB-E14
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-E15:
+    text: SetB-E15
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-E16:
+    text: SetB-E16
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-E17:
+    text: SetB-E17
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-E18:
+    text: SetB-E18
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-E19:
+    text: SetB-E19
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-E2:
+    text: SetB-E2
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-E20:
+    text: SetB-E20
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-E21:
+    text: SetB-E21
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-E22:
+    text: SetB-E22
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-E23:
+    text: SetB-E23
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-E24:
+    text: SetB-E24
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-E3:
+    text: SetB-E3
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-E4:
+    text: SetB-E4
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-E5:
+    text: SetB-E5
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-E6:
+    text: SetB-E6
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-E7:
+    text: SetB-E7
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-E8:
+    text: SetB-E8
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-E9:
+    text: SetB-E9
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-F1:
+    text: SetB-F1
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-F10:
+    text: SetB-F10
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-F11:
+    text: SetB-F11
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-F12:
+    text: SetB-F12
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-F13:
+    text: SetB-F13
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-F14:
+    text: SetB-F14
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-F15:
+    text: SetB-F15
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-F16:
+    text: SetB-F16
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-F17:
+    text: SetB-F17
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-F18:
+    text: SetB-F18
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-F19:
+    text: SetB-F19
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-F2:
+    text: SetB-F2
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-F20:
+    text: SetB-F20
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-F21:
+    text: SetB-F21
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-F22:
+    text: SetB-F22
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-F23:
+    text: SetB-F23
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-F24:
+    text: SetB-F24
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-F3:
+    text: SetB-F3
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-F4:
+    text: SetB-F4
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-F5:
+    text: SetB-F5
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-F6:
+    text: SetB-F6
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-F7:
+    text: SetB-F7
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-F8:
+    text: SetB-F8
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-F9:
+    text: SetB-F9
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-G1:
+    text: SetB-G1
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-G10:
+    text: SetB-G10
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-G11:
+    text: SetB-G11
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-G12:
+    text: SetB-G12
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-G13:
+    text: SetB-G13
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-G14:
+    text: SetB-G14
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-G15:
+    text: SetB-G15
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-G16:
+    text: SetB-G16
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-G17:
+    text: SetB-G17
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-G18:
+    text: SetB-G18
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-G19:
+    text: SetB-G19
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-G2:
+    text: SetB-G2
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-G20:
+    text: SetB-G20
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-G21:
+    text: SetB-G21
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-G22:
+    text: SetB-G22
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-G23:
+    text: SetB-G23
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-G24:
+    text: SetB-G24
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-G3:
+    text: SetB-G3
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-G4:
+    text: SetB-G4
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-G5:
+    text: SetB-G5
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-G6:
+    text: SetB-G6
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-G7:
+    text: SetB-G7
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-G8:
+    text: SetB-G8
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-G9:
+    text: SetB-G9
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-H1:
+    text: SetB-H1
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-H10:
+    text: SetB-H10
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-H11:
+    text: SetB-H11
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-H12:
+    text: SetB-H12
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-H13:
+    text: SetB-H13
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-H14:
+    text: SetB-H14
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-H15:
+    text: SetB-H15
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-H16:
+    text: SetB-H16
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-H17:
+    text: SetB-H17
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-H18:
+    text: SetB-H18
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-H19:
+    text: SetB-H19
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-H2:
+    text: SetB-H2
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-H20:
+    text: SetB-H20
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-H21:
+    text: SetB-H21
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-H22:
+    text: SetB-H22
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-H23:
+    text: SetB-H23
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-H24:
+    text: SetB-H24
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-H3:
+    text: SetB-H3
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-H4:
+    text: SetB-H4
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-H5:
+    text: SetB-H5
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-H6:
+    text: SetB-H6
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-H7:
+    text: SetB-H7
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-H8:
+    text: SetB-H8
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-H9:
+    text: SetB-H9
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-I1:
+    text: SetB-I1
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-I10:
+    text: SetB-I10
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-I11:
+    text: SetB-I11
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-I12:
+    text: SetB-I12
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-I13:
+    text: SetB-I13
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-I14:
+    text: SetB-I14
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-I15:
+    text: SetB-I15
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-I16:
+    text: SetB-I16
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-I17:
+    text: SetB-I17
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-I18:
+    text: SetB-I18
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-I19:
+    text: SetB-I19
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-I2:
+    text: SetB-I2
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-I20:
+    text: SetB-I20
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-I21:
+    text: SetB-I21
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-I22:
+    text: SetB-I22
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-I23:
+    text: SetB-I23
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-I24:
+    text: SetB-I24
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-I3:
+    text: SetB-I3
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-I4:
+    text: SetB-I4
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-I5:
+    text: SetB-I5
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-I6:
+    text: SetB-I6
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-I7:
+    text: SetB-I7
+    description: NeryLab 384_SetB
+    meaning: NIMP:PD-VLLMWZ60
+  SetB-I8:
+    text: SetB-I8
+    description: NeryLab 384_SetB/#
+    meaning: NIMP:PD-VLLMWZ60
+
+
+ +
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/LibraryTechnique/index.html b/LibraryTechnique/index.html new file mode 100644 index 00000000..ae3450d3 --- /dev/null +++ b/LibraryTechnique/index.html @@ -0,0 +1,821 @@ + + + + + + + + + + + + + + + + + + + Enum: LibraryTechnique - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
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+ + + + + + + +

Enum: LibraryTechnique

+

URI: LibraryTechnique

+

Permissible Values

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ValueMeaningDescription
SMARTSeqSCNIMP:PD-AJAJCN35SMARTSeqSC
SmartSeq3NIMP:PD-AJAJCN35SmartSeq3
10xV3.1NIMP:PD-AJAJCN3510xV3
10xV3.1_HTNIMP:PD-AJAJCN3510xV3
10xMultiome;GEXNIMP:PD-AJAJCN3510xMultiome;GEX
10xMultiome;ATACNIMP:PD-AJAJCN3510xMultiome;ATAC
10xATAC_V2.0NIMP:PD-AJAJCN3510xATAC_V2
10XMultiome-CellHashing;GEXNIMP:PD-AJAJCN3510XMultiome-CellHashing;GEX
10XMultiome-CellHashing;ATACNIMP:PD-AJAJCN3510XMultiome-CellHashing;ATAC
10XMultiome-Cell Hashing;BarcodeNIMP:PD-AJAJCN3510XMultiome-Cell Hashing;Barcode
10xV3.1_CellPlex;GEXNIMP:PD-AJAJCN3510xV3
10xV3.1_CellPlex;BarcodeNIMP:PD-AJAJCN3510xV3
10xV3.1_HT_CellPlex;GEXNIMP:PD-AJAJCN3510xV3
10xV3.1_HT_CellPlex;BarcodeNIMP:PD-AJAJCN3510xV3
MethylC-SeqNIMP:PD-AJAJCN35MethylC-Seq
snm3C-seqNIMP:PD-AJAJCN35snm3C-seq
snmCT-seqNIMP:PD-AJAJCN35snmCT-seq
scATAC-seqNIMP:PD-AJAJCN35scATAC-seq
MERFISHNIMP:PD-AJAJCN35MERFISH
Slide-seq MERFISHNIMP:PD-AJAJCN35Slide-seq MERFISH
whole brain MERFISHNIMP:PD-AJAJCN35whole brain MERFISH
DBiT RNA-seqNIMP:PD-AJAJCN35DBiT RNA-seq
DBiT ATAC-seqNIMP:PD-AJAJCN35DBiT ATAC-seq
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

LinkML Source

+
+ +
name: library_technique
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+rank: 1000
+permissible_values:
+  SMARTSeqSC:
+    text: SMARTSeqSC
+    description: SMARTSeqSC
+    meaning: NIMP:PD-AJAJCN35
+  SmartSeq3:
+    text: SmartSeq3
+    description: SmartSeq3
+    meaning: NIMP:PD-AJAJCN35
+  10xV3.1:
+    text: 10xV3.1
+    description: 10xV3.1
+    meaning: NIMP:PD-AJAJCN35
+  10xV3.1_HT:
+    text: 10xV3.1_HT
+    description: 10xV3.1_HT
+    meaning: NIMP:PD-AJAJCN35
+  10xMultiome;GEX:
+    text: 10xMultiome;GEX
+    description: 10xMultiome;GEX
+    meaning: NIMP:PD-AJAJCN35
+  10xMultiome;ATAC:
+    text: 10xMultiome;ATAC
+    description: 10xMultiome;ATAC
+    meaning: NIMP:PD-AJAJCN35
+  10xATAC_V2.0:
+    text: 10xATAC_V2.0
+    description: 10xATAC_V2.0
+    meaning: NIMP:PD-AJAJCN35
+  10XMultiome-CellHashing;GEX:
+    text: 10XMultiome-CellHashing;GEX
+    description: 10XMultiome-CellHashing;GEX
+    meaning: NIMP:PD-AJAJCN35
+  10XMultiome-CellHashing;ATAC:
+    text: 10XMultiome-CellHashing;ATAC
+    description: 10XMultiome-CellHashing;ATAC
+    meaning: NIMP:PD-AJAJCN35
+  10XMultiome-Cell Hashing;Barcode:
+    text: 10XMultiome-Cell Hashing;Barcode
+    description: 10XMultiome-Cell Hashing;Barcode
+    meaning: NIMP:PD-AJAJCN35
+  10xV3.1_CellPlex;GEX:
+    text: 10xV3.1_CellPlex;GEX
+    description: 10xV3.1_CellPlex;GEX
+    meaning: NIMP:PD-AJAJCN35
+  10xV3.1_CellPlex;Barcode:
+    text: 10xV3.1_CellPlex;Barcode
+    description: 10xV3.1_CellPlex;Barcode
+    meaning: NIMP:PD-AJAJCN35
+  10xV3.1_HT_CellPlex;GEX:
+    text: 10xV3.1_HT_CellPlex;GEX
+    description: 10xV3.1_HT_CellPlex;GEX
+    meaning: NIMP:PD-AJAJCN35
+  10xV3.1_HT_CellPlex;Barcode:
+    text: 10xV3.1_HT_CellPlex;Barcode
+    description: 10xV3.1_HT_CellPlex;Barcode
+    meaning: NIMP:PD-AJAJCN35
+  MethylC-Seq:
+    text: MethylC-Seq
+    description: MethylC-Seq
+    meaning: NIMP:PD-AJAJCN35
+  snm3C-seq:
+    text: snm3C-seq
+    description: snm3C-seq
+    meaning: NIMP:PD-AJAJCN35
+  snmCT-seq:
+    text: snmCT-seq
+    description: snmCT-seq
+    meaning: NIMP:PD-AJAJCN35
+  scATAC-seq:
+    text: scATAC-seq
+    description: scATAC-seq
+    meaning: NIMP:PD-AJAJCN35
+  MERFISH:
+    text: MERFISH
+    description: MERFISH
+    meaning: NIMP:PD-AJAJCN35
+  Slide-seq MERFISH:
+    text: Slide-seq MERFISH
+    description: Slide-seq MERFISH
+    meaning: NIMP:PD-AJAJCN35
+  whole brain MERFISH:
+    text: whole brain MERFISH
+    description: whole brain MERFISH
+    meaning: NIMP:PD-AJAJCN35
+  DBiT RNA-seq:
+    text: DBiT RNA-seq
+    description: DBiT RNA-seq
+    meaning: NIMP:PD-AJAJCN35
+  DBiT ATAC-seq:
+    text: DBiT ATAC-seq
+    description: DBiT ATAC-seq
+    meaning: NIMP:PD-AJAJCN35
+
+
+ +
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/MacromolecularMachineMixin/index.html b/MacromolecularMachineMixin/index.html new file mode 100644 index 00000000..61b8c34c --- /dev/null +++ b/MacromolecularMachineMixin/index.html @@ -0,0 +1,473 @@ + + + + + + + + + +Class: MacromolecularMachineMixin - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
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+ +
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+

Class: MacromolecularMachineMixin

+

A union of gene locus, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this.

+

URI: biolink:MacromolecularMachineMixin

+
classDiagram + class MacromolecularMachineMixin + click MacromolecularMachineMixin href "../MacromolecularMachineMixin" + MacromolecularMachineMixin <|-- GeneOrGeneProduct + click GeneOrGeneProduct href "../GeneOrGeneProduct" + + MacromolecularMachineMixin : name + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
name0..1
LabelType		A human-readable name for an attribute or entitydirect
+

Mixin Usage

+ + + + + + + + + + + + + +
mixed intodescription
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:MacromolecularMachineMixin
nativebican:MacromolecularMachineMixin
+

LinkML Source

+ +

Direct

+
+
name: macromolecular machine mixin
+definition_uri: https://w3id.org/biolink/vocab/MacromolecularMachineMixin
+description: A union of gene locus, gene product, and macromolecular complex. These
+  are the basic units of function in a cell. They either carry out individual biological
+  activities, or they encode molecules which do this.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+mixin: true
+slots:
+- name
+class_uri: biolink:MacromolecularMachineMixin
+
+
+
+

Induced

+
+
name: macromolecular machine mixin
+definition_uri: https://w3id.org/biolink/vocab/MacromolecularMachineMixin
+description: A union of gene locus, gene product, and macromolecular complex. These
+  are the basic units of function in a cell. They either carry out individual biological
+  activities, or they encode molecules which do this.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+mixin: true
+attributes:
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: macromolecular machine mixin
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+class_uri: biolink:MacromolecularMachineMixin
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/MaterialSample/index.html b/MaterialSample/index.html new file mode 100644 index 00000000..4a1920fe --- /dev/null +++ b/MaterialSample/index.html @@ -0,0 +1,1065 @@ + + + + + + + + + +Class: MaterialSample - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
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+

Class: MaterialSample

+

A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO]

+

URI: biolink:MaterialSample

+
classDiagram + class MaterialSample + click MaterialSample href "../MaterialSample" + SubjectOfInvestigation <|-- MaterialSample + click SubjectOfInvestigation href "../SubjectOfInvestigation" + PhysicalEntity <|-- MaterialSample + click PhysicalEntity href "../PhysicalEntity" + + MaterialSample : category + + MaterialSample : deprecated + + MaterialSample : description + + MaterialSample : full_name + + MaterialSample : has_attribute + + + + + MaterialSample --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + MaterialSample : id + + MaterialSample : iri + + MaterialSample : name + + MaterialSample : provided_by + + MaterialSample : synonym + + MaterialSample : type + + MaterialSample : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
id1
String		A unique identifier for an entitydirect
iri0..1
IriType		An IRI for an entitydirect
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizeddirect
type*
String		direct
name0..1
LabelType		A human-readable name for an attribute or entitydirect
description0..1
NarrativeText		a human-readable description of an entitydirect
has_attribute*
Attribute		connects any entity to an attributedirect
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...direct
provided_by*
String		The value in this node property represents the knowledge provider that create...direct
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...direct
full_name0..1
LabelType		a long-form human readable name for a thingdirect
synonym*
LabelType		Alternate human-readable names for a thingdirect
+

Aliases

+
    +
  • biospecimen
    • +
  • sample
    • +
  • biosample
    • +
  • physical sample
    • +
+

Identifier and Mapping Information

+

Valid ID Prefixes

+

Instances of this class should have identifiers with one of the following prefixes:

+
    +
  • +

    BIOSAMPLE

    +
    • +
  • +

    GOLD.META

    +
    • +
+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:MaterialSample
nativebican:MaterialSample
exactOBI:0000747, SIO:001050
+

LinkML Source

+ +

Direct

+
+
name: material sample
+id_prefixes:
+- BIOSAMPLE
+- GOLD.META
+definition_uri: https://w3id.org/biolink/vocab/MaterialSample
+description: A sample is a limited quantity of something (e.g. an individual or set
+  of individuals from a population, or a portion of a substance) to be used for testing,
+  analysis, inspection, investigation, demonstration, or trial use. [SIO]
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+aliases:
+- biospecimen
+- sample
+- biosample
+- physical sample
+exact_mappings:
+- OBI:0000747
+- SIO:001050
+is_a: physical entity
+mixins:
+- subject of investigation
+slots:
+- id
+- iri
+- category
+- type
+- name
+- description
+- has attribute
+- deprecated
+- provided by
+- xref
+- full name
+- synonym
+class_uri: biolink:MaterialSample
+
+
+
+

Induced

+
+
name: material sample
+id_prefixes:
+- BIOSAMPLE
+- GOLD.META
+definition_uri: https://w3id.org/biolink/vocab/MaterialSample
+description: A sample is a limited quantity of something (e.g. an individual or set
+  of individuals from a population, or a portion of a substance) to be used for testing,
+  analysis, inspection, investigation, demonstration, or trial use. [SIO]
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+aliases:
+- biospecimen
+- sample
+- biosample
+- physical sample
+exact_mappings:
+- OBI:0000747
+- SIO:001050
+is_a: physical entity
+mixins:
+- subject of investigation
+attributes:
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: material sample
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: material sample
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: material sample
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: material sample
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: material sample
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: material sample
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: material sample
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: material sample
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: material sample
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: material sample
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: material sample
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: material sample
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+class_uri: biolink:MaterialSample
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/ModelOrganismDatabase/index.html b/ModelOrganismDatabase/index.html new file mode 100644 index 00000000..5f2e2e7d --- /dev/null +++ b/ModelOrganismDatabase/index.html @@ -0,0 +1,606 @@ + + + + + + + + + + + + + + + + + + + Subset: ModelOrganismDatabase - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
+
+ + + +
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+ + + + + +
+
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+ + + +
+
+
+ + + +
+
+ + + + + + + +

Subset: ModelOrganismDatabase

+

Subset that is relevant for a typical Model Organism Database (MOD)

+

URI: ModelOrganismDatabase

+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Classes in subset

+ + + + + + + + + + + + + + + + + + + + + +
ClassDescription
GeneA region (or regions) that includes all of the sequence elements necessary to...
GenomeA genome is the sum of genetic material within a cell or virion
OrganismTaxonA classification of a set of organisms
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/NamedThing/index.html b/NamedThing/index.html new file mode 100644 index 00000000..d854ac70 --- /dev/null +++ b/NamedThing/index.html @@ -0,0 +1,1483 @@ + + + + + + + + + +Class: NamedThing - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
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+ +
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+ +
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+ +
+
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+

Class: NamedThing

+

a databased entity or concept/class

+

URI: biolink:NamedThing

+
classDiagram + class NamedThing + click NamedThing href "../NamedThing" + Entity <|-- NamedThing + click Entity href "../Entity" + + + NamedThing <|-- GenomeAssembly + click GenomeAssembly href "../GenomeAssembly" + NamedThing <|-- Attribute + click Attribute href "../Attribute" + NamedThing <|-- OrganismTaxon + click OrganismTaxon href "../OrganismTaxon" + NamedThing <|-- InformationContentEntity + click InformationContentEntity href "../InformationContentEntity" + NamedThing <|-- PhysicalEntity + click PhysicalEntity href "../PhysicalEntity" + NamedThing <|-- Activity + click Activity href "../Activity" + NamedThing <|-- Procedure + click Procedure href "../Procedure" + NamedThing <|-- BiologicalEntity + click BiologicalEntity href "../BiologicalEntity" + + + NamedThing : category + + NamedThing : deprecated + + NamedThing : description + + NamedThing : full_name + + NamedThing : has_attribute + + + + + NamedThing --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + NamedThing : id + + NamedThing : iri + + NamedThing : name + + NamedThing : provided_by + + NamedThing : synonym + + NamedThing : type + + NamedThing : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
id1
String		A unique identifier for an entitydirect
iri0..1
IriType		An IRI for an entitydirect
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizeddirect
type*
String		direct
name0..1
LabelType		A human-readable name for an attribute or entitydirect
description0..1
NarrativeText		a human-readable description of an entitydirect
has_attribute*
Attribute		connects any entity to an attributedirect
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...direct
provided_by*
String		The value in this node property represents the knowledge provider that create...direct
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...direct
full_name0..1
LabelType		a long-form human readable name for a thingdirect
synonym*
LabelType		Alternate human-readable names for a thingdirect
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
GeneAnnotationprovided_bydomainNamedThing
GeneAnnotationfull_namedomainNamedThing
GeneAnnotationsynonymdomainNamedThing
GeneAnnotationsymboldomainNamedThing
GeneAnnotationxrefdomainNamedThing
GeneAnnotationhas_biological_sequencedomainNamedThing
GenomeAnnotationprovided_bydomainNamedThing
GenomeAnnotationxrefdomainNamedThing
GenomeAnnotationfull_namedomainNamedThing
GenomeAnnotationsynonymdomainNamedThing
GenomeAnnotationhas_biological_sequencedomainNamedThing
GenomeAssemblyprovided_bydomainNamedThing
GenomeAssemblyxrefdomainNamedThing
GenomeAssemblyfull_namedomainNamedThing
GenomeAssemblysynonymdomainNamedThing
Attributeprovided_bydomainNamedThing
AttributexrefdomainNamedThing
Attributefull_namedomainNamedThing
AttributesynonymdomainNamedThing
Attributehas_qualitative_valuerangeNamedThing
NamedThingprovided_bydomainNamedThing
NamedThingxrefdomainNamedThing
NamedThingfull_namedomainNamedThing
NamedThingsynonymdomainNamedThing
OrganismTaxonprovided_bydomainNamedThing
OrganismTaxonxrefdomainNamedThing
OrganismTaxonfull_namedomainNamedThing
OrganismTaxonsynonymdomainNamedThing
OrganismTaxonhas_taxonomic_rankdomainNamedThing
InformationContentEntityprovided_bydomainNamedThing
InformationContentEntityxrefdomainNamedThing
InformationContentEntityfull_namedomainNamedThing
InformationContentEntitysynonymdomainNamedThing
InformationContentEntitycreation_datedomainNamedThing
Datasetprovided_bydomainNamedThing
DatasetxrefdomainNamedThing
Datasetfull_namedomainNamedThing
DatasetsynonymdomainNamedThing
Datasetcreation_datedomainNamedThing
PhysicalEntityprovided_bydomainNamedThing
PhysicalEntityxrefdomainNamedThing
PhysicalEntityfull_namedomainNamedThing
PhysicalEntitysynonymdomainNamedThing
Activityprovided_bydomainNamedThing
ActivityxrefdomainNamedThing
Activityfull_namedomainNamedThing
ActivitysynonymdomainNamedThing
Procedureprovided_bydomainNamedThing
ProcedurexrefdomainNamedThing
Procedurefull_namedomainNamedThing
ProceduresynonymdomainNamedThing
MaterialSampleprovided_bydomainNamedThing
MaterialSamplexrefdomainNamedThing
MaterialSamplefull_namedomainNamedThing
MaterialSamplesynonymdomainNamedThing
BiologicalEntityprovided_bydomainNamedThing
BiologicalEntityxrefdomainNamedThing
BiologicalEntityfull_namedomainNamedThing
BiologicalEntitysynonymdomainNamedThing
GenomicEntityhas_biological_sequencedomainNamedThing
Geneprovided_bydomainNamedThing
Genefull_namedomainNamedThing
GenesynonymdomainNamedThing
GenesymboldomainNamedThing
GenexrefdomainNamedThing
Genehas_biological_sequencedomainNamedThing
Genomeprovided_bydomainNamedThing
GenomexrefdomainNamedThing
Genomefull_namedomainNamedThing
GenomesynonymdomainNamedThing
Genomehas_biological_sequencedomainNamedThing
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:NamedThing
nativebican:NamedThing
exactBFO:0000001, WIKIDATA:Q35120, UMLSSG:OBJC, STY:T071, dcid:Thing
+

LinkML Source

+ +

Direct

+
+
name: named thing
+definition_uri: https://w3id.org/biolink/vocab/NamedThing
+description: a databased entity or concept/class
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- BFO:0000001
+- WIKIDATA:Q35120
+- UMLSSG:OBJC
+- STY:T071
+- dcid:Thing
+is_a: entity
+slots:
+- id
+- iri
+- category
+- type
+- name
+- description
+- has attribute
+- deprecated
+- provided by
+- xref
+- full name
+- synonym
+class_uri: biolink:NamedThing
+
+
+
+

Induced

+
+
name: named thing
+definition_uri: https://w3id.org/biolink/vocab/NamedThing
+description: a databased entity or concept/class
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- BFO:0000001
+- WIKIDATA:Q35120
+- UMLSSG:OBJC
+- STY:T071
+- dcid:Thing
+is_a: entity
+attributes:
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: named thing
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: named thing
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: named thing
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: named thing
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: named thing
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: named thing
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: named thing
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: named thing
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: named thing
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: named thing
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: named thing
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: named thing
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+class_uri: biolink:NamedThing
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/NarrativeText/index.html b/NarrativeText/index.html new file mode 100644 index 00000000..18f827e0 --- /dev/null +++ b/NarrativeText/index.html @@ -0,0 +1,613 @@ + + + + + + + + + + + + + + + + + + + Type: NarrativeText - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
+
+ + + +
+
+
+ + + + + +
+
+
+ + + +
+
+
+ + + +
+
+
+ + + +
+
+ + + + + + + +

Type: NarrativeText

+

A string that provides a human-readable description of something

+

URI: xsd:string

+ +

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfxsd:string
nativebican:narrative_text
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/Ncname/index.html b/Ncname/index.html new file mode 100644 index 00000000..78704e13 --- /dev/null +++ b/Ncname/index.html @@ -0,0 +1,613 @@ + + + + + + + + + + + + + + + + + + + Type: Ncname - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
+
+ + + +
+
+
+ + + + + +
+
+
+ + + +
+
+
+ + + +
+
+
+ + + +
+
+ + + + + + + +

Type: Ncname

+

Prefix part of CURIE

+

URI: xsd:string

+
    +
  • +

    base: NCName

    +
    • +
  • +

    uri: xsd:string

    +
    • +
  • +

    repr: str

    +
    • +
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfxsd:string
nativebican:ncname
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/Nodeidentifier/index.html b/Nodeidentifier/index.html new file mode 100644 index 00000000..f0162b2c --- /dev/null +++ b/Nodeidentifier/index.html @@ -0,0 +1,613 @@ + + + + + + + + + + + + + + + + + + + Type: Nodeidentifier - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
+
+ + + +
+
+
+ + + + + +
+
+
+ + + +
+
+
+ + + +
+
+
+ + + +
+
+ + + + + + + +

Type: Nodeidentifier

+

A URI, CURIE or BNODE that represents a node in a model.

+

URI: shex:nonLiteral

+
    +
  • +

    base: NodeIdentifier

    +
    • +
  • +

    uri: shex:nonLiteral

    +
    • +
  • +

    repr: str

    +
    • +
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfshex:nonLiteral
nativebican:nodeidentifier
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/Objectidentifier/index.html b/Objectidentifier/index.html new file mode 100644 index 00000000..72cd9021 --- /dev/null +++ b/Objectidentifier/index.html @@ -0,0 +1,626 @@ + + + + + + + + + + + + + + + + + + + Type: Objectidentifier - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
+
+ + + +
+
+
+ + + + + +
+
+
+ + + +
+
+
+ + + +
+
+
+ + + +
+
+ + + + + + + +

Type: Objectidentifier

+

A URI or CURIE that represents an object in the model.

+

URI: shex:iri

+
    +
  • +

    base: ElementIdentifier

    +
    • +
  • +

    uri: shex:iri

    +
    • +
  • +

    repr: str

    +
    • +
+

Comments

+
    +
  • Used for inheritance and type checking
    • +
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfshex:iri
nativebican:objectidentifier
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/Occurrent/index.html b/Occurrent/index.html new file mode 100644 index 00000000..6abc36d9 --- /dev/null +++ b/Occurrent/index.html @@ -0,0 +1,440 @@ + + + + + + + + + +Class: Occurrent - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: Occurrent

+

A processual entity.

+

URI: biolink:Occurrent

+
classDiagram + class Occurrent + click Occurrent href "../Occurrent" + PhysicalEssenceOrOccurrent <|-- Occurrent + click PhysicalEssenceOrOccurrent href "../PhysicalEssenceOrOccurrent" + + + Occurrent <|-- ActivityAndBehavior + click ActivityAndBehavior href "../ActivityAndBehavior" + + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
+

Mixin Usage

+ + + + + + + + + + + + + +
mixed intodescription
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:Occurrent
nativebican:Occurrent
exactBFO:0000003
+

LinkML Source

+ +

Direct

+
+
name: occurrent
+definition_uri: https://w3id.org/biolink/vocab/Occurrent
+description: A processual entity.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- BFO:0000003
+is_a: physical essence or occurrent
+mixin: true
+class_uri: biolink:Occurrent
+
+
+
+

Induced

+
+
name: occurrent
+definition_uri: https://w3id.org/biolink/vocab/Occurrent
+description: A processual entity.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- BFO:0000003
+is_a: physical essence or occurrent
+mixin: true
+class_uri: biolink:Occurrent
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/OntologyClass/index.html b/OntologyClass/index.html new file mode 100644 index 00000000..c7ee5201 --- /dev/null +++ b/OntologyClass/index.html @@ -0,0 +1,622 @@ + + + + + + + + + +Class: OntologyClass - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
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+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: OntologyClass

+

a concept or class in an ontology, vocabulary or thesaurus. Note that nodes in a biolink compatible KG can be considered both instances of biolink classes, and OWL classes in their own right. In general you should not need to use this class directly. Instead, use the appropriate biolink class. For example, for the GO concept of endocytosis (GO:0006897), use bl:BiologicalProcess as the type.

+

URI: biolink:OntologyClass

+
classDiagram + class OntologyClass + click OntologyClass href "../OntologyClass" + OntologyClass <|-- Attribute + click Attribute href "../Attribute" + OntologyClass <|-- TaxonomicRank + click TaxonomicRank href "../TaxonomicRank" + OntologyClass <|-- Gene + click Gene href "../Gene" + OntologyClass <|-- Genome + click Genome href "../Genome" + + OntologyClass : id + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
id1
String		A unique identifier for an entitydirect
+

Mixin Usage

+ + + + + + + + + + + + + + + + + + + + + +
mixed intodescription
AttributeA property or characteristic of an entity
GeneA region (or regions) that includes all of the sequence elements necessary to...
GenomeA genome is the sum of genetic material within a cell or virion
+

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
Attributehas_attribute_typerangeOntologyClass
+

Examples

+ + + + + + + + + + + +
Value
UBERON:0000955
+

Comments

+
    +
  • This is modeled as a mixin. 'ontology class' should not be the primary type of a node in the KG. Instead you should use an informative bioloink category, such as AnatomicalEntity (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL), etc
    • +
  • Note that formally this is a metaclass. Instances of this class are instances in the graph, but can be the object of 'type' edges. For example, if we had a node in the graph representing a specific brain of a specific patient (e.g brain001), this could have a category of bl:Sample, and by typed more specifically with an ontology class UBERON:nnn, which has as category bl:AnatomicalEntity
    • +
+

See Also

+ +

Identifier and Mapping Information

+

Valid ID Prefixes

+

Instances of this class should have identifiers with one of the following prefixes:

+
    +
  • +

    MESH

    +
    • +
  • +

    UMLS

    +
    • +
  • +

    KEGG.BRITE

    +
    • +
+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:OntologyClass
nativebican:OntologyClass
exactowl:Class, schema:Class
+

LinkML Source

+ +

Direct

+
+
name: ontology class
+id_prefixes:
+- MESH
+- UMLS
+- KEGG.BRITE
+definition_uri: https://w3id.org/biolink/vocab/OntologyClass
+description: a concept or class in an ontology, vocabulary or thesaurus. Note that
+  nodes in a biolink compatible KG can be considered both instances of biolink classes,
+  and OWL classes in their own right. In general you should not need to use this class
+  directly. Instead, use the appropriate biolink class. For example, for the GO concept
+  of endocytosis (GO:0006897), use bl:BiologicalProcess as the type.
+comments:
+- This is modeled as a mixin. 'ontology class' should not be the primary type of a
+  node in the KG. Instead you should use an informative bioloink category, such as
+  AnatomicalEntity (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL),
+  etc
+- Note that formally this is a metaclass. Instances of this class are instances in
+  the graph, but can be the object of 'type' edges. For example, if we had a node
+  in the graph representing a specific brain of a specific patient (e.g brain001),
+  this could have a category of bl:Sample, and by typed more specifically with an
+  ontology class UBERON:nnn, which has as category bl:AnatomicalEntity
+examples:
+- value: UBERON:0000955
+  description: the class 'brain' from the Uberon anatomy ontology
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+see_also:
+- https://github.com/biolink/biolink-model/issues/486
+exact_mappings:
+- owl:Class
+- schema:Class
+mixin: true
+slots:
+- id
+class_uri: biolink:OntologyClass
+
+
+
+

Induced

+
+
name: ontology class
+id_prefixes:
+- MESH
+- UMLS
+- KEGG.BRITE
+definition_uri: https://w3id.org/biolink/vocab/OntologyClass
+description: a concept or class in an ontology, vocabulary or thesaurus. Note that
+  nodes in a biolink compatible KG can be considered both instances of biolink classes,
+  and OWL classes in their own right. In general you should not need to use this class
+  directly. Instead, use the appropriate biolink class. For example, for the GO concept
+  of endocytosis (GO:0006897), use bl:BiologicalProcess as the type.
+comments:
+- This is modeled as a mixin. 'ontology class' should not be the primary type of a
+  node in the KG. Instead you should use an informative bioloink category, such as
+  AnatomicalEntity (for Uberon classes), ChemicalSubstance (for CHEBI or CHEMBL),
+  etc
+- Note that formally this is a metaclass. Instances of this class are instances in
+  the graph, but can be the object of 'type' edges. For example, if we had a node
+  in the graph representing a specific brain of a specific patient (e.g brain001),
+  this could have a category of bl:Sample, and by typed more specifically with an
+  ontology class UBERON:nnn, which has as category bl:AnatomicalEntity
+examples:
+- value: UBERON:0000955
+  description: the class 'brain' from the Uberon anatomy ontology
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+see_also:
+- https://github.com/biolink/biolink-model/issues/486
+exact_mappings:
+- owl:Class
+- schema:Class
+mixin: true
+attributes:
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: ontology class
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+class_uri: biolink:OntologyClass
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/OrganismTaxon/index.html b/OrganismTaxon/index.html new file mode 100644 index 00000000..6230f889 --- /dev/null +++ b/OrganismTaxon/index.html @@ -0,0 +1,1167 @@ + + + + + + + + + +Class: OrganismTaxon - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: OrganismTaxon

+

A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies.

+

URI: biolink:OrganismTaxon

+
classDiagram + class OrganismTaxon + click OrganismTaxon href "../OrganismTaxon" + NamedThing <|-- OrganismTaxon + click NamedThing href "../NamedThing" + + OrganismTaxon : category + + OrganismTaxon : deprecated + + OrganismTaxon : description + + OrganismTaxon : full_name + + OrganismTaxon : has_attribute + + + + + OrganismTaxon --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + OrganismTaxon : has_taxonomic_rank + + + + + OrganismTaxon --> "0..1" TaxonomicRank : has_taxonomic_rank + click TaxonomicRank href "../TaxonomicRank" + + + OrganismTaxon : id + + OrganismTaxon : iri + + OrganismTaxon : name + + OrganismTaxon : provided_by + + OrganismTaxon : synonym + + OrganismTaxon : type + + OrganismTaxon : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
id1
String		A unique identifier for an entitydirect
iri0..1
IriType		An IRI for an entitydirect
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizeddirect
type*
String		direct
name0..1
LabelType		A human-readable name for an attribute or entitydirect
description0..1
NarrativeText		a human-readable description of an entitydirect
has_attribute*
Attribute		connects any entity to an attributedirect
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...direct
provided_by*
String		The value in this node property represents the knowledge provider that create...direct
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...direct
full_name0..1
LabelType		a long-form human readable name for a thingdirect
synonym*
LabelType		Alternate human-readable names for a thingdirect
has_taxonomic_rank0..1
TaxonomicRank		direct
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
GeneAnnotationin_taxonrangeOrganismTaxon
GenomeAnnotationin_taxonrangeOrganismTaxon
GenomeAssemblyin_taxonrangeOrganismTaxon
ThingWithTaxonin_taxonrangeOrganismTaxon
BiologicalEntityin_taxonrangeOrganismTaxon
Genein_taxonrangeOrganismTaxon
Genomein_taxonrangeOrganismTaxon
+

Aliases

+
    +
  • taxon
    • +
  • taxonomic classification
    • +
+

Identifier and Mapping Information

+

Valid ID Prefixes

+

Instances of this class should have identifiers with one of the following prefixes:

+
    +
  • +

    NCBITaxon

    +
    • +
  • +

    MESH

    +
    • +
  • +

    UMLS

    +
    • +
+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:OrganismTaxon
nativebican:OrganismTaxon
exactWIKIDATA:Q16521, STY:T001, bioschemas:Taxon
narrowdcid:BiologicalSpecies
+

LinkML Source

+ +

Direct

+
+
name: organism taxon
+id_prefixes:
+- NCBITaxon
+- MESH
+- UMLS
+definition_uri: https://w3id.org/biolink/vocab/OrganismTaxon
+description: 'A classification of a set of organisms. Example instances: NCBITaxon:9606
+  (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or
+  subspecies.'
+in_subset:
+- model_organism_database
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+aliases:
+- taxon
+- taxonomic classification
+exact_mappings:
+- WIKIDATA:Q16521
+- STY:T001
+- bioschemas:Taxon
+narrow_mappings:
+- dcid:BiologicalSpecies
+is_a: named thing
+values_from:
+- NCBITaxon
+slots:
+- id
+- iri
+- category
+- type
+- name
+- description
+- has attribute
+- deprecated
+- provided by
+- xref
+- full name
+- synonym
+- has taxonomic rank
+class_uri: biolink:OrganismTaxon
+
+
+
+

Induced

+
+
name: organism taxon
+id_prefixes:
+- NCBITaxon
+- MESH
+- UMLS
+definition_uri: https://w3id.org/biolink/vocab/OrganismTaxon
+description: 'A classification of a set of organisms. Example instances: NCBITaxon:9606
+  (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or
+  subspecies.'
+in_subset:
+- model_organism_database
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+aliases:
+- taxon
+- taxonomic classification
+exact_mappings:
+- WIKIDATA:Q16521
+- STY:T001
+- bioschemas:Taxon
+narrow_mappings:
+- dcid:BiologicalSpecies
+is_a: named thing
+values_from:
+- NCBITaxon
+attributes:
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: organism taxon
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: organism taxon
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: organism taxon
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: organism taxon
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: organism taxon
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: organism taxon
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: organism taxon
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: organism taxon
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: organism taxon
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: organism taxon
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: organism taxon
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: organism taxon
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+  has taxonomic rank:
+    name: has taxonomic rank
+    definition_uri: https://w3id.org/biolink/vocab/has_taxonomic_rank
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    mappings:
+    - WIKIDATA:P105
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:has_taxonomic_rank
+    alias: has_taxonomic_rank
+    owner: organism taxon
+    domain_of:
+    - organism taxon
+    range: taxonomic rank
+    multivalued: false
+class_uri: biolink:OrganismTaxon
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/ParcellationAnnotation/index.html b/ParcellationAnnotation/index.html new file mode 100644 index 00000000..102ff47c --- /dev/null +++ b/ParcellationAnnotation/index.html @@ -0,0 +1,500 @@ + + + + + + + + + +Class: ParcellationAnnotation - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: ParcellationAnnotation

+

A parcellation annotation defines a specific segment of an anatomical space denoted by an internal identifier and is a unique and exclusive member of a versioned release anatomical annotation set. For example, in the case where the anatomical annotation set is a single multi-value image mask (e.g. Allen Mouse CCF), a specific annotation corresponds to a specific label index (internal identifier) in the mask.

+

URI: AnS:ParcellationAnnotation

+
classDiagram + class ParcellationAnnotation + click ParcellationAnnotation href "../ParcellationAnnotation" + ParcellationAnnotation : internal_identifier + + ParcellationAnnotation : part_of_anatomical_annotation_set + + ParcellationAnnotation : voxel_count + + +
+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
part_of_anatomical_annotation_set1
String or 
AnatomicalAnnotationSet or 
String		direct
internal_identifier1
String		An identifier that uniquely denotes a specific parcellation annotation within...direct
voxel_count0..1
Integer		The number of voxels (3D pixels) spanned by the parcellation annotation (opti...direct
+

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
ParcellationAnnotationTermMapsubject_parcellation_annotationany_of[range]ParcellationAnnotation
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/my-org/anatomical-structure-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfAnS:ParcellationAnnotation
nativeAnS:ParcellationAnnotation
+

LinkML Source

+ +

Direct

+
+
name: ParcellationAnnotation
+description: A parcellation annotation defines a specific segment of an anatomical
+  space denoted by an internal  identifier and is a unique and exclusive member of
+  a versioned release anatomical annotation set.  For example, in the case where the
+  anatomical annotation set is a single multi-value image mask (e.g. Allen Mouse CCF),
+  a specific annotation corresponds to a specific label index (internal identifier)
+  in the mask.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+attributes:
+  part_of_anatomical_annotation_set:
+    name: part_of_anatomical_annotation_set
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ParcellationAnnotation
+    required: true
+    any_of:
+    - range: AnatomicalAnnotationSet
+    - range: string
+  internal_identifier:
+    name: internal_identifier
+    description: An identifier that uniquely denotes a specific parcellation annotation
+      within the context of an anatomical annotation set
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ParcellationAnnotation
+    required: true
+  voxel_count:
+    name: voxel_count
+    description: The number of voxels (3D pixels) spanned by the parcellation annotation
+      (optional).
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ParcellationAnnotation
+    range: integer
+    minimum_value: 0
+
+
+
+

Induced

+
+
name: ParcellationAnnotation
+description: A parcellation annotation defines a specific segment of an anatomical
+  space denoted by an internal  identifier and is a unique and exclusive member of
+  a versioned release anatomical annotation set.  For example, in the case where the
+  anatomical annotation set is a single multi-value image mask (e.g. Allen Mouse CCF),
+  a specific annotation corresponds to a specific label index (internal identifier)
+  in the mask.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+attributes:
+  part_of_anatomical_annotation_set:
+    name: part_of_anatomical_annotation_set
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: part_of_anatomical_annotation_set
+    owner: ParcellationAnnotation
+    domain_of:
+    - ParcellationAnnotation
+    range: string
+    required: true
+    any_of:
+    - range: AnatomicalAnnotationSet
+    - range: string
+  internal_identifier:
+    name: internal_identifier
+    description: An identifier that uniquely denotes a specific parcellation annotation
+      within the context of an anatomical annotation set
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: internal_identifier
+    owner: ParcellationAnnotation
+    domain_of:
+    - ParcellationAnnotation
+    range: string
+    required: true
+  voxel_count:
+    name: voxel_count
+    description: The number of voxels (3D pixels) spanned by the parcellation annotation
+      (optional).
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: voxel_count
+    owner: ParcellationAnnotation
+    domain_of:
+    - ParcellationAnnotation
+    range: integer
+    minimum_value: 0
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/ParcellationAnnotationTermMap/index.html b/ParcellationAnnotationTermMap/index.html new file mode 100644 index 00000000..5920923d --- /dev/null +++ b/ParcellationAnnotationTermMap/index.html @@ -0,0 +1,454 @@ + + + + + + + + + +Class: ParcellationAnnotationTermMap - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: ParcellationAnnotationTermMap

+

The parcellation annotation term map table defines the relationship between parcellation annotations and parcellation terms. A parcellation term is uniquely denoted by a parcellation term identifier and the parcellation terminology it belongs to. A parcellation term can be spatially parameterized by the union of one or more parcellation annotations within a versioned release of an anatomical annotation set. For example, annotations defining individual cortical layers in cortical region R (R1, R2/3, R4, etc) can be combined to define the parent region R.

+

URI: AnS:ParcellationAnnotationTermMap

+
classDiagram + class ParcellationAnnotationTermMap + click ParcellationAnnotationTermMap href "../ParcellationAnnotationTermMap" + ParcellationAnnotationTermMap : subject_parcellation_annotation + + ParcellationAnnotationTermMap : subject_parcellation_term + + +
+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
subject_parcellation_annotation1
String or 
ParcellationAnnotation or 
String		Reference to the parcellation annotation that is the subject of the associati...direct
subject_parcellation_term1
String or 
ParcellationTerm or 
String		Reference to the parcellation term that is the subject of the associationdirect
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/my-org/anatomical-structure-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfAnS:ParcellationAnnotationTermMap
nativeAnS:ParcellationAnnotationTermMap
+

LinkML Source

+ +

Direct

+
+
name: ParcellationAnnotationTermMap
+description: The parcellation annotation term map table defines the relationship between
+  parcellation annotations and parcellation terms.  A parcellation term is uniquely
+  denoted by a parcellation term identifier and the parcellation terminology it belongs
+  to.  A parcellation term can be spatially parameterized by the union of one or more
+  parcellation annotations within a versioned  release of an anatomical annotation
+  set. For example, annotations defining individual cortical layers in cortical region  R
+  (R1, R2/3, R4, etc) can be combined to define the parent region R.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+attributes:
+  subject_parcellation_annotation:
+    name: subject_parcellation_annotation
+    description: Reference to the parcellation annotation that is the subject of the
+      association.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ParcellationAnnotationTermMap
+    required: true
+    any_of:
+    - range: ParcellationAnnotation
+    - range: string
+  subject_parcellation_term:
+    name: subject_parcellation_term
+    description: Reference to the parcellation term that is the subject of the association.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    domain_of:
+    - ParcellationColorAssignment
+    - ParcellationAnnotationTermMap
+    required: true
+    any_of:
+    - range: ParcellationTerm
+    - range: string
+
+
+
+

Induced

+
+
name: ParcellationAnnotationTermMap
+description: The parcellation annotation term map table defines the relationship between
+  parcellation annotations and parcellation terms.  A parcellation term is uniquely
+  denoted by a parcellation term identifier and the parcellation terminology it belongs
+  to.  A parcellation term can be spatially parameterized by the union of one or more
+  parcellation annotations within a versioned  release of an anatomical annotation
+  set. For example, annotations defining individual cortical layers in cortical region  R
+  (R1, R2/3, R4, etc) can be combined to define the parent region R.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+attributes:
+  subject_parcellation_annotation:
+    name: subject_parcellation_annotation
+    description: Reference to the parcellation annotation that is the subject of the
+      association.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: subject_parcellation_annotation
+    owner: ParcellationAnnotationTermMap
+    domain_of:
+    - ParcellationAnnotationTermMap
+    range: string
+    required: true
+    any_of:
+    - range: ParcellationAnnotation
+    - range: string
+  subject_parcellation_term:
+    name: subject_parcellation_term
+    description: Reference to the parcellation term that is the subject of the association.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    alias: subject_parcellation_term
+    owner: ParcellationAnnotationTermMap
+    domain_of:
+    - ParcellationColorAssignment
+    - ParcellationAnnotationTermMap
+    range: string
+    required: true
+    any_of:
+    - range: ParcellationTerm
+    - range: string
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/ParcellationAtlas/index.html b/ParcellationAtlas/index.html new file mode 100644 index 00000000..54033c00 --- /dev/null +++ b/ParcellationAtlas/index.html @@ -0,0 +1,711 @@ + + + + + + + + + +Class: ParcellationAtlas - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: ParcellationAtlas

+

A parcellation atlas is a versioned release reference used to guide experiments or deal with the spatial relationship between objects or the location of objects within the context of some anatomical structure. An atlas is minimally defined by a notion of space (either implicit or explicit) and an annotation set. Reference atlases usually have additional parts that make them more useful in certain situations, such as a well defined coordinate system, delineations indicating the boundaries of various regions or cell populations, landmarks, and labels and names to make it easier to communicate about well known and useful locations (ref: ILX:0777109, RRID:SCR_023499).

+

URI: AnS:ParcellationAtlas

+
classDiagram + class ParcellationAtlas + click ParcellationAtlas href "../ParcellationAtlas" + VersionedNamedThing <|-- ParcellationAtlas + click VersionedNamedThing href "../VersionedNamedThing" + + ParcellationAtlas : category + + ParcellationAtlas : description + + ParcellationAtlas : has_anatomical_annotation_set + + ParcellationAtlas : has_anatomical_space + + ParcellationAtlas : has_parcellation_terminology + + ParcellationAtlas : id + + ParcellationAtlas : name + + ParcellationAtlas : revision_of + + + + + ParcellationAtlas --> "0..1" VersionedNamedThing : revision_of + click VersionedNamedThing href "../VersionedNamedThing" + + + ParcellationAtlas : specialization_of + + ParcellationAtlas : version + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
has_anatomical_space1
String or 
AnatomicalSpace or 
String		Reference to the anatomical space component of the parcellation atlasdirect
has_anatomical_annotation_set1
String or 
AnatomicalAnnotationSet or 
String		Reference to the anatomical annotation set component of the parcellation atla...direct
has_parcellation_terminology1
String or 
ParcellationTerminology or 
String		Reference to the parcellation terminology component of the parcellation atlasdirect
specialization_of0..1
String or 
ParcellationAtlas or 
String		Reference to the general (non versioned) parcellation atlas for which the par...direct
version1
String		VersionedNamedThing
revision_of0..1
VersionedNamedThing or 
ParcellationAtlas or 
String		VersionedNamedThing
id1
Uriorcurie		NamedThing
name1
String		NamedThing
description1
String		NamedThing
category*
Uriorcurie		NamedThing
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
ParcellationAtlasspecialization_ofany_of[range]ParcellationAtlas
ParcellationAtlasrevision_ofany_of[range]ParcellationAtlas
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/my-org/anatomical-structure-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfAnS:ParcellationAtlas
nativeAnS:ParcellationAtlas
+

LinkML Source

+ +

Direct

+
+
name: ParcellationAtlas
+description: 'A parcellation atlas is a versioned release reference used to guide
+  experiments or deal with the spatial relationship between  objects or the location
+  of objects within the context of some anatomical structure. An atlas is minimally
+  defined by a notion  of space (either implicit or explicit) and an annotation set.
+  Reference atlases usually have additional parts that make them  more useful in certain
+  situations, such as a well defined coordinate system, delineations indicating the
+  boundaries of various  regions or cell populations, landmarks, and labels and names
+  to make it easier to communicate about well known and useful  locations (ref: ILX:0777109,
+  RRID:SCR_023499).'
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: VersionedNamedThing
+slot_usage:
+  revision_of:
+    name: revision_of
+    any_of:
+    - range: ParcellationAtlas
+    - range: string
+attributes:
+  has_anatomical_space:
+    name: has_anatomical_space
+    description: Reference to the anatomical space component of the parcellation atlas
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ParcellationAtlas
+    required: true
+    any_of:
+    - range: AnatomicalSpace
+    - range: string
+  has_anatomical_annotation_set:
+    name: has_anatomical_annotation_set
+    description: Reference to the anatomical annotation set component of the parcellation
+      atlas
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ParcellationAtlas
+    required: true
+    any_of:
+    - range: AnatomicalAnnotationSet
+    - range: string
+  has_parcellation_terminology:
+    name: has_parcellation_terminology
+    description: Reference to the parcellation terminology component of the parcellation
+      atlas
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ParcellationAtlas
+    required: true
+    any_of:
+    - range: ParcellationTerminology
+    - range: string
+  specialization_of:
+    name: specialization_of
+    description: Reference to the general (non versioned) parcellation atlas for which
+      the parcellation atlas is a specific  version release of.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ParcellationAtlas
+    any_of:
+    - range: ParcellationAtlas
+    - range: string
+
+
+
+

Induced

+
+
name: ParcellationAtlas
+description: 'A parcellation atlas is a versioned release reference used to guide
+  experiments or deal with the spatial relationship between  objects or the location
+  of objects within the context of some anatomical structure. An atlas is minimally
+  defined by a notion  of space (either implicit or explicit) and an annotation set.
+  Reference atlases usually have additional parts that make them  more useful in certain
+  situations, such as a well defined coordinate system, delineations indicating the
+  boundaries of various  regions or cell populations, landmarks, and labels and names
+  to make it easier to communicate about well known and useful  locations (ref: ILX:0777109,
+  RRID:SCR_023499).'
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: VersionedNamedThing
+slot_usage:
+  revision_of:
+    name: revision_of
+    any_of:
+    - range: ParcellationAtlas
+    - range: string
+attributes:
+  has_anatomical_space:
+    name: has_anatomical_space
+    description: Reference to the anatomical space component of the parcellation atlas
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: has_anatomical_space
+    owner: ParcellationAtlas
+    domain_of:
+    - ParcellationAtlas
+    range: string
+    required: true
+    any_of:
+    - range: AnatomicalSpace
+    - range: string
+  has_anatomical_annotation_set:
+    name: has_anatomical_annotation_set
+    description: Reference to the anatomical annotation set component of the parcellation
+      atlas
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: has_anatomical_annotation_set
+    owner: ParcellationAtlas
+    domain_of:
+    - ParcellationAtlas
+    range: string
+    required: true
+    any_of:
+    - range: AnatomicalAnnotationSet
+    - range: string
+  has_parcellation_terminology:
+    name: has_parcellation_terminology
+    description: Reference to the parcellation terminology component of the parcellation
+      atlas
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: has_parcellation_terminology
+    owner: ParcellationAtlas
+    domain_of:
+    - ParcellationAtlas
+    range: string
+    required: true
+    any_of:
+    - range: ParcellationTerminology
+    - range: string
+  specialization_of:
+    name: specialization_of
+    description: Reference to the general (non versioned) parcellation atlas for which
+      the parcellation atlas is a specific  version release of.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: specialization_of
+    owner: ParcellationAtlas
+    domain_of:
+    - ParcellationAtlas
+    range: string
+    any_of:
+    - range: ParcellationAtlas
+    - range: string
+  version:
+    name: version
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: version
+    owner: ParcellationAtlas
+    domain_of:
+    - VersionedNamedThing
+    range: string
+    required: true
+  revision_of:
+    name: revision_of
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: revision_of
+    owner: ParcellationAtlas
+    domain_of:
+    - VersionedNamedThing
+    range: VersionedNamedThing
+    any_of:
+    - range: ParcellationAtlas
+    - range: string
+  id:
+    name: id
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    identifier: true
+    alias: id
+    owner: ParcellationAtlas
+    domain_of:
+    - NamedThing
+    range: uriorcurie
+    required: true
+  name:
+    name: name
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: name
+    owner: ParcellationAtlas
+    domain_of:
+    - NamedThing
+    range: string
+    required: true
+  description:
+    name: description
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: description
+    owner: ParcellationAtlas
+    domain_of:
+    - NamedThing
+    range: string
+    required: true
+  category:
+    name: category
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    designates_type: true
+    alias: category
+    owner: ParcellationAtlas
+    domain_of:
+    - NamedThing
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/ParcellationColorAssignment/index.html b/ParcellationColorAssignment/index.html new file mode 100644 index 00000000..f7e8fdb7 --- /dev/null +++ b/ParcellationColorAssignment/index.html @@ -0,0 +1,482 @@ + + + + + + + + + +Class: ParcellationColorAssignment - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: ParcellationColorAssignment

+

The parcellation color assignment associates hex color value to a parcellation term within a versioned release of a color scheme. A parcellation term is uniquely denoted by a parcellation term identifier and the parcellation terminology it belongs to.

+

URI: AnS:ParcellationColorAssignment

+
classDiagram + class ParcellationColorAssignment + click ParcellationColorAssignment href "../ParcellationColorAssignment" + ParcellationColorAssignment : color + + ParcellationColorAssignment : part_of_parcellation_color_scheme + + ParcellationColorAssignment : subject_parcellation_term + + +
+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
part_of_parcellation_color_scheme1
String or 
ParcellationColorScheme or 
String		Reference to the parcellation color scheme for which the color assignment is ...direct
subject_parcellation_term1
String or 
ParcellationTerm or 
String		Reference to the parcellation term identifier for which the color assignment ...direct
color0..1
String		A string representing to hex triplet code of a colordirect
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/my-org/anatomical-structure-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfAnS:ParcellationColorAssignment
nativeAnS:ParcellationColorAssignment
+

LinkML Source

+ +

Direct

+
+
name: ParcellationColorAssignment
+description: The parcellation color assignment associates hex color value to a parcellation
+  term within a  versioned release of a color scheme. A parcellation term is uniquely
+  denoted by a parcellation  term identifier and the parcellation terminology it belongs
+  to.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+attributes:
+  part_of_parcellation_color_scheme:
+    name: part_of_parcellation_color_scheme
+    description: Reference to the parcellation color scheme for which the color assignment
+      is part of.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ParcellationColorAssignment
+    required: true
+    any_of:
+    - range: ParcellationColorScheme
+    - range: string
+  subject_parcellation_term:
+    name: subject_parcellation_term
+    description: Reference to the parcellation term identifier for which the color
+      assignment is about.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ParcellationColorAssignment
+    - ParcellationAnnotationTermMap
+    required: true
+    any_of:
+    - range: ParcellationTerm
+    - range: string
+  color:
+    name: color
+    description: A string representing to hex triplet code of a color
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ParcellationColorAssignment
+    range: string
+    structured_pattern:
+      syntax: '{ColorHexTriplet}'
+
+
+
+

Induced

+
+
name: ParcellationColorAssignment
+description: The parcellation color assignment associates hex color value to a parcellation
+  term within a  versioned release of a color scheme. A parcellation term is uniquely
+  denoted by a parcellation  term identifier and the parcellation terminology it belongs
+  to.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+attributes:
+  part_of_parcellation_color_scheme:
+    name: part_of_parcellation_color_scheme
+    description: Reference to the parcellation color scheme for which the color assignment
+      is part of.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: part_of_parcellation_color_scheme
+    owner: ParcellationColorAssignment
+    domain_of:
+    - ParcellationColorAssignment
+    range: string
+    required: true
+    any_of:
+    - range: ParcellationColorScheme
+    - range: string
+  subject_parcellation_term:
+    name: subject_parcellation_term
+    description: Reference to the parcellation term identifier for which the color
+      assignment is about.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: subject_parcellation_term
+    owner: ParcellationColorAssignment
+    domain_of:
+    - ParcellationColorAssignment
+    - ParcellationAnnotationTermMap
+    range: string
+    required: true
+    any_of:
+    - range: ParcellationTerm
+    - range: string
+  color:
+    name: color
+    description: A string representing to hex triplet code of a color
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: color
+    owner: ParcellationColorAssignment
+    domain_of:
+    - ParcellationColorAssignment
+    range: string
+    structured_pattern:
+      syntax: '{ColorHexTriplet}'
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/ParcellationColorScheme/index.html b/ParcellationColorScheme/index.html new file mode 100644 index 00000000..dace22e1 --- /dev/null +++ b/ParcellationColorScheme/index.html @@ -0,0 +1,604 @@ + + + + + + + + + +Class: ParcellationColorScheme - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: ParcellationColorScheme

+

A parcellation color scheme is a versioned release color palette that can be used to visualize a parcellation terminology or its related parcellation annotation. A parcellation terminology may have zero or more parcellation color schemes and each color scheme is in context of a specific parcellation terminology, where each parcellation term is assigned a hex color value. A parcellation color scheme is defined as a part of one and only one parcellation terminology.

+

URI: AnS:ParcellationColorScheme

+
classDiagram + class ParcellationColorScheme + click ParcellationColorScheme href "../ParcellationColorScheme" + VersionedNamedThing <|-- ParcellationColorScheme + click VersionedNamedThing href "../VersionedNamedThing" + + ParcellationColorScheme : category + + ParcellationColorScheme : description + + ParcellationColorScheme : id + + ParcellationColorScheme : name + + ParcellationColorScheme : revision_of + + + + + ParcellationColorScheme --> "0..1" VersionedNamedThing : revision_of + click VersionedNamedThing href "../VersionedNamedThing" + + + ParcellationColorScheme : subject_parcellation_terminology + + ParcellationColorScheme : version + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
subject_parcellation_terminology1
String or 
ParcellationTerminology or 
String		Reference to the parcellation terminology for which the parcellation color sc...direct
version1
String		VersionedNamedThing
revision_of0..1
VersionedNamedThing or 
ParcellationColorScheme or 
String		VersionedNamedThing
id1
Uriorcurie		NamedThing
name1
String		NamedThing
description1
String		NamedThing
category*
Uriorcurie		NamedThing
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
ParcellationColorSchemerevision_ofany_of[range]ParcellationColorScheme
ParcellationColorAssignmentpart_of_parcellation_color_schemeany_of[range]ParcellationColorScheme
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/my-org/anatomical-structure-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfAnS:ParcellationColorScheme
nativeAnS:ParcellationColorScheme
+

LinkML Source

+ +

Direct

+
+
name: ParcellationColorScheme
+description: A parcellation color scheme is a versioned release color palette that
+  can be used to visualize a  parcellation terminology or its related parcellation
+  annotation. A parcellation terminology may  have zero or more parcellation color
+  schemes and each color scheme is in context of a specific  parcellation terminology,
+  where each parcellation term is assigned a hex color value. A parcellation  color
+  scheme is defined as a part of one and only one parcellation terminology.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: VersionedNamedThing
+slot_usage:
+  revision_of:
+    name: revision_of
+    any_of:
+    - range: ParcellationColorScheme
+    - range: string
+attributes:
+  subject_parcellation_terminology:
+    name: subject_parcellation_terminology
+    description: Reference to the parcellation terminology for which the parcellation
+      color scheme is in  context of.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ParcellationColorScheme
+    required: true
+    any_of:
+    - range: ParcellationTerminology
+    - range: string
+
+
+
+

Induced

+
+
name: ParcellationColorScheme
+description: A parcellation color scheme is a versioned release color palette that
+  can be used to visualize a  parcellation terminology or its related parcellation
+  annotation. A parcellation terminology may  have zero or more parcellation color
+  schemes and each color scheme is in context of a specific  parcellation terminology,
+  where each parcellation term is assigned a hex color value. A parcellation  color
+  scheme is defined as a part of one and only one parcellation terminology.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: VersionedNamedThing
+slot_usage:
+  revision_of:
+    name: revision_of
+    any_of:
+    - range: ParcellationColorScheme
+    - range: string
+attributes:
+  subject_parcellation_terminology:
+    name: subject_parcellation_terminology
+    description: Reference to the parcellation terminology for which the parcellation
+      color scheme is in  context of.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: subject_parcellation_terminology
+    owner: ParcellationColorScheme
+    domain_of:
+    - ParcellationColorScheme
+    range: string
+    required: true
+    any_of:
+    - range: ParcellationTerminology
+    - range: string
+  version:
+    name: version
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: version
+    owner: ParcellationColorScheme
+    domain_of:
+    - VersionedNamedThing
+    range: string
+    required: true
+  revision_of:
+    name: revision_of
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: revision_of
+    owner: ParcellationColorScheme
+    domain_of:
+    - VersionedNamedThing
+    range: VersionedNamedThing
+    any_of:
+    - range: ParcellationColorScheme
+    - range: string
+  id:
+    name: id
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    identifier: true
+    alias: id
+    owner: ParcellationColorScheme
+    domain_of:
+    - NamedThing
+    range: uriorcurie
+    required: true
+  name:
+    name: name
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: name
+    owner: ParcellationColorScheme
+    domain_of:
+    - NamedThing
+    range: string
+    required: true
+  description:
+    name: description
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: description
+    owner: ParcellationColorScheme
+    domain_of:
+    - NamedThing
+    range: string
+    required: true
+  category:
+    name: category
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    designates_type: true
+    alias: category
+    owner: ParcellationColorScheme
+    domain_of:
+    - NamedThing
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/ParcellationTerm/index.html b/ParcellationTerm/index.html new file mode 100644 index 00000000..bb8d5c19 --- /dev/null +++ b/ParcellationTerm/index.html @@ -0,0 +1,640 @@ + + + + + + + + + +Class: ParcellationTerm - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: ParcellationTerm

+

A parcellation term is an individual term within a specific parcellation terminology describing a single anatomical entity by a persistent identifier, name, symbol and description. A parcellation term is a unique and exclusive member of a versioned release parcellation terminology. Although term identifiers must be unique within the context of one versioned release of a parcellation terminology, they can be reused in different parcellation terminology versions enabling the representation of terminology updates and modifications over time.

+

URI: AnS:ParcellationTerm

+
classDiagram + class ParcellationTerm + click ParcellationTerm href "../ParcellationTerm" + NamedThing <|-- ParcellationTerm + click NamedThing href "../NamedThing" + + ParcellationTerm : category + + ParcellationTerm : description + + ParcellationTerm : has_parent_parcellation_term + + ParcellationTerm : id + + ParcellationTerm : name + + ParcellationTerm : ordinal + + ParcellationTerm : part_of_parcellation_term_set + + ParcellationTerm : symbol + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
symbol0..1
String		Symbol representing a parcellation termdirect
part_of_parcellation_term_set1
String or 
ParcellationTermSet or 
String		Reference to the parcellation term set for which the parcellation term is par...direct
ordinal0..1
Integer		Ordinal of the parcellation term among other terms within the context of the ...direct
has_parent_parcellation_term0..1
String or 
ParcellationTerm or 
String		Reference to the parent parcellation term for which the parcellation term is ...direct
id1
Uriorcurie		NamedThing
name1
String		NamedThing
description1
String		NamedThing
category*
Uriorcurie		NamedThing
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
ParcellationTermhas_parent_parcellation_termany_of[range]ParcellationTerm
ParcellationColorAssignmentsubject_parcellation_termany_of[range]ParcellationTerm
ParcellationAnnotationTermMapsubject_parcellation_termany_of[range]ParcellationTerm
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/my-org/anatomical-structure-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfAnS:ParcellationTerm
nativeAnS:ParcellationTerm
+

LinkML Source

+ +

Direct

+
+
name: ParcellationTerm
+description: A parcellation term is an individual term within a specific parcellation
+  terminology describing a  single anatomical entity by a persistent identifier, name,
+  symbol and description.  A parcellation  term is a unique and exclusive member of
+  a versioned release parcellation terminology. Although term  identifiers must be
+  unique within the context of one versioned release of a parcellation terminology,  they
+  can be reused in different parcellation terminology versions enabling the representation
+  of  terminology updates and modifications over time.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: NamedThing
+attributes:
+  symbol:
+    name: symbol
+    description: Symbol representing a parcellation term.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ParcellationTerm
+  part_of_parcellation_term_set:
+    name: part_of_parcellation_term_set
+    description: Reference to the parcellation term set for which the parcellation
+      term is part of.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ParcellationTerm
+    required: true
+    any_of:
+    - range: ParcellationTermSet
+    - range: string
+  ordinal:
+    name: ordinal
+    description: Ordinal of the parcellation term among other terms within the context
+      of the associated  parcellation terminology.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    domain_of:
+    - ParcellationTermSet
+    - ParcellationTerm
+    range: integer
+    minimum_value: 0
+  has_parent_parcellation_term:
+    name: has_parent_parcellation_term
+    description: Reference to the parent parcellation term for which the parcellation
+      term is a child ( spatially part) of
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ParcellationTerm
+    any_of:
+    - range: ParcellationTerm
+    - range: string
+
+
+
+

Induced

+
+
name: ParcellationTerm
+description: A parcellation term is an individual term within a specific parcellation
+  terminology describing a  single anatomical entity by a persistent identifier, name,
+  symbol and description.  A parcellation  term is a unique and exclusive member of
+  a versioned release parcellation terminology. Although term  identifiers must be
+  unique within the context of one versioned release of a parcellation terminology,  they
+  can be reused in different parcellation terminology versions enabling the representation
+  of  terminology updates and modifications over time.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: NamedThing
+attributes:
+  symbol:
+    name: symbol
+    description: Symbol representing a parcellation term.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: symbol
+    owner: ParcellationTerm
+    domain_of:
+    - ParcellationTerm
+    range: string
+  part_of_parcellation_term_set:
+    name: part_of_parcellation_term_set
+    description: Reference to the parcellation term set for which the parcellation
+      term is part of.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: part_of_parcellation_term_set
+    owner: ParcellationTerm
+    domain_of:
+    - ParcellationTerm
+    range: string
+    required: true
+    any_of:
+    - range: ParcellationTermSet
+    - range: string
+  ordinal:
+    name: ordinal
+    description: Ordinal of the parcellation term among other terms within the context
+      of the associated  parcellation terminology.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    alias: ordinal
+    owner: ParcellationTerm
+    domain_of:
+    - ParcellationTermSet
+    - ParcellationTerm
+    range: integer
+    minimum_value: 0
+  has_parent_parcellation_term:
+    name: has_parent_parcellation_term
+    description: Reference to the parent parcellation term for which the parcellation
+      term is a child ( spatially part) of
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: has_parent_parcellation_term
+    owner: ParcellationTerm
+    domain_of:
+    - ParcellationTerm
+    range: string
+    any_of:
+    - range: ParcellationTerm
+    - range: string
+  id:
+    name: id
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    identifier: true
+    alias: id
+    owner: ParcellationTerm
+    domain_of:
+    - NamedThing
+    range: uriorcurie
+    required: true
+  name:
+    name: name
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: name
+    owner: ParcellationTerm
+    domain_of:
+    - NamedThing
+    range: string
+    required: true
+  description:
+    name: description
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: description
+    owner: ParcellationTerm
+    domain_of:
+    - NamedThing
+    range: string
+    required: true
+  category:
+    name: category
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    designates_type: true
+    alias: category
+    owner: ParcellationTerm
+    domain_of:
+    - NamedThing
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/ParcellationTermSet/index.html b/ParcellationTermSet/index.html new file mode 100644 index 00000000..ddd87849 --- /dev/null +++ b/ParcellationTermSet/index.html @@ -0,0 +1,611 @@ + + + + + + + + + +Class: ParcellationTermSet - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
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+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: ParcellationTermSet

+

A parcellation term set is the set of parcellation terms within a specific parcellation terminology. A parcellation term set belongs to one and only one parcellation terminology and each parcellation term in a parcellation terminology belongs to one and only one term set. If the parcellation terminology is a taxonomy, parcellation term sets can be used to represent taxonomic ranks. For consistency, if the terminology does not have the notion of taxonomic ranks, all terms are grouped into a single parcellation term set.

+

URI: AnS:ParcellationTermSet

+
classDiagram + class ParcellationTermSet + click ParcellationTermSet href "../ParcellationTermSet" + NamedThing <|-- ParcellationTermSet + click NamedThing href "../NamedThing" + + ParcellationTermSet : category + + ParcellationTermSet : description + + ParcellationTermSet : has_parent_parcellation_term_set + + ParcellationTermSet : id + + ParcellationTermSet : name + + ParcellationTermSet : ordinal + + ParcellationTermSet : part_of_parcellation_terminology + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
part_of_parcellation_terminology1
String or 
ParcellationTerminology or 
String		Reference to the parcellation terminology for which the parcellation term set...direct
ordinal0..1
Integer		Ordinal of the parcellation term set among other term sets within the context...direct
has_parent_parcellation_term_set0..1
String or 
ParcellationTermSet or 
String		Reference to the parent parcellation term set for which the parcellation term...direct
id1
Uriorcurie		NamedThing
name1
String		NamedThing
description1
String		NamedThing
category*
Uriorcurie		NamedThing
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
ParcellationTermSethas_parent_parcellation_term_setany_of[range]ParcellationTermSet
ParcellationTermpart_of_parcellation_term_setany_of[range]ParcellationTermSet
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/my-org/anatomical-structure-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfAnS:ParcellationTermSet
nativeAnS:ParcellationTermSet
+

LinkML Source

+ +

Direct

+
+
name: ParcellationTermSet
+description: A parcellation term set is the set of parcellation terms within a specific
+  parcellation terminology.  A parcellation term set belongs to one and only one parcellation
+  terminology and each parcellation  term in a parcellation terminology belongs to
+  one and only one term set.  If the parcellation terminology is a taxonomy, parcellation
+  term sets can be used to represent  taxonomic ranks. For consistency, if the terminology
+  does not have the notion of taxonomic ranks,  all terms are grouped into a single
+  parcellation term set.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: NamedThing
+attributes:
+  part_of_parcellation_terminology:
+    name: part_of_parcellation_terminology
+    description: Reference to the parcellation terminology for which the parcellation
+      term set partitions.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ParcellationTermSet
+    required: true
+    any_of:
+    - range: ParcellationTerminology
+    - range: string
+  ordinal:
+    name: ordinal
+    description: Ordinal of the parcellation term set among other term sets within
+      the context of the  associated parcellation terminology.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ParcellationTermSet
+    - ParcellationTerm
+    range: integer
+    minimum_value: 0
+  has_parent_parcellation_term_set:
+    name: has_parent_parcellation_term_set
+    description: Reference to the parent parcellation term set for which the parcellation
+      term set is a child  (lower taxonomic rank) of.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    domain_of:
+    - ParcellationTermSet
+    any_of:
+    - range: ParcellationTermSet
+    - range: string
+
+
+
+

Induced

+
+
name: ParcellationTermSet
+description: A parcellation term set is the set of parcellation terms within a specific
+  parcellation terminology.  A parcellation term set belongs to one and only one parcellation
+  terminology and each parcellation  term in a parcellation terminology belongs to
+  one and only one term set.  If the parcellation terminology is a taxonomy, parcellation
+  term sets can be used to represent  taxonomic ranks. For consistency, if the terminology
+  does not have the notion of taxonomic ranks,  all terms are grouped into a single
+  parcellation term set.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: NamedThing
+attributes:
+  part_of_parcellation_terminology:
+    name: part_of_parcellation_terminology
+    description: Reference to the parcellation terminology for which the parcellation
+      term set partitions.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: part_of_parcellation_terminology
+    owner: ParcellationTermSet
+    domain_of:
+    - ParcellationTermSet
+    range: string
+    required: true
+    any_of:
+    - range: ParcellationTerminology
+    - range: string
+  ordinal:
+    name: ordinal
+    description: Ordinal of the parcellation term set among other term sets within
+      the context of the  associated parcellation terminology.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: ordinal
+    owner: ParcellationTermSet
+    domain_of:
+    - ParcellationTermSet
+    - ParcellationTerm
+    range: integer
+    minimum_value: 0
+  has_parent_parcellation_term_set:
+    name: has_parent_parcellation_term_set
+    description: Reference to the parent parcellation term set for which the parcellation
+      term set is a child  (lower taxonomic rank) of.
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: has_parent_parcellation_term_set
+    owner: ParcellationTermSet
+    domain_of:
+    - ParcellationTermSet
+    range: string
+    any_of:
+    - range: ParcellationTermSet
+    - range: string
+  id:
+    name: id
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    identifier: true
+    alias: id
+    owner: ParcellationTermSet
+    domain_of:
+    - NamedThing
+    range: uriorcurie
+    required: true
+  name:
+    name: name
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: name
+    owner: ParcellationTermSet
+    domain_of:
+    - NamedThing
+    range: string
+    required: true
+  description:
+    name: description
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: description
+    owner: ParcellationTermSet
+    domain_of:
+    - NamedThing
+    range: string
+    required: true
+  category:
+    name: category
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    designates_type: true
+    alias: category
+    owner: ParcellationTermSet
+    domain_of:
+    - NamedThing
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/ParcellationTerminology/index.html b/ParcellationTerminology/index.html new file mode 100644 index 00000000..0a262696 --- /dev/null +++ b/ParcellationTerminology/index.html @@ -0,0 +1,582 @@ + + + + + + + + + +Class: ParcellationTerminology - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
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+ +
+
+
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+
+
+ +
+
+
+
+
+

Class: ParcellationTerminology

+

A parcellation terminology is a versioned release set of terms that can be used to label annotations in an atlas, providing human readability and context and allowing communication about brain locations and structural properties. Typically, a terminology is a set of descriptive anatomical terms following a specific naming convention and/or approach to organization scheme. The terminology may be a flat list of controlled vocabulary, a taxonomy and partonomy, or an ontology (ref: ILX:0777107, RRID:SCR_023499)

+

URI: AnS:ParcellationTerminology

+
classDiagram + class ParcellationTerminology + click ParcellationTerminology href "../ParcellationTerminology" + VersionedNamedThing <|-- ParcellationTerminology + click VersionedNamedThing href "../VersionedNamedThing" + + ParcellationTerminology : category + + ParcellationTerminology : description + + ParcellationTerminology : id + + ParcellationTerminology : name + + ParcellationTerminology : revision_of + + + + + ParcellationTerminology --> "0..1" VersionedNamedThing : revision_of + click VersionedNamedThing href "../VersionedNamedThing" + + + ParcellationTerminology : version + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
version1
String		VersionedNamedThing
revision_of0..1
VersionedNamedThing or 
ParcellationTerminology or 
String		VersionedNamedThing
id1
Uriorcurie		NamedThing
name1
String		NamedThing
description1
String		NamedThing
category*
Uriorcurie		NamedThing
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
ParcellationTerminologyrevision_ofany_of[range]ParcellationTerminology
ParcellationTermSetpart_of_parcellation_terminologyany_of[range]ParcellationTerminology
ParcellationColorSchemesubject_parcellation_terminologyany_of[range]ParcellationTerminology
ParcellationAtlashas_parcellation_terminologyany_of[range]ParcellationTerminology
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/my-org/anatomical-structure-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfAnS:ParcellationTerminology
nativeAnS:ParcellationTerminology
+

LinkML Source

+ +

Direct

+
+
name: ParcellationTerminology
+description: 'A parcellation terminology is a versioned release set of terms that
+  can be used to label  annotations in an atlas, providing human readability and context
+  and allowing communication  about brain locations and structural properties. Typically,
+  a terminology is a set of  descriptive anatomical terms following a specific naming
+  convention and/or approach to  organization scheme. The terminology may be a flat
+  list of controlled vocabulary, a taxonomy  and partonomy, or an ontology (ref: ILX:0777107,
+  RRID:SCR_023499)'
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: VersionedNamedThing
+slot_usage:
+  revision_of:
+    name: revision_of
+    any_of:
+    - range: ParcellationTerminology
+    - range: string
+
+
+
+

Induced

+
+
name: ParcellationTerminology
+description: 'A parcellation terminology is a versioned release set of terms that
+  can be used to label  annotations in an atlas, providing human readability and context
+  and allowing communication  about brain locations and structural properties. Typically,
+  a terminology is a set of  descriptive anatomical terms following a specific naming
+  convention and/or approach to  organization scheme. The terminology may be a flat
+  list of controlled vocabulary, a taxonomy  and partonomy, or an ontology (ref: ILX:0777107,
+  RRID:SCR_023499)'
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: VersionedNamedThing
+slot_usage:
+  revision_of:
+    name: revision_of
+    any_of:
+    - range: ParcellationTerminology
+    - range: string
+attributes:
+  version:
+    name: version
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: version
+    owner: ParcellationTerminology
+    domain_of:
+    - VersionedNamedThing
+    range: string
+    required: true
+  revision_of:
+    name: revision_of
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: revision_of
+    owner: ParcellationTerminology
+    domain_of:
+    - VersionedNamedThing
+    range: VersionedNamedThing
+    any_of:
+    - range: ParcellationTerminology
+    - range: string
+  id:
+    name: id
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    identifier: true
+    alias: id
+    owner: ParcellationTerminology
+    domain_of:
+    - NamedThing
+    range: uriorcurie
+    required: true
+  name:
+    name: name
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: name
+    owner: ParcellationTerminology
+    domain_of:
+    - NamedThing
+    range: string
+    required: true
+  description:
+    name: description
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: description
+    owner: ParcellationTerminology
+    domain_of:
+    - NamedThing
+    range: string
+    required: true
+  category:
+    name: category
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    designates_type: true
+    alias: category
+    owner: ParcellationTerminology
+    domain_of:
+    - NamedThing
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/PercentageFrequencyValue/index.html b/PercentageFrequencyValue/index.html new file mode 100644 index 00000000..4ea24842 --- /dev/null +++ b/PercentageFrequencyValue/index.html @@ -0,0 +1,612 @@ + + + + + + + + + + + + + + + + + + + Type: PercentageFrequencyValue - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
+
+ + + +
+
+
+ + + + + +
+
+
+ + + +
+
+
+ + + +
+
+
+ + + +
+
+ + + + + + + +

Type: PercentageFrequencyValue

+

URI: UO:0000187

+ +

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfUO:0000187
nativebican:percentage_frequency_value
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/PhysicalEntity/index.html b/PhysicalEntity/index.html new file mode 100644 index 00000000..3a611c56 --- /dev/null +++ b/PhysicalEntity/index.html @@ -0,0 +1,1025 @@ + + + + + + + + + +Class: PhysicalEntity - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: PhysicalEntity

+

An entity that has material reality (a.k.a. physical essence).

+

URI: biolink:PhysicalEntity

+
classDiagram + class PhysicalEntity + click PhysicalEntity href "../PhysicalEntity" + PhysicalEssence <|-- PhysicalEntity + click PhysicalEssence href "../PhysicalEssence" + NamedThing <|-- PhysicalEntity + click NamedThing href "../NamedThing" + + + PhysicalEntity <|-- MaterialSample + click MaterialSample href "../MaterialSample" + + + PhysicalEntity : category + + PhysicalEntity : deprecated + + PhysicalEntity : description + + PhysicalEntity : full_name + + PhysicalEntity : has_attribute + + + + + PhysicalEntity --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + PhysicalEntity : id + + PhysicalEntity : iri + + PhysicalEntity : name + + PhysicalEntity : provided_by + + PhysicalEntity : synonym + + PhysicalEntity : type + + PhysicalEntity : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
id1
String		A unique identifier for an entitydirect
iri0..1
IriType		An IRI for an entitydirect
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizeddirect
type*
String		direct
name0..1
LabelType		A human-readable name for an attribute or entitydirect
description0..1
NarrativeText		a human-readable description of an entitydirect
has_attribute*
Attribute		connects any entity to an attributedirect
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...direct
provided_by*
String		The value in this node property represents the knowledge provider that create...direct
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...direct
full_name0..1
LabelType		a long-form human readable name for a thingdirect
synonym*
LabelType		Alternate human-readable names for a thingdirect
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:PhysicalEntity
nativebican:PhysicalEntity
exactSTY:T072
narrowSTY:T073
+

LinkML Source

+ +

Direct

+
+
name: physical entity
+definition_uri: https://w3id.org/biolink/vocab/PhysicalEntity
+description: An entity that has material reality (a.k.a. physical essence).
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- STY:T072
+narrow_mappings:
+- STY:T073
+is_a: named thing
+mixins:
+- physical essence
+slots:
+- id
+- iri
+- category
+- type
+- name
+- description
+- has attribute
+- deprecated
+- provided by
+- xref
+- full name
+- synonym
+class_uri: biolink:PhysicalEntity
+
+
+
+

Induced

+
+
name: physical entity
+definition_uri: https://w3id.org/biolink/vocab/PhysicalEntity
+description: An entity that has material reality (a.k.a. physical essence).
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- STY:T072
+narrow_mappings:
+- STY:T073
+is_a: named thing
+mixins:
+- physical essence
+attributes:
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: physical entity
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: physical entity
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: physical entity
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: physical entity
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: physical entity
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: physical entity
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: physical entity
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: physical entity
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: physical entity
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: physical entity
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: physical entity
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: physical entity
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+class_uri: biolink:PhysicalEntity
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/PhysicalEssence/index.html b/PhysicalEssence/index.html new file mode 100644 index 00000000..a50feb81 --- /dev/null +++ b/PhysicalEssence/index.html @@ -0,0 +1,443 @@ + + + + + + + + + +Class: PhysicalEssence - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
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+ +
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+ +
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+ +
+
+
+
+
+

Class: PhysicalEssence

+

Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge.

+

URI: biolink:PhysicalEssence

+
classDiagram + class PhysicalEssence + click PhysicalEssence href "../PhysicalEssence" + PhysicalEssenceOrOccurrent <|-- PhysicalEssence + click PhysicalEssenceOrOccurrent href "../PhysicalEssenceOrOccurrent" + + + PhysicalEssence <|-- PhysicalEntity + click PhysicalEntity href "../PhysicalEntity" + PhysicalEssence <|-- Gene + click Gene href "../Gene" + PhysicalEssence <|-- Genome + click Genome href "../Genome" + + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
+

Mixin Usage

+ + + + + + + + + + + + + + + + + + + + + +
mixed intodescription
PhysicalEntityAn entity that has material reality (a
GeneA region (or regions) that includes all of the sequence elements necessary to...
GenomeA genome is the sum of genetic material within a cell or virion
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:PhysicalEssence
nativebican:PhysicalEssence
+

LinkML Source

+ +

Direct

+
+
name: physical essence
+definition_uri: https://w3id.org/biolink/vocab/PhysicalEssence
+description: Semantic mixin concept.  Pertains to entities that have physical properties
+  such as mass, volume, or charge.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: physical essence or occurrent
+mixin: true
+class_uri: biolink:PhysicalEssence
+
+
+
+

Induced

+
+
name: physical essence
+definition_uri: https://w3id.org/biolink/vocab/PhysicalEssence
+description: Semantic mixin concept.  Pertains to entities that have physical properties
+  such as mass, volume, or charge.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: physical essence or occurrent
+mixin: true
+class_uri: biolink:PhysicalEssence
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/PhysicalEssenceOrOccurrent/index.html b/PhysicalEssenceOrOccurrent/index.html new file mode 100644 index 00000000..9d889181 --- /dev/null +++ b/PhysicalEssenceOrOccurrent/index.html @@ -0,0 +1,425 @@ + + + + + + + + + +Class: PhysicalEssenceOrOccurrent - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
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+ +
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+ +
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+ +
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+
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+
+

Class: PhysicalEssenceOrOccurrent

+

Either a physical or processual entity.

+

URI: biolink:PhysicalEssenceOrOccurrent

+
classDiagram + class PhysicalEssenceOrOccurrent + click PhysicalEssenceOrOccurrent href "../PhysicalEssenceOrOccurrent" + PhysicalEssenceOrOccurrent <|-- PhysicalEssence + click PhysicalEssence href "../PhysicalEssence" + PhysicalEssenceOrOccurrent <|-- Occurrent + click Occurrent href "../Occurrent" + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
+

Mixin Usage

+ + + + + + + + + + + + + +
mixed intodescription
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:PhysicalEssenceOrOccurrent
nativebican:PhysicalEssenceOrOccurrent
+

LinkML Source

+ +

Direct

+
+
name: physical essence or occurrent
+definition_uri: https://w3id.org/biolink/vocab/PhysicalEssenceOrOccurrent
+description: Either a physical or processual entity.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+mixin: true
+class_uri: biolink:PhysicalEssenceOrOccurrent
+
+
+
+

Induced

+
+
name: physical essence or occurrent
+definition_uri: https://w3id.org/biolink/vocab/PhysicalEssenceOrOccurrent
+description: Either a physical or processual entity.
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+mixin: true
+class_uri: biolink:PhysicalEssenceOrOccurrent
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/PredicateType/index.html b/PredicateType/index.html new file mode 100644 index 00000000..fc087f72 --- /dev/null +++ b/PredicateType/index.html @@ -0,0 +1,616 @@ + + + + + + + + + + + + + + + + + + + Type: PredicateType - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
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+ + + + + +
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+ + + +
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+ + + + + + + +

Type: PredicateType

+

A CURIE from the biolink related_to hierarchy. For example, biolink:related_to, biolink:causes, biolink:treats.

+

URI: xsd:anyURI

+ +

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfxsd:anyURI
nativebican:predicate_type
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/Procedure/index.html b/Procedure/index.html new file mode 100644 index 00000000..8a1aac35 --- /dev/null +++ b/Procedure/index.html @@ -0,0 +1,1041 @@ + + + + + + + + + +Class: Procedure - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
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+ +
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+ +
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+ +
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+

Class: Procedure

+

A series of actions conducted in a certain order or manner

+

URI: biolink:Procedure

+
classDiagram + class Procedure + click Procedure href "../Procedure" + ActivityAndBehavior <|-- Procedure + click ActivityAndBehavior href "../ActivityAndBehavior" + NamedThing <|-- Procedure + click NamedThing href "../NamedThing" + + Procedure : category + + Procedure : deprecated + + Procedure : description + + Procedure : full_name + + Procedure : has_attribute + + + + + Procedure --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + Procedure : id + + Procedure : iri + + Procedure : name + + Procedure : provided_by + + Procedure : synonym + + Procedure : type + + Procedure : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
id1
String		A unique identifier for an entitydirect
iri0..1
IriType		An IRI for an entitydirect
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizeddirect
type*
String		direct
name0..1
LabelType		A human-readable name for an attribute or entitydirect
description0..1
NarrativeText		a human-readable description of an entitydirect
has_attribute*
Attribute		connects any entity to an attributedirect
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...direct
provided_by*
String		The value in this node property represents the knowledge provider that create...direct
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...direct
full_name0..1
LabelType		a long-form human readable name for a thingdirect
synonym*
LabelType		Alternate human-readable names for a thingdirect
+

Identifier and Mapping Information

+

Valid ID Prefixes

+

Instances of this class should have identifiers with one of the following prefixes:

+
    +
  • CPT
    • +
+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:Procedure
nativebican:Procedure
exactUMLSSG:PROC, dcid:MedicalProcedure
narrowSTY:T059, STY:T060, STY:T061, STY:T063
+

LinkML Source

+ +

Direct

+
+
name: procedure
+id_prefixes:
+- CPT
+definition_uri: https://w3id.org/biolink/vocab/Procedure
+description: A series of actions conducted in a certain order or manner
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- UMLSSG:PROC
+- dcid:MedicalProcedure
+narrow_mappings:
+- STY:T059
+- STY:T060
+- STY:T061
+- STY:T063
+is_a: named thing
+mixins:
+- activity and behavior
+slots:
+- id
+- iri
+- category
+- type
+- name
+- description
+- has attribute
+- deprecated
+- provided by
+- xref
+- full name
+- synonym
+class_uri: biolink:Procedure
+
+
+
+

Induced

+
+
name: procedure
+id_prefixes:
+- CPT
+definition_uri: https://w3id.org/biolink/vocab/Procedure
+description: A series of actions conducted in a certain order or manner
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+exact_mappings:
+- UMLSSG:PROC
+- dcid:MedicalProcedure
+narrow_mappings:
+- STY:T059
+- STY:T060
+- STY:T061
+- STY:T063
+is_a: named thing
+mixins:
+- activity and behavior
+attributes:
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: procedure
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: procedure
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: procedure
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: procedure
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: procedure
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: procedure
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: procedure
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: procedure
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: procedure
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: procedure
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: procedure
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: procedure
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+class_uri: biolink:Procedure
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/ProcessingElements/index.html b/ProcessingElements/index.html new file mode 100644 index 00000000..3b1a1f22 --- /dev/null +++ b/ProcessingElements/index.html @@ -0,0 +1,574 @@ + + + + + + + + + + + + + + + + + + + Subset: ProcessingElements - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
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+ + + +
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+ + + + + +
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+ + + +
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+ + + +
+
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+ + + +
+
+ + + + + + + +

Subset: ProcessingElements

+

A subset of classes that are associated with processing.

+

URI: ProcessingElements

+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/ProvActivity/index.html b/ProvActivity/index.html new file mode 100644 index 00000000..aa880a2b --- /dev/null +++ b/ProvActivity/index.html @@ -0,0 +1,482 @@ + + + + + + + + + +Class: ProvActivity - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
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+ +
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+ +
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+ +
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+

Class: ProvActivity

+

An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities.

+

URI: prov:Activity

+
classDiagram + class ProvActivity + click ProvActivity href "../ProvActivity" + ProvActivity <|-- DissectionRoiDelineation + click DissectionRoiDelineation href "../DissectionRoiDelineation" + ProvActivity <|-- TissueDissection + click TissueDissection href "../TissueDissection" + ProvActivity <|-- CellDissociation + click CellDissociation href "../CellDissociation" + ProvActivity <|-- CellEnrichment + click CellEnrichment href "../CellEnrichment" + ProvActivity <|-- EnrichedCellSampleSplitting + click EnrichedCellSampleSplitting href "../EnrichedCellSampleSplitting" + ProvActivity <|-- CellBarcoding + click CellBarcoding href "../CellBarcoding" + ProvActivity <|-- CdnaAmplification + click CdnaAmplification href "../CdnaAmplification" + ProvActivity <|-- LibraryConstruction + click LibraryConstruction href "../LibraryConstruction" + ProvActivity <|-- LibraryPooling + click LibraryPooling href "../LibraryPooling" + + ProvActivity : used + + +
+ +

Slots

+ + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
used0..1
String		direct
+

Mixin Usage

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
mixed intodescription
DissectionRoiDelineationThe process of outlining a region of interest on a brain slab image to guide ...
TissueDissectionThe process of dissecting a tissue sample from a brain slab guided by a disse...
CellDissociationThe process of generating dissociated cells from an input tissue sample
CellEnrichmentThe process of enriching a dissociated cell sample by including or excluding ...
EnrichedCellSampleSplittingThe process of splitting an enriched cell sample into several portions
CellBarcodingThe process of adding a molecular barcode to individual cells in a sample
CdnaAmplificationThe process of creating a collection of cDNA molecules derived and amplified ...
LibraryConstructionThe process of constructing a library from input material (such as amplified ...
LibraryPoolingThe process of constructing of a libray pool by combining library aliquots fr...
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfprov:Activity
nativebican:ProvActivity
+

LinkML Source

+ +

Direct

+
+
name: ProvActivity
+description: An activity is something that occurs over a period of time and acts upon
+  or with entities;  it may include consuming, processing, transforming, modifying,
+  relocating, using, or generating entities.
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+mixin: true
+slots:
+- used
+class_uri: prov:Activity
+
+
+
+

Induced

+
+
name: ProvActivity
+description: An activity is something that occurs over a period of time and acts upon
+  or with entities;  it may include consuming, processing, transforming, modifying,
+  relocating, using, or generating entities.
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+mixin: true
+attributes:
+  used:
+    name: used
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: used
+    owner: ProvActivity
+    domain_of:
+    - DissectionRoiDelineation
+    - TissueDissection
+    - CellDissociation
+    - CellEnrichment
+    - EnrichedCellSampleSplitting
+    - CellBarcoding
+    - CdnaAmplification
+    - LibraryConstruction
+    - LibraryPooling
+    - ProvActivity
+    range: string
+class_uri: prov:Activity
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/ProvEntity/index.html b/ProvEntity/index.html new file mode 100644 index 00000000..006dfda6 --- /dev/null +++ b/ProvEntity/index.html @@ -0,0 +1,525 @@ + + + + + + + + + +Class: ProvEntity - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
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+ +
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+ +
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+ +
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+

Class: ProvEntity

+

An entity is a physical, digital, conceptual, or other kind of thing with some fixed aspects; entities may be real or imaginary.

+

URI: prov:Entity

+
classDiagram + class ProvEntity + click ProvEntity href "../ProvEntity" + ProvEntity <|-- Donor + click Donor href "../Donor" + ProvEntity <|-- BrainSlab + click BrainSlab href "../BrainSlab" + ProvEntity <|-- TissueSample + click TissueSample href "../TissueSample" + ProvEntity <|-- DissociatedCellSample + click DissociatedCellSample href "../DissociatedCellSample" + ProvEntity <|-- EnrichedCellSample + click EnrichedCellSample href "../EnrichedCellSample" + ProvEntity <|-- BarcodedCellSample + click BarcodedCellSample href "../BarcodedCellSample" + ProvEntity <|-- AmplifiedCdna + click AmplifiedCdna href "../AmplifiedCdna" + ProvEntity <|-- Library + click Library href "../Library" + ProvEntity <|-- LibraryAliquot + click LibraryAliquot href "../LibraryAliquot" + ProvEntity <|-- LibraryPool + click LibraryPool href "../LibraryPool" + ProvEntity <|-- DissectionRoiPolygon + click DissectionRoiPolygon href "../DissectionRoiPolygon" + ProvEntity <|-- DigitalAsset + click DigitalAsset href "../DigitalAsset" + + ProvEntity : was_derived_from + + ProvEntity : was_generated_by + + +
+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
was_derived_from0..1
String		direct
was_generated_by0..1
String		direct
+

Mixin Usage

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
mixed intodescription
DonorA person or organism that is the source of a biological sample for scientific...
BrainSlabA thick flat piece of brain tissue obtained by slicing a whole brain, brain h...
TissueSampleThe final intact piece of tissue before cell or nuclei prep
DissociatedCellSampleA collection of dissociated cells or nuclei derived from dissociation of a ti...
EnrichedCellSampleA collection of enriched cells or nuclei after enrichment process, usually vi...
BarcodedCellSampleA collection of molecularly barcoded cells
AmplifiedCdnaA collection of cDNA molecules derived and amplified from an input barcoded c...
LibraryA collection of fragmented and barcode-indexed DNA molecules for sequencing
LibraryAliquotOne library in the library pool
LibraryPoolA library pool is made up of library aliquots from multiple libraries
DissectionRoiPolygonA polygon annotated on a brain slab image delineating a region of interest (R...
DigitalAsset
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfprov:Entity
nativebican:ProvEntity
+

LinkML Source

+ +

Direct

+
+
name: ProvEntity
+description: An entity is a physical, digital, conceptual, or other kind of thing
+  with some fixed aspects;  entities may be real or imaginary.
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+mixin: true
+slots:
+- was_derived_from
+- was_generated_by
+class_uri: prov:Entity
+
+
+
+

Induced

+
+
name: ProvEntity
+description: An entity is a physical, digital, conceptual, or other kind of thing
+  with some fixed aspects;  entities may be real or imaginary.
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+mixin: true
+attributes:
+  was_derived_from:
+    name: was_derived_from
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: was_derived_from
+    owner: ProvEntity
+    domain_of:
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DigitalAsset
+    - ProvEntity
+    range: string
+  was_generated_by:
+    name: was_generated_by
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: was_generated_by
+    owner: ProvEntity
+    domain_of:
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryPool
+    - DissectionRoiPolygon
+    - ProvEntity
+    range: string
+class_uri: prov:Entity
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/QuantityValue/index.html b/QuantityValue/index.html new file mode 100644 index 00000000..0f01b671 --- /dev/null +++ b/QuantityValue/index.html @@ -0,0 +1,500 @@ + + + + + + + + + +Class: QuantityValue - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
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+ +
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+ +
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+
+
+ +
+
+
+
+
+

Class: QuantityValue

+

A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value

+

URI: biolink:QuantityValue

+
classDiagram + class QuantityValue + click QuantityValue href "../QuantityValue" + Annotation <|-- QuantityValue + click Annotation href "../Annotation" + + QuantityValue : has_numeric_value + + QuantityValue : has_unit + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
has_unit0..1
Unit		connects a quantity value to a unitdirect
has_numeric_value0..1
Double		connects a quantity value to a numberdirect
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
QuantityValuehas_unitdomainQuantityValue
QuantityValuehas_numeric_valuedomainQuantityValue
Attributehas_quantitative_valuerangeQuantityValue
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:QuantityValue
nativebican:QuantityValue
+

LinkML Source

+ +

Direct

+
+
name: quantity value
+definition_uri: https://w3id.org/biolink/vocab/QuantityValue
+description: A value of an attribute that is quantitative and measurable, expressed
+  as a combination of a unit and a numeric value
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: annotation
+slots:
+- has unit
+- has numeric value
+class_uri: biolink:QuantityValue
+
+
+
+

Induced

+
+
name: quantity value
+definition_uri: https://w3id.org/biolink/vocab/QuantityValue
+description: A value of an attribute that is quantitative and measurable, expressed
+  as a combination of a unit and a numeric value
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+is_a: annotation
+attributes:
+  has unit:
+    name: has unit
+    definition_uri: https://w3id.org/biolink/vocab/has_unit
+    description: connects a quantity value to a unit
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - qud:unit
+    - IAO:0000039
+    close_mappings:
+    - EFO:0001697
+    - UO-PROPERTY:is_unit_of
+    narrow_mappings:
+    - SNOMED:has_concentration_strength_denominator_unit
+    - SNOMED:has_concentration_strength_numerator_unit
+    - SNOMED:has_presentation_strength_denominator_unit
+    - SNOMED:has_presentation_strength_numerator_unit
+    - SNOMED:has_unit_of_presentation
+    rank: 1000
+    domain: quantity value
+    slot_uri: biolink:has_unit
+    alias: has_unit
+    owner: quantity value
+    domain_of:
+    - quantity value
+    range: unit
+    multivalued: false
+  has numeric value:
+    name: has numeric value
+    definition_uri: https://w3id.org/biolink/vocab/has_numeric_value
+    description: connects a quantity value to a number
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - qud:quantityValue
+    rank: 1000
+    domain: quantity value
+    slot_uri: biolink:has_numeric_value
+    alias: has_numeric_value
+    owner: quantity value
+    domain_of:
+    - quantity value
+    range: double
+    multivalued: false
+class_uri: biolink:QuantityValue
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/Quotient/index.html b/Quotient/index.html new file mode 100644 index 00000000..ab1f985a --- /dev/null +++ b/Quotient/index.html @@ -0,0 +1,625 @@ + + + + + + + + + + + + + + + + + + + Type: Quotient - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
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+ + + + + +
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+ + + +
+
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+ + + +
+
+
+ + + +
+
+ + + + + + + +

Type: Quotient

+

URI: UO:0010006

+ +

Aliases

+
    +
  • ratio
    • +
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfUO:0010006
nativebican:quotient
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/Samples/index.html b/Samples/index.html new file mode 100644 index 00000000..306aa5e1 --- /dev/null +++ b/Samples/index.html @@ -0,0 +1,716 @@ + + + + + + + + + + + + + + + + + + + Subset: Samples - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
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+ + + + + +
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+ + + +
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+ + + +
+
+
+ + + +
+
+ + + + + + + +

Subset: Samples

+

Sample/biosample datamodel

+

URI: Samples

+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Classes in subset

+ + + + + + + + + + + + + +
ClassDescription
AttributeA property or characteristic of an entity
+

Slots from Attribute also in samples

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescription
attribute_name0..1
LabelType		The human-readable 'attribute name' can be set to a string which reflects its...
has_attribute*
Attribute		connects any entity to an attribute
has_attribute_type1
OntologyClass		connects an attribute to a class that describes it
has_qualitative_value0..1
NamedThing		connects an attribute to a value
has_quantitative_value*
QuantityValue		connects an attribute to a value
iri0..1
IriType		An IRI for an entity
name0..1
LabelType		The human-readable 'attribute name' can be set to a string which reflects its...
+

Slots in subset

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
SlotDescription
attribute_nameThe human-readable 'attribute name' can be set to a string which reflects its...
has_attributeconnects any entity to an attribute
has_attribute_typeconnects an attribute to a class that describes it
has_numeric_valueconnects a quantity value to a number
has_qualitative_valueconnects an attribute to a value
has_quantitative_valueconnects an attribute to a value
has_unitconnects a quantity value to a unit
iriAn IRI for an entity
nameA human-readable name for an attribute or entity
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/SequencingElements/index.html b/SequencingElements/index.html new file mode 100644 index 00000000..bb8ddd33 --- /dev/null +++ b/SequencingElements/index.html @@ -0,0 +1,574 @@ + + + + + + + + + + + + + + + + + + + Subset: SequencingElements - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
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+ + + +
+
+ + + + + + + +

Subset: SequencingElements

+

A subset of classes that are associated with sequencing.

+

URI: SequencingElements

+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/Sex/index.html b/Sex/index.html new file mode 100644 index 00000000..85ba3b9c --- /dev/null +++ b/Sex/index.html @@ -0,0 +1,683 @@ + + + + + + + + + + + + + + + + + + + Enum: Sex - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
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+ + + +
+
+ + + + + + + +

Enum: Sex

+

URI: Sex

+

Permissible Values

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ValueMeaningDescription
1NIMP:PD-LXUBTM45Male
2NIMP:PD-LXUBTM45Female
7NIMP:PD-LXUBTM45Other
8NIMP:PD-LXUBTM45Unknown
9NIMP:PD-LXUBTM45Not Reported
+

Slots

+ + + + + + + + + + + + + +
NameDescription
biological_sexBiological sex of donor at birth
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

LinkML Source

+
+ +
name: sex
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+rank: 1000
+permissible_values:
+  '1':
+    text: '1'
+    description: Male
+    meaning: NIMP:PD-LXUBTM45
+  '2':
+    text: '2'
+    description: Female
+    meaning: NIMP:PD-LXUBTM45
+  '7':
+    text: '7'
+    description: Other
+    meaning: NIMP:PD-LXUBTM45
+  '8':
+    text: '8'
+    description: Unknown
+    meaning: NIMP:PD-LXUBTM45
+  '9':
+    text: '9'
+    description: Not Reported
+    meaning: NIMP:PD-LXUBTM45
+
+
+ +
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/Sparqlpath/index.html b/Sparqlpath/index.html new file mode 100644 index 00000000..7cd57165 --- /dev/null +++ b/Sparqlpath/index.html @@ -0,0 +1,613 @@ + + + + + + + + + + + + + + + + + + + Type: Sparqlpath - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
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+ + + + + +
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+ + + +
+
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+ + + +
+
+ + + + + + + +

Type: Sparqlpath

+

A string encoding a SPARQL Property Path. The value of the string MUST conform to SPARQL syntax and SHOULD dereference to zero or more valid objects within the current instance document when encoded as RDF.

+

URI: xsd:string

+ +

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfxsd:string
nativebican:sparqlpath
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/String/index.html b/String/index.html new file mode 100644 index 00000000..bb6fe1e4 --- /dev/null +++ b/String/index.html @@ -0,0 +1,614 @@ + + + + + + + + + + + + + + + + + + + Type: String - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
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+ + + + + +
+
+
+ + + +
+
+
+ + + +
+
+
+ + + +
+
+ + + + + + + +

Type: String

+

A character string

+

URI: xsd:string

+
    +
  • +

    base: str

    +
    • +
  • +

    uri: xsd:string

    +
    • +
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfxsd:string
nativebican:string
exactschema:Text
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/SubjectOfInvestigation/index.html b/SubjectOfInvestigation/index.html new file mode 100644 index 00000000..405c292e --- /dev/null +++ b/SubjectOfInvestigation/index.html @@ -0,0 +1,411 @@ + + + + + + + + + +Class: SubjectOfInvestigation - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+

Class: SubjectOfInvestigation

+

An entity that has the role of being studied in an investigation, study, or experiment

+

URI: biolink:SubjectOfInvestigation

+
classDiagram + class SubjectOfInvestigation + click SubjectOfInvestigation href "../SubjectOfInvestigation" + SubjectOfInvestigation <|-- MaterialSample + click MaterialSample href "../MaterialSample" + + +
+ +

Slots

+ + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
+

Mixin Usage

+ + + + + + + + + + + + + +
mixed intodescription
MaterialSampleA sample is a limited quantity of something (e
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:SubjectOfInvestigation
nativebican:SubjectOfInvestigation
+

LinkML Source

+ +

Direct

+
+
name: subject of investigation
+definition_uri: https://w3id.org/biolink/vocab/SubjectOfInvestigation
+description: An entity that has the role of being studied in an investigation, study,
+  or experiment
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+mixin: true
+class_uri: biolink:SubjectOfInvestigation
+
+
+
+

Induced

+
+
name: subject of investigation
+definition_uri: https://w3id.org/biolink/vocab/SubjectOfInvestigation
+description: An entity that has the role of being studied in an investigation, study,
+  or experiment
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+mixin: true
+class_uri: biolink:SubjectOfInvestigation
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/SymbolType/index.html b/SymbolType/index.html new file mode 100644 index 00000000..2179257b --- /dev/null +++ b/SymbolType/index.html @@ -0,0 +1,612 @@ + + + + + + + + + + + + + + + + + + + Type: SymbolType - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
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+ + + + + + + +

Type: SymbolType

+

URI: xsd:string

+ +

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfxsd:string
nativebican:symbol_type
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/TaxonomicRank/index.html b/TaxonomicRank/index.html new file mode 100644 index 00000000..02c4b3ff --- /dev/null +++ b/TaxonomicRank/index.html @@ -0,0 +1,493 @@ + + + + + + + + + +Class: TaxonomicRank - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
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+ +
+
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+
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+
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+ +
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+
+
+ +
+
+
+
+
+

Class: TaxonomicRank

+

A descriptor for the rank within a taxonomic classification. Example instance: TAXRANK:0000017 (kingdom)

+

URI: biolink:TaxonomicRank

+
classDiagram + class TaxonomicRank + click TaxonomicRank href "../TaxonomicRank" + OntologyClass <|-- TaxonomicRank + click OntologyClass href "../OntologyClass" + + TaxonomicRank : id + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
id1
String		A unique identifier for an entitydirect
+

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
OrganismTaxonhas_taxonomic_rankrangeTaxonomicRank
+

Identifier and Mapping Information

+

Valid ID Prefixes

+

Instances of this class should have identifiers with one of the following prefixes:

+
    +
  • TAXRANK
    • +
+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:TaxonomicRank
nativebican:TaxonomicRank
undefinedWIKIDATA:Q427626
+

LinkML Source

+ +

Direct

+
+
name: taxonomic rank
+id_prefixes:
+- TAXRANK
+definition_uri: https://w3id.org/biolink/vocab/TaxonomicRank
+description: 'A descriptor for the rank within a taxonomic classification. Example
+  instance: TAXRANK:0000017 (kingdom)'
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+mappings:
+- WIKIDATA:Q427626
+is_a: ontology class
+slots:
+- id
+class_uri: biolink:TaxonomicRank
+
+
+
+

Induced

+
+
name: taxonomic rank
+id_prefixes:
+- TAXRANK
+definition_uri: https://w3id.org/biolink/vocab/TaxonomicRank
+description: 'A descriptor for the rank within a taxonomic classification. Example
+  instance: TAXRANK:0000017 (kingdom)'
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+mappings:
+- WIKIDATA:Q427626
+is_a: ontology class
+attributes:
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: taxonomic rank
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+class_uri: biolink:TaxonomicRank
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/Testing/index.html b/Testing/index.html new file mode 100644 index 00000000..df6bd211 --- /dev/null +++ b/Testing/index.html @@ -0,0 +1,574 @@ + + + + + + + + + + + + + + + + + + + Subset: Testing - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
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Subset: Testing

+

TBD

+

URI: Testing

+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/ThingWithTaxon/index.html b/ThingWithTaxon/index.html new file mode 100644 index 00000000..4bff899f --- /dev/null +++ b/ThingWithTaxon/index.html @@ -0,0 +1,606 @@ + + + + + + + + + +Class: ThingWithTaxon - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
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Class: ThingWithTaxon

+

A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes

+

URI: biolink:ThingWithTaxon

+
classDiagram + class ThingWithTaxon + click ThingWithTaxon href "../ThingWithTaxon" + ThingWithTaxon <|-- GenomeAssembly + click GenomeAssembly href "../GenomeAssembly" + ThingWithTaxon <|-- BiologicalEntity + click BiologicalEntity href "../BiologicalEntity" + + ThingWithTaxon : in_taxon + + + + + ThingWithTaxon --> "*" OrganismTaxon : in_taxon + click OrganismTaxon href "../OrganismTaxon" + + + ThingWithTaxon : in_taxon_label + + +
+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
in_taxon*
OrganismTaxon		connects an entity to its taxonomic classificationdirect
in_taxon_label0..1
LabelType		The human readable scientific name for the taxon of the entitydirect
+

Mixin Usage

+ + + + + + + + + + + + + + + + + +
mixed intodescription
GenomeAssemblyGenome assembly to contain version and label information
BiologicalEntity
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
GeneAnnotationin_taxondomainThingWithTaxon
GeneAnnotationin_taxon_labeldomainThingWithTaxon
GenomeAnnotationin_taxondomainThingWithTaxon
GenomeAnnotationin_taxon_labeldomainThingWithTaxon
GenomeAssemblyin_taxondomainThingWithTaxon
GenomeAssemblyin_taxon_labeldomainThingWithTaxon
ThingWithTaxonin_taxondomainThingWithTaxon
ThingWithTaxonin_taxon_labeldomainThingWithTaxon
BiologicalEntityin_taxondomainThingWithTaxon
BiologicalEntityin_taxon_labeldomainThingWithTaxon
Genein_taxondomainThingWithTaxon
Genein_taxon_labeldomainThingWithTaxon
Genomein_taxondomainThingWithTaxon
Genomein_taxon_labeldomainThingWithTaxon
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbiolink:ThingWithTaxon
nativebican:ThingWithTaxon
+

LinkML Source

+ +

Direct

+
+
name: thing with taxon
+definition_uri: https://w3id.org/biolink/vocab/ThingWithTaxon
+description: A mixin that can be used on any entity that can be taxonomically classified.
+  This includes individual organisms; genes, their products and other molecular entities;
+  body parts; biological processes
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+mixin: true
+slots:
+- in taxon
+- in taxon label
+class_uri: biolink:ThingWithTaxon
+
+
+
+

Induced

+
+
name: thing with taxon
+definition_uri: https://w3id.org/biolink/vocab/ThingWithTaxon
+description: A mixin that can be used on any entity that can be taxonomically classified.
+  This includes individual organisms; genes, their products and other molecular entities;
+  body parts; biological processes
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+mixin: true
+attributes:
+  in taxon:
+    name: in taxon
+    definition_uri: https://w3id.org/biolink/vocab/in_taxon
+    annotations:
+      canonical_predicate:
+        tag: canonical_predicate
+        value: true
+    description: connects an entity to its taxonomic classification. Only certain
+      kinds of entities can be taxonomically classified; see 'thing with taxon'
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    aliases:
+    - instance of
+    - is organism source of gene product
+    - organism has gene
+    - gene found in organism
+    - gene product has organism source
+    exact_mappings:
+    - RO:0002162
+    - WIKIDATA_PROPERTY:P703
+    narrow_mappings:
+    - RO:0002160
+    rank: 1000
+    is_a: related to at instance level
+    domain: thing with taxon
+    slot_uri: biolink:in_taxon
+    inherited: true
+    alias: in_taxon
+    owner: thing with taxon
+    domain_of:
+    - thing with taxon
+    - biological entity
+    - gene
+    - genome
+    range: organism taxon
+    multivalued: true
+  in taxon label:
+    name: in taxon label
+    definition_uri: https://w3id.org/biolink/vocab/in_taxon_label
+    annotations:
+      denormalized:
+        tag: denormalized
+        value: true
+    description: The human readable scientific name for the taxon of the entity.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P225
+    rank: 1000
+    is_a: node property
+    domain: thing with taxon
+    slot_uri: biolink:in_taxon_label
+    alias: in_taxon_label
+    owner: thing with taxon
+    domain_of:
+    - thing with taxon
+    - biological entity
+    - gene
+    - genome
+    range: label type
+class_uri: biolink:ThingWithTaxon
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/Time/index.html b/Time/index.html new file mode 100644 index 00000000..c6e8aed3 --- /dev/null +++ b/Time/index.html @@ -0,0 +1,617 @@ + + + + + + + + + + + + + + + + + + + Type: Time - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
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+ + + + + + + +

Type: Time

+

A time object represents a (local) time of day, independent of any particular day

+

URI: xsd:time

+
    +
  • +

    base: XSDTime

    +
    • +
  • +

    uri: xsd:time

    +
    • +
  • +

    repr: str

    +
    • +
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfxsd:time
nativebican:time
exactschema:Time
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/TimeType/index.html b/TimeType/index.html new file mode 100644 index 00000000..f53cc4b4 --- /dev/null +++ b/TimeType/index.html @@ -0,0 +1,615 @@ + + + + + + + + + + + + + + + + + + + Type: TimeType - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
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+ +
+ + + + + + +
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+ + + + + +
+
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+ + + +
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+ + + +
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+
+ + + + + + + +

Type: TimeType

+

URI: xsd:time

+ +

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfxsd:time
nativebican:time_type
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/TissueDissection/index.html b/TissueDissection/index.html new file mode 100644 index 00000000..e15473d4 --- /dev/null +++ b/TissueDissection/index.html @@ -0,0 +1,1119 @@ + + + + + + + + + +Class: TissueDissection - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
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+ +
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+ +
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+

Class: TissueDissection

+

The process of dissecting a tissue sample from a brain slab guided by a dissection region of interest (ROI) delineation.

+

URI: bican:TissueDissection

+
classDiagram + class TissueDissection + click TissueDissection href "../TissueDissection" + ProvActivity <|-- TissueDissection + click ProvActivity href "../ProvActivity" + Procedure <|-- TissueDissection + click Procedure href "../Procedure" + + TissueDissection : category + + TissueDissection : deprecated + + TissueDissection : description + + TissueDissection : full_name + + TissueDissection : has_attribute + + + + + TissueDissection --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + TissueDissection : id + + TissueDissection : iri + + TissueDissection : name + + TissueDissection : provided_by + + TissueDissection : synonym + + TissueDissection : type + + TissueDissection : used + + + + + TissueDissection --> "0..1" BrainSlab : used + click BrainSlab href "../BrainSlab" + + + TissueDissection : was_guided_by + + + + + TissueDissection --> "0..1" DissectionRoiPolygon : was_guided_by + click DissectionRoiPolygon href "../DissectionRoiPolygon" + + + TissueDissection : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
used0..1
BrainSlab		The brain slab from which the tissue sample was dissected fromdirect
was_guided_by0..1
DissectionRoiPolygon		The dissection ROI polygon which was used to guide the tissue dissectiondirect
id1
String		A unique identifier for an entityProcedure, NamedThing, Entity
iri0..1
IriType		An IRI for an entityProcedure, NamedThing, Entity
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizedProcedure, NamedThing, Entity
type*
String		Procedure, NamedThing, Entity
name0..1
LabelType		A human-readable name for an attribute or entityProcedure, NamedThing, Entity
description0..1
NarrativeText		a human-readable description of an entityProcedure, NamedThing, Entity
has_attribute*
Attribute		connects any entity to an attributeProcedure, NamedThing, Entity
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...Procedure, NamedThing, Entity
provided_by*
String		The value in this node property represents the knowledge provider that create...Procedure, NamedThing
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...Procedure, NamedThing
full_name0..1
LabelType		a long-form human readable name for a thingProcedure, NamedThing
synonym*
LabelType		Alternate human-readable names for a thingProcedure, NamedThing
+

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
TissueSamplewas_generated_byrangeTissueDissection
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:TissueDissection
nativebican:TissueDissection
+

LinkML Source

+ +

Direct

+
+
name: TissueDissection
+description: The process of dissecting a tissue sample from a brain slab guided by
+  a dissection region of interest (ROI) delineation.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slots:
+- used
+slot_usage:
+  used:
+    name: used
+    description: The brain slab from which the tissue sample was dissected from.
+    range: BrainSlab
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  was_guided_by:
+    name: was_guided_by
+    description: The dissection ROI polygon which was used to guide the tissue dissection.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    domain_of:
+    - TissueDissection
+    range: DissectionRoiPolygon
+
+
+
+

Induced

+
+
name: TissueDissection
+description: The process of dissecting a tissue sample from a brain slab guided by
+  a dissection region of interest (ROI) delineation.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+is_a: procedure
+mixins:
+- ProvActivity
+slot_usage:
+  used:
+    name: used
+    description: The brain slab from which the tissue sample was dissected from.
+    range: BrainSlab
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  was_guided_by:
+    name: was_guided_by
+    description: The dissection ROI polygon which was used to guide the tissue dissection.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: was_guided_by
+    owner: TissueDissection
+    domain_of:
+    - TissueDissection
+    range: DissectionRoiPolygon
+  used:
+    name: used
+    description: The brain slab from which the tissue sample was dissected from.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: used
+    owner: TissueDissection
+    domain_of:
+    - DissectionRoiDelineation
+    - TissueDissection
+    - CellDissociation
+    - CellEnrichment
+    - EnrichedCellSampleSplitting
+    - CellBarcoding
+    - CdnaAmplification
+    - LibraryConstruction
+    - LibraryPooling
+    - ProvActivity
+    range: BrainSlab
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: TissueDissection
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: TissueDissection
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: TissueDissection
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+    pattern: ^bican:[A-Z][A-Za-z]+$
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: TissueDissection
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    description: A human-readable name for an attribute or entity.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - gff3:Name
+    - gpi:DB_Object_Name
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: rdfs:label
+    alias: name
+    owner: TissueDissection
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - Donor
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DissectionRoiPolygon
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: TissueDissection
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: TissueDissection
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: TissueDissection
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: TissueDissection
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: TissueDissection
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: TissueDissection
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: TissueDissection
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/TissueSample/index.html b/TissueSample/index.html new file mode 100644 index 00000000..b0bffa5e --- /dev/null +++ b/TissueSample/index.html @@ -0,0 +1,1263 @@ + + + + + + + + + +Class: TissueSample - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
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+
+

Class: TissueSample

+

The final intact piece of tissue before cell or nuclei prep. This piece of tissue will be used in dissociation and has an region of interest polygon (ROI) associated with it.

+

URI: bican:TissueSample

+
classDiagram + class TissueSample + click TissueSample href "../TissueSample" + ProvEntity <|-- TissueSample + click ProvEntity href "../ProvEntity" + MaterialSample <|-- TissueSample + click MaterialSample href "../MaterialSample" + + TissueSample : category + + TissueSample : deprecated + + TissueSample : description + + TissueSample : dissection_was_guided_by + + + + + TissueSample --> "0..1" DissectionRoiPolygon : dissection_was_guided_by + click DissectionRoiPolygon href "../DissectionRoiPolygon" + + + TissueSample : full_name + + TissueSample : has_attribute + + + + + TissueSample --> "*" Attribute : has_attribute + click Attribute href "../Attribute" + + + TissueSample : id + + TissueSample : iri + + TissueSample : name + + TissueSample : provided_by + + TissueSample : structure + + TissueSample : synonym + + TissueSample : type + + TissueSample : was_derived_from + + + + + TissueSample --> "0..1" Donor : was_derived_from + click Donor href "../Donor" + + + TissueSample : was_generated_by + + + + + TissueSample --> "0..1" TissueDissection : was_generated_by + click TissueDissection href "../TissueDissection" + + + TissueSample : xref + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
was_derived_from0..1
Donor		The donor or brain slab from which the tissue sample was derived fromdirect
was_generated_by0..1
TissueDissection		The dissection process from which the tissue sample was generated bydirect
name0..1
LabelType		Identifier name for final intact piece of tissue before cell or nuclei prepdirect
dissection_was_guided_by0..1
DissectionRoiPolygon		The dissection ROI polygon that was used to guide the dissectiondirect
structure*
String		Strucure of tissue sampledirect
id1
String		A unique identifier for an entityNamedThing, MaterialSample, PhysicalEntity, Entity
iri0..1
IriType		An IRI for an entityNamedThing, MaterialSample, PhysicalEntity, Entity
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorizedNamedThing, MaterialSample, PhysicalEntity, Entity
type*
String		NamedThing, MaterialSample, PhysicalEntity, Entity
description0..1
NarrativeText		a human-readable description of an entityNamedThing, MaterialSample, PhysicalEntity, Entity
has_attribute*
Attribute		connects any entity to an attributeNamedThing, MaterialSample, PhysicalEntity, Entity
deprecated0..1
Boolean		A boolean flag indicating that an entity is no longer considered current or v...NamedThing, MaterialSample, PhysicalEntity, Entity
provided_by*
String		The value in this node property represents the knowledge provider that create...NamedThing, MaterialSample, PhysicalEntity
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...NamedThing, MaterialSample, PhysicalEntity
full_name0..1
LabelType		a long-form human readable name for a thingNamedThing, MaterialSample, PhysicalEntity
synonym*
LabelType		Alternate human-readable names for a thingNamedThing, MaterialSample, PhysicalEntity
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
DissociatedCellSamplewas_derived_fromrangeTissueSample
CellDissociationusedrangeTissueSample
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:TissueSample
nativebican:TissueSample
exactNIMP:Tissue
+

LinkML Source

+ +

Direct

+
+
name: TissueSample
+description: The final intact piece of tissue before cell or nuclei prep. This piece
+  of tissue will be used in dissociation and has an region of interest polygon (ROI)
+  associated with it.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Tissue
+is_a: material sample
+mixins:
+- ProvEntity
+slots:
+- was_derived_from
+- was_generated_by
+- name
+slot_usage:
+  was_derived_from:
+    name: was_derived_from
+    description: The donor or brain slab from which the tissue sample was derived
+      from.
+    exact_mappings:
+    - NIMP:has_parent
+    range: Donor
+  was_generated_by:
+    name: was_generated_by
+    description: The dissection process from which the tissue sample was generated
+      by.
+    range: TissueDissection
+  name:
+    name: name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: tissue_sample_local_name
+    description: Identifier name for final intact piece of tissue before cell or nuclei
+      prep.  This piece of tissue will be used in dissociation and has an ROI associated
+      with it.
+    exact_mappings:
+    - NIMP:PD-LJCRCC35
+    slot_uri: bican:2e4ca2fc-2d77-4d19-af45-d0fb7bbc2269
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  dissection_was_guided_by:
+    name: dissection_was_guided_by
+    description: The dissection ROI polygon that was used to guide the dissection.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:has_parent
+    rank: 1000
+    domain_of:
+    - TissueSample
+    range: DissectionRoiPolygon
+  structure:
+    name: structure
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: structure
+    description: Strucure of tissue sample.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: tissue_sample_structure
+    domain_of:
+    - TissueSample
+    multivalued: true
+
+
+
+

Induced

+
+
name: TissueSample
+description: The final intact piece of tissue before cell or nuclei prep. This piece
+  of tissue will be used in dissociation and has an region of interest polygon (ROI)
+  associated with it.
+in_subset:
+- bican
+- library_generation
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:Tissue
+is_a: material sample
+mixins:
+- ProvEntity
+slot_usage:
+  was_derived_from:
+    name: was_derived_from
+    description: The donor or brain slab from which the tissue sample was derived
+      from.
+    exact_mappings:
+    - NIMP:has_parent
+    range: Donor
+  was_generated_by:
+    name: was_generated_by
+    description: The dissection process from which the tissue sample was generated
+      by.
+    range: TissueDissection
+  name:
+    name: name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: tissue_sample_local_name
+    description: Identifier name for final intact piece of tissue before cell or nuclei
+      prep.  This piece of tissue will be used in dissociation and has an ROI associated
+      with it.
+    exact_mappings:
+    - NIMP:PD-LJCRCC35
+    slot_uri: bican:2e4ca2fc-2d77-4d19-af45-d0fb7bbc2269
+  category:
+    name: category
+    pattern: ^bican:[A-Z][A-Za-z]+$
+attributes:
+  dissection_was_guided_by:
+    name: dissection_was_guided_by
+    description: The dissection ROI polygon that was used to guide the dissection.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:has_parent
+    rank: 1000
+    alias: dissection_was_guided_by
+    owner: TissueSample
+    domain_of:
+    - TissueSample
+    range: DissectionRoiPolygon
+  structure:
+    name: structure
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: structure
+    description: Strucure of tissue sample.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: tissue_sample_structure
+    owner: TissueSample
+    domain_of:
+    - TissueSample
+    range: string
+    multivalued: true
+  was_derived_from:
+    name: was_derived_from
+    description: The donor or brain slab from which the tissue sample was derived
+      from.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - NIMP:has_parent
+    rank: 1000
+    alias: was_derived_from
+    owner: TissueSample
+    domain_of:
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DigitalAsset
+    - ProvEntity
+    range: Donor
+  was_generated_by:
+    name: was_generated_by
+    description: The dissection process from which the tissue sample was generated
+      by.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    alias: was_generated_by
+    owner: TissueSample
+    domain_of:
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryPool
+    - DissectionRoiPolygon
+    - ProvEntity
+    range: TissueDissection
+  name:
+    name: name
+    definition_uri: https://w3id.org/biolink/vocab/name
+    local_names:
+      NIMP:
+        local_name_source: NIMP
+        local_name_value: tissue_sample_local_name
+    description: Identifier name for final intact piece of tissue before cell or nuclei
+      prep.  This piece of tissue will be used in dissociation and has an ROI associated
+      with it.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - label
+    - display name
+    - title
+    mappings:
+    - rdfs:label
+    exact_mappings:
+    - NIMP:PD-LJCRCC35
+    narrow_mappings:
+    - dct:title
+    - WIKIDATA_PROPERTY:P1476
+    rank: 1000
+    domain: entity
+    slot_uri: bican:2e4ca2fc-2d77-4d19-af45-d0fb7bbc2269
+    alias: name
+    owner: TissueSample
+    domain_of:
+    - attribute
+    - entity
+    - macromolecular machine mixin
+    - Donor
+    - BrainSlab
+    - TissueSample
+    - DissociatedCellSample
+    - EnrichedCellSample
+    - BarcodedCellSample
+    - AmplifiedCdna
+    - Library
+    - LibraryAliquot
+    - LibraryPool
+    - DissectionRoiPolygon
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene or gene product
+    - gene
+    - genome
+    range: label type
+  id:
+    name: id
+    definition_uri: https://w3id.org/biolink/vocab/id
+    description: A unique identifier for an entity. Must be either a CURIE shorthand
+      for a URI or a complete URI
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - AGRKB:primaryId
+    - gff3:ID
+    - gpi:DB_Object_ID
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:id
+    identifier: true
+    alias: id
+    owner: TissueSample
+    domain_of:
+    - ontology class
+    - entity
+    - attribute
+    - named thing
+    - taxonomic rank
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    required: true
+  iri:
+    name: iri
+    definition_uri: https://w3id.org/biolink/vocab/iri
+    description: An IRI for an entity. This is determined by the id using expansion
+      rules.
+    in_subset:
+    - translator_minimal
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - WIKIDATA_PROPERTY:P854
+    rank: 1000
+    slot_uri: biolink:iri
+    alias: iri
+    owner: TissueSample
+    domain_of:
+    - attribute
+    - entity
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: iri type
+  category:
+    name: category
+    definition_uri: https://w3id.org/biolink/vocab/category
+    description: Name of the high level ontology class in which this entity is categorized.
+      Corresponds to the label for the biolink entity type class. In a neo4j database
+      this MAY correspond to the neo4j label tag. In an RDF database it should be
+      a biolink model class URI. This field is multi-valued. It should include values
+      for ancestors of the biolink class; for example, a protein such as Shh would
+      have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
+      In an RDF database, nodes will typically have an rdf:type triples. This can
+      be to the most specific biolink class, or potentially to a class more specific
+      than something in biolink. For example, a sequence feature `f` may have a rdf:type
+      assertion to a SO class such as TF_binding_site, which is more specific than
+      anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity,
+      biolink:NamedThing}
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: type
+    domain: entity
+    slot_uri: biolink:category
+    designates_type: true
+    alias: category
+    owner: TissueSample
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+    pattern: ^bican:[A-Z][A-Za-z]+$
+  type:
+    name: type
+    definition_uri: https://w3id.org/biolink/vocab/type
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    mappings:
+    - rdf:type
+    exact_mappings:
+    - gff3:type
+    - gpi:DB_Object_Type
+    rank: 1000
+    domain: entity
+    slot_uri: rdf:type
+    alias: type
+    owner: TissueSample
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  description:
+    name: description
+    definition_uri: https://w3id.org/biolink/vocab/description
+    description: a human-readable description of an entity
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - definition
+    mappings:
+    - dct:description
+    exact_mappings:
+    - IAO:0000115
+    - skos:definitions
+    narrow_mappings:
+    - gff3:Description
+    rank: 1000
+    slot_uri: dct:description
+    alias: description
+    owner: TissueSample
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: narrative text
+  has attribute:
+    name: has attribute
+    definition_uri: https://w3id.org/biolink/vocab/has_attribute
+    description: connects any entity to an attribute
+    in_subset:
+    - samples
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - SIO:000008
+    close_mappings:
+    - OBI:0001927
+    narrow_mappings:
+    - OBAN:association_has_subject_property
+    - OBAN:association_has_object_property
+    - CPT:has_possibly_included_panel_element
+    - DRUGBANK:category
+    - EFO:is_executed_in
+    - HANCESTRO:0301
+    - LOINC:has_action_guidance
+    - LOINC:has_adjustment
+    - LOINC:has_aggregation_view
+    - LOINC:has_approach_guidance
+    - LOINC:has_divisor
+    - LOINC:has_exam
+    - LOINC:has_method
+    - LOINC:has_modality_subtype
+    - LOINC:has_object_guidance
+    - LOINC:has_scale
+    - LOINC:has_suffix
+    - LOINC:has_time_aspect
+    - LOINC:has_time_modifier
+    - LOINC:has_timing_of
+    - NCIT:R88
+    - NCIT:eo_disease_has_property_or_attribute
+    - NCIT:has_data_element
+    - NCIT:has_pharmaceutical_administration_method
+    - NCIT:has_pharmaceutical_basic_dose_form
+    - NCIT:has_pharmaceutical_intended_site
+    - NCIT:has_pharmaceutical_release_characteristics
+    - NCIT:has_pharmaceutical_state_of_matter
+    - NCIT:has_pharmaceutical_transformation
+    - NCIT:is_qualified_by
+    - NCIT:qualifier_applies_to
+    - NCIT:role_has_domain
+    - NCIT:role_has_range
+    - INO:0000154
+    - HANCESTRO:0308
+    - OMIM:has_inheritance_type
+    - orphanet:C016
+    - orphanet:C017
+    - RO:0000053
+    - RO:0000086
+    - RO:0000087
+    - SNOMED:has_access
+    - SNOMED:has_clinical_course
+    - SNOMED:has_count_of_base_of_active_ingredient
+    - SNOMED:has_dose_form_administration_method
+    - SNOMED:has_dose_form_release_characteristic
+    - SNOMED:has_dose_form_transformation
+    - SNOMED:has_finding_context
+    - SNOMED:has_finding_informer
+    - SNOMED:has_inherent_attribute
+    - SNOMED:has_intent
+    - SNOMED:has_interpretation
+    - SNOMED:has_laterality
+    - SNOMED:has_measurement_method
+    - SNOMED:has_method
+    - SNOMED:has_priority
+    - SNOMED:has_procedure_context
+    - SNOMED:has_process_duration
+    - SNOMED:has_property
+    - SNOMED:has_revision_status
+    - SNOMED:has_scale_type
+    - SNOMED:has_severity
+    - SNOMED:has_specimen
+    - SNOMED:has_state_of_matter
+    - SNOMED:has_subject_relationship_context
+    - SNOMED:has_surgical_approach
+    - SNOMED:has_technique
+    - SNOMED:has_temporal_context
+    - SNOMED:has_time_aspect
+    - SNOMED:has_units
+    - UMLS:has_structural_class
+    - UMLS:has_supported_concept_property
+    - UMLS:has_supported_concept_relationship
+    - UMLS:may_be_qualified_by
+    rank: 1000
+    domain: entity
+    slot_uri: biolink:has_attribute
+    alias: has_attribute
+    owner: TissueSample
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: attribute
+    multivalued: true
+  deprecated:
+    name: deprecated
+    definition_uri: https://w3id.org/biolink/vocab/deprecated
+    description: A boolean flag indicating that an entity is no longer considered
+      current or valid.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    exact_mappings:
+    - oboInOwl:ObsoleteClass
+    rank: 1000
+    slot_uri: biolink:deprecated
+    alias: deprecated
+    owner: TissueSample
+    domain_of:
+    - entity
+    - attribute
+    - named thing
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: boolean
+  provided by:
+    name: provided by
+    definition_uri: https://w3id.org/biolink/vocab/provided_by
+    description: The value in this node property represents the knowledge provider
+      that created or assembled the node and all of its attributes.  Used internally
+      to represent how a particular node made its way into a knowledge provider or
+      graph.
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:provided_by
+    alias: provided_by
+    owner: TissueSample
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: string
+    multivalued: true
+  xref:
+    name: xref
+    definition_uri: https://w3id.org/biolink/vocab/xref
+    description: A database cross reference or alternative identifier for a NamedThing
+      or edge between two NamedThings.  This property should point to a database record
+      or webpage that supports the existence of the edge, or gives more detail about
+      the edge. This property can be used on a node or edge to provide multiple URIs
+      or CURIE cross references.
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - dbxref
+    - Dbxref
+    - DbXref
+    - record_url
+    - source_record_urls
+    narrow_mappings:
+    - gff3:Dbxref
+    - gpi:DB_Xrefs
+    rank: 1000
+    domain: named thing
+    slot_uri: biolink:xref
+    alias: xref
+    owner: TissueSample
+    domain_of:
+    - named thing
+    - gene
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - genome
+    range: uriorcurie
+    multivalued: true
+  full name:
+    name: full name
+    definition_uri: https://w3id.org/biolink/vocab/full_name
+    description: a long-form human readable name for a thing
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:full_name
+    alias: full_name
+    owner: TissueSample
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+  synonym:
+    name: synonym
+    definition_uri: https://w3id.org/biolink/vocab/synonym
+    description: Alternate human-readable names for a thing
+    in_subset:
+    - translator_minimal
+    from_schema: https://identifiers.org/brain-bican/library-generation-schema
+    aliases:
+    - alias
+    narrow_mappings:
+    - skos:altLabel
+    - gff3:Alias
+    - AGRKB:synonyms
+    - gpi:DB_Object_Synonyms
+    - HANCESTRO:0330
+    - IAO:0000136
+    - RXNORM:has_tradename
+    rank: 1000
+    is_a: node property
+    domain: named thing
+    slot_uri: biolink:synonym
+    alias: synonym
+    owner: TissueSample
+    domain_of:
+    - named thing
+    - attribute
+    - organism taxon
+    - information content entity
+    - dataset
+    - physical entity
+    - activity
+    - procedure
+    - material sample
+    - biological entity
+    - gene
+    - genome
+    range: label type
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/TissueSpecimen/index.html b/TissueSpecimen/index.html new file mode 100644 index 00000000..ad400a2a --- /dev/null +++ b/TissueSpecimen/index.html @@ -0,0 +1,602 @@ + + + + + + + + + + + + + + + + + + + Subset: TissueSpecimen - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
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+ +
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+ + + + + +
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+ + + +
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+ + + +
+
+
+ + + +
+
+ + + + + + + +

Subset: TissueSpecimen

+

A subset of classes that are associated with tissue specimens.

+

URI: TissueSpecimen

+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Classes in subset

+ + + + + + + + + + + + + + + + + +
ClassDescription
BrainSlabA thick flat piece of brain tissue obtained by slicing a whole brain, brain h...
DissectionRoiPolygonA polygon annotated on a brain slab image delineating a region of interest (R...
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/Tracking/index.html b/Tracking/index.html new file mode 100644 index 00000000..3f59906f --- /dev/null +++ b/Tracking/index.html @@ -0,0 +1,606 @@ + + + + + + + + + + + + + + + + + + + Subset: Tracking - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
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+ +
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+
+ + + +
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+ + + +
+
+
+ + + +
+
+ + + + + + + +

Subset: Tracking

+

A subset of slots/attributes that are required for tracking.

+

URI: Tracking

+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Slots in subset

+ + + + + + + + + + + + + + + + + + + + + +
SlotDescription
cell_prep_typeThe type of cell preparation
local_tube_idLibrary Pool Tube local name
r1_r2_indexName of the pair of library indexes used for sequencing
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/TranslatorMinimal/index.html b/TranslatorMinimal/index.html new file mode 100644 index 00000000..24de57ae --- /dev/null +++ b/TranslatorMinimal/index.html @@ -0,0 +1,734 @@ + + + + + + + + + + + + + + + + + + + Subset: TranslatorMinimal - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
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+ +
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+ + + +
+
+
+ + + +
+
+ + + + + + + +

Subset: TranslatorMinimal

+

Minimum subset of translator work

+

URI: TranslatorMinimal

+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Classes in subset

+ + + + + + + + + + + + + + + + + +
ClassDescription
GeneA region (or regions) that includes all of the sequence elements necessary to...
GenomicEntity
+

Slots from Gene also in translator_minimal

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescription
category*
Uriorcurie		Name of the high level ontology class in which this entity is categorized
description0..1
NarrativeText		a human-readable description of an entity
id1
String		A unique identifier for an entity identifier
in_taxon*
OrganismTaxon		connects an entity to its taxonomic classification
in_taxon_label0..1
LabelType		The human readable scientific name for the taxon of the entity
iri0..1
IriType		An IRI for an entity
name0..1
LabelType		A human-readable name for an attribute or entity
synonym*
LabelType		Alternate human-readable names for a thing
xref*
Uriorcurie		A database cross reference or alternative identifier for a NamedThing or edge...
+

Slots in subset

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
SlotDescription
attribute_nameThe human-readable 'attribute name' can be set to a string which reflects its...
categoryName of the high level ontology class in which this entity is categorized
descriptiona human-readable description of an entity
idA unique identifier for an entity
in_taxonconnects an entity to its taxonomic classification
in_taxon_labelThe human readable scientific name for the taxon of the entity
iriAn IRI for an entity
nameA human-readable name for an attribute or entity
synonymAlternate human-readable names for a thing
xrefA database cross reference or alternative identifier for a NamedThing or edge...
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/Unit/index.html b/Unit/index.html new file mode 100644 index 00000000..8e32bb3f --- /dev/null +++ b/Unit/index.html @@ -0,0 +1,630 @@ + + + + + + + + + + + + + + + + + + + Type: Unit - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
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+ + + +
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+ + + +
+
+
+ + + +
+
+ + + + + + + +

Type: Unit

+

URI: UO:0000000

+ +

Identifier and Mapping Information

+

Valid ID Prefixes

+

Instances of this class should have identifiers with one of the following prefixes:

+
    +
  • UO
    • +
+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfUO:0000000
nativebican:unit
exactqud:Unit
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/Uri/index.html b/Uri/index.html new file mode 100644 index 00000000..73cbf5c9 --- /dev/null +++ b/Uri/index.html @@ -0,0 +1,630 @@ + + + + + + + + + + + + + + + + + + + Type: Uri - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
+
+ + + +
+
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+ + + + + +
+
+
+ + + +
+
+
+ + + +
+
+
+ + + +
+
+ + + + + + + +

Type: Uri

+

a complete URI

+

URI: xsd:anyURI

+ +

Comments

+
    +
  • in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node
    • +
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfxsd:anyURI
nativebican:uri
closeschema:URL
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/Uriorcurie/index.html b/Uriorcurie/index.html new file mode 100644 index 00000000..c35e3478 --- /dev/null +++ b/Uriorcurie/index.html @@ -0,0 +1,613 @@ + + + + + + + + + + + + + + + + + + + Type: Uriorcurie - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
+ + + + + + +
+ + +
+ +
+ + + + + + +
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+ + + + + +
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+ + + +
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+ + + +
+
+
+ + + +
+
+ + + + + + + +

Type: Uriorcurie

+

a URI or a CURIE

+

URI: xsd:anyURI

+
    +
  • +

    base: URIorCURIE

    +
    • +
  • +

    uri: xsd:anyURI

    +
    • +
  • +

    repr: str

    +
    • +
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfxsd:anyURI
nativebican:uriorcurie
+ + + + + + + + + + + + + +
+
+ + + + + +
+ +
+ + + +
+
+
+
+ + + + + + + + + + \ No newline at end of file diff --git a/VersionedNamedThing/index.html b/VersionedNamedThing/index.html new file mode 100644 index 00000000..aaa5f781 --- /dev/null +++ b/VersionedNamedThing/index.html @@ -0,0 +1,603 @@ + + + + + + + + + +Class: VersionedNamedThing - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + +
+ + Skip to content + +
+
+
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+ +
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+
+
+ +
+
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+
+ +
+
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+
+
+

Class: VersionedNamedThing

+

Core base entity for Anatomical Structure schema representing an versioned named thing.

+
    +
  • NOTE: this is an abstract class and should not be instantiated directly
    • +
+

URI: AnS:VersionedNamedThing

+
classDiagram + class VersionedNamedThing + click VersionedNamedThing href "../VersionedNamedThing" + NamedThing <|-- VersionedNamedThing + click NamedThing href "../NamedThing" + + + VersionedNamedThing <|-- ImageDataset + click ImageDataset href "../ImageDataset" + VersionedNamedThing <|-- AnatomicalSpace + click AnatomicalSpace href "../AnatomicalSpace" + VersionedNamedThing <|-- ParcellationTerminology + click ParcellationTerminology href "../ParcellationTerminology" + VersionedNamedThing <|-- ParcellationColorScheme + click ParcellationColorScheme href "../ParcellationColorScheme" + VersionedNamedThing <|-- AnatomicalAnnotationSet + click AnatomicalAnnotationSet href "../AnatomicalAnnotationSet" + VersionedNamedThing <|-- ParcellationAtlas + click ParcellationAtlas href "../ParcellationAtlas" + + + VersionedNamedThing : category + + VersionedNamedThing : description + + VersionedNamedThing : id + + VersionedNamedThing : name + + VersionedNamedThing : revision_of + + + + + VersionedNamedThing --> "0..1" VersionedNamedThing : revision_of + click VersionedNamedThing href "../VersionedNamedThing" + + + VersionedNamedThing : version + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
version1
String		direct
revision_of0..1
VersionedNamedThing		direct
id1
Uriorcurie		NamedThing
name1
String		NamedThing
description1
String		NamedThing
category*
Uriorcurie		NamedThing
+

Usages

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
used byused intypeused
ImageDatasetrevision_ofrangeVersionedNamedThing
AnatomicalSpacerevision_ofrangeVersionedNamedThing
ParcellationTerminologyrevision_ofrangeVersionedNamedThing
ParcellationColorSchemerevision_ofrangeVersionedNamedThing
AnatomicalAnnotationSetrevision_ofrangeVersionedNamedThing
ParcellationAtlasrevision_ofrangeVersionedNamedThing
VersionedNamedThingrevision_ofrangeVersionedNamedThing
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://w3id.org/my-org/anatomical-structure-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfAnS:VersionedNamedThing
nativeAnS:VersionedNamedThing
+

LinkML Source

+ +

Direct

+
+
name: VersionedNamedThing
+description: Core base entity for Anatomical Structure schema representing an versioned
+  named thing.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: NamedThing
+abstract: true
+slots:
+- version
+- revision_of
+
+
+
+

Induced

+
+
name: VersionedNamedThing
+description: Core base entity for Anatomical Structure schema representing an versioned
+  named thing.
+from_schema: https://w3id.org/my-org/anatomical-structure-schema
+is_a: NamedThing
+abstract: true
+attributes:
+  version:
+    name: version
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: version
+    owner: VersionedNamedThing
+    domain_of:
+    - VersionedNamedThing
+    range: string
+    required: true
+  revision_of:
+    name: revision_of
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: revision_of
+    owner: VersionedNamedThing
+    domain_of:
+    - VersionedNamedThing
+    range: VersionedNamedThing
+  id:
+    name: id
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    identifier: true
+    alias: id
+    owner: VersionedNamedThing
+    domain_of:
+    - NamedThing
+    range: uriorcurie
+    required: true
+  name:
+    name: name
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: name
+    owner: VersionedNamedThing
+    domain_of:
+    - NamedThing
+    range: string
+    required: true
+  description:
+    name: description
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    alias: description
+    owner: VersionedNamedThing
+    domain_of:
+    - NamedThing
+    range: string
+    required: true
+  category:
+    name: category
+    from_schema: https://w3id.org/my-org/anatomical-structure-schema
+    rank: 1000
+    designates_type: true
+    alias: category
+    owner: VersionedNamedThing
+    domain_of:
+    - NamedThing
+    is_class_field: true
+    range: uriorcurie
+    multivalued: true
+
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/age_at_death_description/index.html b/age_at_death_description/index.html new file mode 100644 index 00000000..ef1943d2 --- /dev/null +++ b/age_at_death_description/index.html @@ -0,0 +1,680 @@ + + + + + + + + + + + + + + + + + + + Slot: age_at_death_description - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + Skip to content + + +
+
+ +
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+ +
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Slot: age_at_death_description

+

Text description of the age of death following typical scientific convention for the species or developmental stage. For example: P56, E11.5

+

URI: bican:0630a265-4a63-48f4-8853-66b929002306

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
DonorA person or organism that is the source of a biological sample for scientific...no
+

Properties

+ +

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:0630a265-4a63-48f4-8853-66b929002306
nativebican:age_at_death_description
exactNIMP:PD-ZJZJLE33
+

LinkML Source

+
+ +
name: age_at_death_description
+local_names:
+  NIMP:
+    local_name_source: NIMP
+    local_name_value: age_at_death_description
+description: 'Text description of the age of death following typical scientific convention
+  for the species or developmental stage. For example: P56, E11.5'
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:PD-ZJZJLE33
+rank: 1000
+slot_uri: bican:0630a265-4a63-48f4-8853-66b929002306
+alias: age_at_death_description
+owner: Donor
+domain_of:
+- Donor
+range: string
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+ + + + + + + + + + \ No newline at end of file diff --git a/age_at_death_reference_point/index.html b/age_at_death_reference_point/index.html new file mode 100644 index 00000000..e37de931 --- /dev/null +++ b/age_at_death_reference_point/index.html @@ -0,0 +1,707 @@ + + + + + + + + + + + + + + + + + + + Slot: age_at_death_reference_point - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Slot: age_at_death_reference_point

+

The reference point for an age interval; for example, birth or conception.

+

URI: bican:3bed1f94-9d82-4ed7-afdf-79d896b24dbb

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
DonorA person or organism that is the source of a biological sample for scientific...no
+

Properties

+ +

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
Donorage_at_death_reference_pointrangeage_at_death_reference_point
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:3bed1f94-9d82-4ed7-afdf-79d896b24dbb
nativebican:age_at_death_reference_point
exactNIMP:PD-RARAGG39
+

LinkML Source

+
+ +
name: age_at_death_reference_point
+local_names:
+  NIMP:
+    local_name_source: NIMP
+    local_name_value: age_at_death_reference_point
+description: The reference point for an age interval; for example, birth or conception.
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:PD-RARAGG39
+rank: 1000
+slot_uri: bican:3bed1f94-9d82-4ed7-afdf-79d896b24dbb
+alias: age_at_death_reference_point
+owner: Donor
+domain_of:
+- Donor
+range: age_at_death_reference_point
+
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+ + + + + + + + + + \ No newline at end of file diff --git a/age_at_death_unit/index.html b/age_at_death_unit/index.html new file mode 100644 index 00000000..0a7bbc7d --- /dev/null +++ b/age_at_death_unit/index.html @@ -0,0 +1,707 @@ + + + + + + + + + + + + + + + + + + + Slot: age_at_death_unit - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Slot: age_at_death_unit

+

The unit used for representing the donor age from the reference point.

+

URI: bican:b5436e99-f0a7-4c30-825d-56b88ee2ac1d

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
DonorA person or organism that is the source of a biological sample for scientific...no
+

Properties

+ +

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
Donorage_at_death_unitrangeage_at_death_unit
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:b5436e99-f0a7-4c30-825d-56b88ee2ac1d
nativebican:age_at_death_unit
exactNIMP:PD-AVAVEV39
+

LinkML Source

+
+ +
name: age_at_death_unit
+local_names:
+  NIMP:
+    local_name_source: NIMP
+    local_name_value: age_at_death_unit
+description: The unit used for representing the donor age from the reference point.
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:PD-AVAVEV39
+rank: 1000
+slot_uri: bican:b5436e99-f0a7-4c30-825d-56b88ee2ac1d
+alias: age_at_death_unit
+owner: Donor
+domain_of:
+- Donor
+range: age_at_death_unit
+
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+ + + + + + + + + + \ No newline at end of file diff --git a/age_at_death_value/index.html b/age_at_death_value/index.html new file mode 100644 index 00000000..ffe6c344 --- /dev/null +++ b/age_at_death_value/index.html @@ -0,0 +1,679 @@ + + + + + + + + + + + + + + + + + + + Slot: age_at_death_value - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Slot: age_at_death_value

+

The value representing the donor age from the reference point.

+

URI: bican:57e24d3c-c9c7-4ef3-9809-a35802d563ec

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
DonorA person or organism that is the source of a biological sample for scientific...no
+

Properties

+ +

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:57e24d3c-c9c7-4ef3-9809-a35802d563ec
nativebican:age_at_death_value
exactNIMP:PD-FTFTCP24
+

LinkML Source

+
+ +
name: age_at_death_value
+local_names:
+  NIMP:
+    local_name_source: NIMP
+    local_name_value: age_at_death
+description: The value representing the donor age from the reference point.
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:PD-FTFTCP24
+rank: 1000
+slot_uri: bican:57e24d3c-c9c7-4ef3-9809-a35802d563ec
+alias: age_at_death_value
+owner: Donor
+domain_of:
+- Donor
+range: float
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+ + + + + + + + + + \ No newline at end of file diff --git a/anatomical-structure-schema/index.html b/anatomical-structure-schema/index.html new file mode 100644 index 00000000..85f5fff2 --- /dev/null +++ b/anatomical-structure-schema/index.html @@ -0,0 +1,537 @@ + + + + + + + + + + + + + + + + + + + anatomical-structure-schema - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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anatomical-structure-schema

+

The Anatomical Structure schema is designed to represent types and relationships of anatomical brain structures.

+

URI: https://w3id.org/my-org/anatomical-structure-schema

+ + + + + + + + + + + + + +
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Anatomical Structure

+
erDiagram +NamedThing { + uriorcurie id + string name + string description + uriorcurieList category +} +VersionedNamedThing { + string version + uriorcurie id + string name + string description + uriorcurieList category +} +ImageDataset { + ANATOMICAL_DIRECTION x_direction + ANATOMICAL_DIRECTION y_direction + ANATOMICAL_DIRECTION z_direction + integer x_size + integer y_size + integer z_size + float x_resolution + float y_resolution + float z_resolution + DISTANCE_UNIT unit + string version + uriorcurie id + string name + string description + uriorcurieList category +} +AnatomicalSpace { + string measures + string version + uriorcurie id + string name + string description + uriorcurieList category +} +ParcellationTerminology { + string version + uriorcurie id + string name + string description + uriorcurieList category +} +ParcellationTermSet { + string part_of_parcellation_terminology + integer ordinal + string has_parent_parcellation_term_set + uriorcurie id + string name + string description + uriorcurieList category +} +ParcellationTerm { + string symbol + string part_of_parcellation_term_set + integer ordinal + string has_parent_parcellation_term + uriorcurie id + string name + string description + uriorcurieList category +} +ParcellationColorScheme { + string subject_parcellation_terminology + string version + uriorcurie id + string name + string description + uriorcurieList category +} +ParcellationColorAssignment { + string part_of_parcellation_color_scheme + string subject_parcellation_term + string color +} +AnatomicalAnnotationSet { + string parameterizes + string version + uriorcurie id + string name + string description + uriorcurieList category +} +ParcellationAnnotation { + string part_of_anatomical_annotation_set + string internal_identifier + integer voxel_count +} +ParcellationAnnotationTermMap { + string subject_parcellation_annotation + string subject_parcellation_term +} +ParcellationAtlas { + string has_anatomical_space + string has_anatomical_annotation_set + string has_parcellation_terminology + string specialization_of + string version + uriorcurie id + string name + string description + uriorcurieList category +} + +VersionedNamedThing ||--|o VersionedNamedThing : "revision_of" +ImageDataset ||--|o VersionedNamedThing : "revision_of" +AnatomicalSpace ||--|o VersionedNamedThing : "revision_of" +ParcellationTerminology ||--|o VersionedNamedThing : "revision_of" +ParcellationColorScheme ||--|o VersionedNamedThing : "revision_of" +AnatomicalAnnotationSet ||--|o VersionedNamedThing : "revision_of" +ParcellationAtlas ||--|o VersionedNamedThing : "revision_of" + +
+
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+ + + + \ No newline at end of file diff --git a/annotates/index.html b/annotates/index.html new file mode 100644 index 00000000..fbc5e3e1 --- /dev/null +++ b/annotates/index.html @@ -0,0 +1,674 @@ + + + + + + + + + + + + + + + + + + + Slot: annotates - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Slot: annotates

+

The brain slab that was annotated by the delineation process.

+

URI: bican:annotates

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
DissectionRoiPolygonA polygon annotated on a brain slab image delineating a region of interest (R...no
+

Properties

+ +

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/library-generation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:annotates
nativebican:annotates
exactNIMP:has_parent
+

LinkML Source

+
+ +
name: annotates
+description: The brain slab that was annotated by the delineation process.
+from_schema: https://identifiers.org/brain-bican/library-generation-schema
+exact_mappings:
+- NIMP:has_parent
+rank: 1000
+alias: annotates
+owner: DissectionRoiPolygon
+domain_of:
+- DissectionRoiPolygon
+range: BrainSlab
+
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+ + + + + + + + + + \ No newline at end of file diff --git a/annotations/index.html b/annotations/index.html new file mode 100644 index 00000000..20b014a4 --- /dev/null +++ b/annotations/index.html @@ -0,0 +1,674 @@ + + + + + + + + + + + + + + + + + + + Slot: annotations - BICAN Knowledge Graph Models Documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Slot: annotations

+

URI: bican:annotations

+ + +

Applicable Classes

+ + + + + + + + + + + + + + + +
NameDescriptionModifies Slot
AnnotationCollectionno
+

Properties

+ +

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://identifiers.org/brain-bican/genome-annotation-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfbican:annotations
nativebican:annotations
+

LinkML Source

+
+ +
name: annotations
+from_schema: https://identifiers.org/brain-bican/genome-annotation-schema
+rank: 1000
+alias: annotations
+owner: annotation collection
+domain_of:
+- annotation collection
+range: gene annotation
+multivalued: true
+inlined: true
+inlined_as_list: true
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circle{fill:var(--md-mermaid-label-bg-color)}.actor{fill:var(--md-mermaid-sequence-actor-bg-color);stroke:var(--md-mermaid-sequence-actor-border-color)}text.actor>tspan{fill:var(--md-mermaid-sequence-actor-fg-color);font-family:var(--md-mermaid-font-family)}line{stroke:var(--md-mermaid-sequence-actor-line-color)}.actor-man circle,.actor-man line{fill:var(--md-mermaid-sequence-actorman-bg-color);stroke:var(--md-mermaid-sequence-actorman-line-color)}.messageLine0,.messageLine1{stroke:var(--md-mermaid-sequence-message-line-color)}.note{fill:var(--md-mermaid-sequence-note-bg-color);stroke:var(--md-mermaid-sequence-note-border-color)}.loopText,.loopText>tspan,.messageText,.noteText>tspan{stroke:none;font-family:var(--md-mermaid-font-family)!important}.messageText{fill:var(--md-mermaid-sequence-message-fg-color)}.loopText,.loopText>tspan{fill:var(--md-mermaid-sequence-loop-fg-color)}.noteText>tspan{fill:var(--md-mermaid-sequence-note-fg-color)}#arrowhead 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l=R(`label[for="${c.id}"]`);l.replaceChildren(x("a",{href:`#${l.htmlFor}`,tabIndex:-1},...Array.from(l.childNodes))),h(l.firstElementChild,"click").pipe(W(p),b(f=>!(f.metaKey||f.ctrlKey)),w(f=>{f.preventDefault(),f.stopPropagation()})).subscribe(()=>{history.replaceState({},"",`#${l.htmlFor}`),l.click()})}return B("content.tabs.link")&&s.pipe(Ce(1),re(t)).subscribe(([{active:c},{offset:l}])=>{let f=c.innerText.trim();if(c.hasAttribute("data-md-switching"))c.removeAttribute("data-md-switching");else{let u=e.offsetTop-l.y;for(let y of P("[data-tabs]"))for(let L of P(":scope > input",y)){let X=R(`label[for="${L.id}"]`);if(X!==c&&X.innerText.trim()===f){X.setAttribute("data-md-switching",""),L.click();break}}window.scrollTo({top:e.offsetTop-u});let d=__md_get("__tabs")||[];__md_set("__tabs",[...new Set([f,...d])])}}),s.pipe(W(p)).subscribe(()=>{for(let c of P("audio, video",e))c.pause()}),Ya(n).pipe(w(c=>s.next(c)),_(()=>s.complete()),m(c=>$({ref:e},c)))}).pipe(Ke(se))}function zn(e,{viewport$:t,target$:r,print$:o}){return O(...P(".annotate:not(.highlight)",e).map(n=>Pn(n,{target$:r,print$:o})),...P("pre:not(.mermaid) > code",e).map(n=>jn(n,{target$:r,print$:o})),...P("pre.mermaid",e).map(n=>Wn(n)),...P("table:not([class])",e).map(n=>Vn(n)),...P("details",e).map(n=>Fn(n,{target$:r,print$:o})),...P("[data-tabs]",e).map(n=>Nn(n,{viewport$:t,target$:r})),...P("[title]",e).filter(()=>B("content.tooltips")).map(n=>mt(n,{viewport$:t})))}function Ba(e,{alert$:t}){return t.pipe(v(r=>O(I(!0),I(!1).pipe(Ge(2e3))).pipe(m(o=>({message:r,active:o})))))}function qn(e,t){let r=R(".md-typeset",e);return C(()=>{let o=new g;return o.subscribe(({message:n,active:i})=>{e.classList.toggle("md-dialog--active",i),r.textContent=n}),Ba(e,t).pipe(w(n=>o.next(n)),_(()=>o.complete()),m(n=>$({ref:e},n)))})}var Ga=0;function Ja(e,t){document.body.append(e);let{width:r}=ce(e);e.style.setProperty("--md-tooltip-width",`${r}px`),e.remove();let o=cr(t),n=typeof 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Xa({viewport$:e}){if(!B("header.autohide"))return I(!1);let t=e.pipe(m(({offset:{y:n}})=>n),Be(2,1),m(([n,i])=>[nMath.abs(i-n.y)>100),m(([,[n]])=>n),K()),o=ze("search");return z([e,o]).pipe(m(([{offset:n},i])=>n.y>400&&!i),K(),v(n=>n?r:I(!1)),Q(!1))}function Kn(e,t){return C(()=>z([ge(e),Xa(t)])).pipe(m(([{height:r},o])=>({height:r,hidden:o})),K((r,o)=>r.height===o.height&&r.hidden===o.hidden),G(1))}function Yn(e,{header$:t,main$:r}){return C(()=>{let o=new g,n=o.pipe(Z(),ie(!0));o.pipe(ee("active"),He(t)).subscribe(([{active:a},{hidden:s}])=>{e.classList.toggle("md-header--shadow",a&&!s),e.hidden=s});let i=ue(P("[title]",e)).pipe(b(()=>B("content.tooltips")),ne(a=>Qn(a)));return r.subscribe(o),t.pipe(W(n),m(a=>$({ref:e},a)),Re(i.pipe(W(n))))})}function Za(e,{viewport$:t,header$:r}){return mr(e,{viewport$:t,header$:r}).pipe(m(({offset:{y:o}})=>{let{height:n}=ce(e);return{active:o>=n}}),ee("active"))}function Bn(e,t){return C(()=>{let r=new g;r.subscribe({next({active:n}){e.classList.toggle("md-header__title--active",n)},complete(){e.classList.remove("md-header__title--active")}});let o=fe(".md-content h1");return typeof o=="undefined"?S:Za(o,t).pipe(w(n=>r.next(n)),_(()=>r.complete()),m(n=>$({ref:e},n)))})}function Gn(e,{viewport$:t,header$:r}){let o=r.pipe(m(({height:i})=>i),K()),n=o.pipe(v(()=>ge(e).pipe(m(({height:i})=>({top:e.offsetTop,bottom:e.offsetTop+i})),ee("bottom"))));return z([o,n,t]).pipe(m(([i,{top:a,bottom:s},{offset:{y:p},size:{height:c}}])=>(c=Math.max(0,c-Math.max(0,a-p,i)-Math.max(0,c+p-s)),{offset:a-i,height:c,active:a-i<=p})),K((i,a)=>i.offset===a.offset&&i.height===a.height&&i.active===a.active))}function es(e){let t=__md_get("__palette")||{index:e.findIndex(o=>matchMedia(o.getAttribute("data-md-color-media")).matches)},r=Math.max(0,Math.min(t.index,e.length-1));return 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g,n=on(e.parentElement).pipe(b(Boolean)),i=e.parentElement,a=R(":scope > :first-child",e),s=R(":scope > :last-child",e);ze("search").subscribe(l=>s.setAttribute("role",l?"list":"presentation")),o.pipe(re(r),Wr(t.pipe(Ae(jt)))).subscribe(([{items:l},{value:f}])=>{switch(l.length){case 0:a.textContent=f.length?Ee("search.result.none"):Ee("search.result.placeholder");break;case 1:a.textContent=Ee("search.result.one");break;default:let u=sr(l.length);a.textContent=Ee("search.result.other",u)}});let p=o.pipe(w(()=>s.innerHTML=""),v(({items:l})=>O(I(...l.slice(0,10)),I(...l.slice(10)).pipe(Be(4),Vr(n),v(([f])=>f)))),m(Mn),pe());return p.subscribe(l=>s.appendChild(l)),p.pipe(ne(l=>{let f=fe("details",l);return typeof f=="undefined"?S:h(f,"toggle").pipe(W(o),m(()=>f))})).subscribe(l=>{l.open===!1&&l.offsetTop<=i.scrollTop&&i.scrollTo({top:l.offsetTop})}),t.pipe(b(dr),m(({data:l})=>l)).pipe(w(l=>o.next(l)),_(()=>o.complete()),m(l=>$({ref:e},l)))}function ms(e,{query$:t}){return t.pipe(m(({value:r})=>{let o=ye();return o.hash="",r=r.replace(/\s+/g,"+").replace(/&/g,"%26").replace(/=/g,"%3D"),o.search=`q=${r}`,{url:o}}))}function mi(e,t){let r=new g,o=r.pipe(Z(),ie(!0));return r.subscribe(({url:n})=>{e.setAttribute("data-clipboard-text",e.href),e.href=`${n}`}),h(e,"click").pipe(W(o)).subscribe(n=>n.preventDefault()),ms(e,t).pipe(w(n=>r.next(n)),_(()=>r.complete()),m(n=>$({ref:e},n)))}function fi(e,{worker$:t,keyboard$:r}){let o=new g,n=Se("search-query"),i=O(h(n,"keydown"),h(n,"focus")).pipe(ve(se),m(()=>n.value),K());return o.pipe(He(i),m(([{suggest:s},p])=>{let c=p.split(/([\s-]+)/);if(s!=null&&s.length&&c[c.length-1]){let l=s[s.length-1];l.startsWith(c[c.length-1])&&(c[c.length-1]=l)}else c.length=0;return c})).subscribe(s=>e.innerHTML=s.join("").replace(/\s/g," ")),r.pipe(b(({mode:s})=>s==="search")).subscribe(s=>{switch(s.type){case"ArrowRight":e.innerText.length&&n.selectionStart===n.value.length&&(n.value=e.innerText);break}}),t.pipe(b(dr),m(({data:s})=>s)).pipe(w(s=>o.next(s)),_(()=>o.complete()),m(()=>({ref:e})))}function ui(e,{index$:t,keyboard$:r}){let o=xe();try{let n=ai(o.search,t),i=Se("search-query",e),a=Se("search-result",e);h(e,"click").pipe(b(({target:p})=>p instanceof Element&&!!p.closest("a"))).subscribe(()=>Je("search",!1)),r.pipe(b(({mode:p})=>p==="search")).subscribe(p=>{let c=Ie();switch(p.type){case"Enter":if(c===i){let l=new Map;for(let f of P(":first-child [href]",a)){let u=f.firstElementChild;l.set(f,parseFloat(u.getAttribute("data-md-score")))}if(l.size){let[[f]]=[...l].sort(([,u],[,d])=>d-u);f.click()}p.claim()}break;case"Escape":case"Tab":Je("search",!1),i.blur();break;case"ArrowUp":case"ArrowDown":if(typeof c=="undefined")i.focus();else{let l=[i,...P(":not(details) > [href], summary, details[open] [href]",a)],f=Math.max(0,(Math.max(0,l.indexOf(c))+l.length+(p.type==="ArrowUp"?-1:1))%l.length);l[f].focus()}p.claim();break;default:i!==Ie()&&i.focus()}}),r.pipe(b(({mode:p})=>p==="global")).subscribe(p=>{switch(p.type){case"f":case"s":case"/":i.focus(),i.select(),p.claim();break}});let s=pi(i,{worker$:n});return O(s,li(a,{worker$:n,query$:s})).pipe(Re(...ae("search-share",e).map(p=>mi(p,{query$:s})),...ae("search-suggest",e).map(p=>fi(p,{worker$:n,keyboard$:r}))))}catch(n){return e.hidden=!0,Ye}}function di(e,{index$:t,location$:r}){return z([t,r.pipe(Q(ye()),b(o=>!!o.searchParams.get("h")))]).pipe(m(([o,n])=>ii(o.config)(n.searchParams.get("h"))),m(o=>{var a;let n=new Map,i=document.createNodeIterator(e,NodeFilter.SHOW_TEXT);for(let s=i.nextNode();s;s=i.nextNode())if((a=s.parentElement)!=null&&a.offsetHeight){let p=s.textContent,c=o(p);c.length>p.length&&n.set(s,c)}for(let[s,p]of n){let{childNodes:c}=x("span",null,p);s.replaceWith(...Array.from(c))}return{ref:e,nodes:n}}))}function fs(e,{viewport$:t,main$:r}){let o=e.closest(".md-grid"),n=o.offsetTop-o.parentElement.offsetTop;return z([r,t]).pipe(m(([{offset:i,height:a},{offset:{y:s}}])=>(a=a+Math.min(n,Math.max(0,s-i))-n,{height:a,locked:s>=i+n})),K((i,a)=>i.height===a.height&&i.locked===a.locked))}function Zr(e,o){var n=o,{header$:t}=n,r=so(n,["header$"]);let i=R(".md-sidebar__scrollwrap",e),{y:a}=Ve(i);return C(()=>{let s=new g,p=s.pipe(Z(),ie(!0)),c=s.pipe(Me(0,me));return c.pipe(re(t)).subscribe({next([{height:l},{height:f}]){i.style.height=`${l-2*a}px`,e.style.top=`${f}px`},complete(){i.style.height="",e.style.top=""}}),c.pipe(Ae()).subscribe(()=>{for(let l of P(".md-nav__link--active[href]",e)){if(!l.clientHeight)continue;let f=l.closest(".md-sidebar__scrollwrap");if(typeof f!="undefined"){let u=l.offsetTop-f.offsetTop,{height:d}=ce(f);f.scrollTo({top:u-d/2})}}}),ue(P("label[tabindex]",e)).pipe(ne(l=>h(l,"click").pipe(ve(se),m(()=>l),W(p)))).subscribe(l=>{let f=R(`[id="${l.htmlFor}"]`);R(`[aria-labelledby="${l.id}"]`).setAttribute("aria-expanded",`${f.checked}`)}),fs(e,r).pipe(w(l=>s.next(l)),_(()=>s.complete()),m(l=>$({ref:e},l)))})}function hi(e,t){if(typeof t!="undefined"){let r=`https://api.github.com/repos/${e}/${t}`;return st(je(`${r}/releases/latest`).pipe(de(()=>S),m(o=>({version:o.tag_name})),De({})),je(r).pipe(de(()=>S),m(o=>({stars:o.stargazers_count,forks:o.forks_count})),De({}))).pipe(m(([o,n])=>$($({},o),n)))}else{let r=`https://api.github.com/users/${e}`;return je(r).pipe(m(o=>({repositories:o.public_repos})),De({}))}}function bi(e,t){let r=`https://${e}/api/v4/projects/${encodeURIComponent(t)}`;return st(je(`${r}/releases/permalink/latest`).pipe(de(()=>S),m(({tag_name:o})=>({version:o})),De({})),je(r).pipe(de(()=>S),m(({star_count:o,forks_count:n})=>({stars:o,forks:n})),De({}))).pipe(m(([o,n])=>$($({},o),n)))}function vi(e){let t=e.match(/^.+github\.com\/([^/]+)\/?([^/]+)?/i);if(t){let[,r,o]=t;return hi(r,o)}if(t=e.match(/^.+?([^/]*gitlab[^/]+)\/(.+?)\/?$/i),t){let[,r,o]=t;return bi(r,o)}return S}var us;function ds(e){return us||(us=C(()=>{let t=__md_get("__source",sessionStorage);if(t)return I(t);if(ae("consent").length){let o=__md_get("__consent");if(!(o&&o.github))return S}return vi(e.href).pipe(w(o=>__md_set("__source",o,sessionStorage)))}).pipe(de(()=>S),b(t=>Object.keys(t).length>0),m(t=>({facts:t})),G(1)))}function gi(e){let t=R(":scope > :last-child",e);return C(()=>{let r=new g;return r.subscribe(({facts:o})=>{t.appendChild(_n(o)),t.classList.add("md-source__repository--active")}),ds(e).pipe(w(o=>r.next(o)),_(()=>r.complete()),m(o=>$({ref:e},o)))})}function hs(e,{viewport$:t,header$:r}){return ge(document.body).pipe(v(()=>mr(e,{header$:r,viewport$:t})),m(({offset:{y:o}})=>({hidden:o>=10})),ee("hidden"))}function yi(e,t){return C(()=>{let r=new g;return r.subscribe({next({hidden:o}){e.hidden=o},complete(){e.hidden=!1}}),(B("navigation.tabs.sticky")?I({hidden:!1}):hs(e,t)).pipe(w(o=>r.next(o)),_(()=>r.complete()),m(o=>$({ref:e},o)))})}function bs(e,{viewport$:t,header$:r}){let o=new Map,n=P(".md-nav__link",e);for(let s of n){let p=decodeURIComponent(s.hash.substring(1)),c=fe(`[id="${p}"]`);typeof c!="undefined"&&o.set(s,c)}let i=r.pipe(ee("height"),m(({height:s})=>{let p=Se("main"),c=R(":scope > :first-child",p);return s+.8*(c.offsetTop-p.offsetTop)}),pe());return ge(document.body).pipe(ee("height"),v(s=>C(()=>{let p=[];return I([...o].reduce((c,[l,f])=>{for(;p.length&&o.get(p[p.length-1]).tagName>=f.tagName;)p.pop();let u=f.offsetTop;for(;!u&&f.parentElement;)f=f.parentElement,u=f.offsetTop;let d=f.offsetParent;for(;d;d=d.offsetParent)u+=d.offsetTop;return c.set([...p=[...p,l]].reverse(),u)},new Map))}).pipe(m(p=>new Map([...p].sort(([,c],[,l])=>c-l))),He(i),v(([p,c])=>t.pipe(Fr(([l,f],{offset:{y:u},size:d})=>{let y=u+d.height>=Math.floor(s.height);for(;f.length;){let[,L]=f[0];if(L-c=u&&!y)f=[l.pop(),...f];else break}return[l,f]},[[],[...p]]),K((l,f)=>l[0]===f[0]&&l[1]===f[1])))))).pipe(m(([s,p])=>({prev:s.map(([c])=>c),next:p.map(([c])=>c)})),Q({prev:[],next:[]}),Be(2,1),m(([s,p])=>s.prev.length{let i=new g,a=i.pipe(Z(),ie(!0));if(i.subscribe(({prev:s,next:p})=>{for(let[c]of p)c.classList.remove("md-nav__link--passed"),c.classList.remove("md-nav__link--active");for(let[c,[l]]of s.entries())l.classList.add("md-nav__link--passed"),l.classList.toggle("md-nav__link--active",c===s.length-1)}),B("toc.follow")){let s=O(t.pipe(_e(1),m(()=>{})),t.pipe(_e(250),m(()=>"smooth")));i.pipe(b(({prev:p})=>p.length>0),He(o.pipe(ve(se))),re(s)).subscribe(([[{prev:p}],c])=>{let[l]=p[p.length-1];if(l.offsetHeight){let f=cr(l);if(typeof f!="undefined"){let u=l.offsetTop-f.offsetTop,{height:d}=ce(f);f.scrollTo({top:u-d/2,behavior:c})}}})}return B("navigation.tracking")&&t.pipe(W(a),ee("offset"),_e(250),Ce(1),W(n.pipe(Ce(1))),ct({delay:250}),re(i)).subscribe(([,{prev:s}])=>{let p=ye(),c=s[s.length-1];if(c&&c.length){let[l]=c,{hash:f}=new URL(l.href);p.hash!==f&&(p.hash=f,history.replaceState({},"",`${p}`))}else p.hash="",history.replaceState({},"",`${p}`)}),bs(e,{viewport$:t,header$:r}).pipe(w(s=>i.next(s)),_(()=>i.complete()),m(s=>$({ref:e},s)))})}function vs(e,{viewport$:t,main$:r,target$:o}){let n=t.pipe(m(({offset:{y:a}})=>a),Be(2,1),m(([a,s])=>a>s&&s>0),K()),i=r.pipe(m(({active:a})=>a));return z([i,n]).pipe(m(([a,s])=>!(a&&s)),K(),W(o.pipe(Ce(1))),ie(!0),ct({delay:250}),m(a=>({hidden:a})))}function Ei(e,{viewport$:t,header$:r,main$:o,target$:n}){let i=new g,a=i.pipe(Z(),ie(!0));return i.subscribe({next({hidden:s}){e.hidden=s,s?(e.setAttribute("tabindex","-1"),e.blur()):e.removeAttribute("tabindex")},complete(){e.style.top="",e.hidden=!0,e.removeAttribute("tabindex")}}),r.pipe(W(a),ee("height")).subscribe(({height:s})=>{e.style.top=`${s+16}px`}),h(e,"click").subscribe(s=>{s.preventDefault(),window.scrollTo({top:0})}),vs(e,{viewport$:t,main$:o,target$:n}).pipe(w(s=>i.next(s)),_(()=>i.complete()),m(s=>$({ref:e},s)))}function wi({document$:e,viewport$:t}){e.pipe(v(()=>P(".md-ellipsis")),ne(r=>tt(r).pipe(W(e.pipe(Ce(1))),b(o=>o),m(()=>r),Te(1))),b(r=>r.offsetWidth{let o=r.innerText,n=r.closest("a")||r;return n.title=o,B("content.tooltips")?mt(n,{viewport$:t}).pipe(W(e.pipe(Ce(1))),_(()=>n.removeAttribute("title"))):S})).subscribe(),B("content.tooltips")&&e.pipe(v(()=>P(".md-status")),ne(r=>mt(r,{viewport$:t}))).subscribe()}function Ti({document$:e,tablet$:t}){e.pipe(v(()=>P(".md-toggle--indeterminate")),w(r=>{r.indeterminate=!0,r.checked=!1}),ne(r=>h(r,"change").pipe(Dr(()=>r.classList.contains("md-toggle--indeterminate")),m(()=>r))),re(t)).subscribe(([r,o])=>{r.classList.remove("md-toggle--indeterminate"),o&&(r.checked=!1)})}function gs(){return/(iPad|iPhone|iPod)/.test(navigator.userAgent)}function Si({document$:e}){e.pipe(v(()=>P("[data-md-scrollfix]")),w(t=>t.removeAttribute("data-md-scrollfix")),b(gs),ne(t=>h(t,"touchstart").pipe(m(()=>t)))).subscribe(t=>{let r=t.scrollTop;r===0?t.scrollTop=1:r+t.offsetHeight===t.scrollHeight&&(t.scrollTop=r-1)})}function Oi({viewport$:e,tablet$:t}){z([ze("search"),t]).pipe(m(([r,o])=>r&&!o),v(r=>I(r).pipe(Ge(r?400:100))),re(e)).subscribe(([r,{offset:{y:o}}])=>{if(r)document.body.setAttribute("data-md-scrolllock",""),document.body.style.top=`-${o}px`;else{let 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URL("search/search_index.js",eo.base)}`).pipe(m(()=>__index),G(1)):je(new URL("search/search_index.json",eo.base))}document.documentElement.classList.remove("no-js");document.documentElement.classList.add("js");var ot=Go(),Ut=sn(),Lt=ln(Ut),to=an(),Oe=gn(),hr=Pt("(min-width: 960px)"),Mi=Pt("(min-width: 1220px)"),_i=mn(),eo=xe(),Ai=document.forms.namedItem("search")?ys():Ye,ro=new g;Zn({alert$:ro});var oo=new g;B("navigation.instant")&&oi({location$:Ut,viewport$:Oe,progress$:oo}).subscribe(ot);var Li;((Li=eo.version)==null?void 0:Li.provider)==="mike"&&ci({document$:ot});O(Ut,Lt).pipe(Ge(125)).subscribe(()=>{Je("drawer",!1),Je("search",!1)});to.pipe(b(({mode:e})=>e==="global")).subscribe(e=>{switch(e.type){case"p":case",":let t=fe("link[rel=prev]");typeof t!="undefined"&<(t);break;case"n":case".":let r=fe("link[rel=next]");typeof r!="undefined"&<(r);break;case"Enter":let o=Ie();o instanceof 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rt=Kn(Se("header"),{viewport$:Oe}),Ft=ot.pipe(m(()=>Se("main")),v(e=>Gn(e,{viewport$:Oe,header$:rt})),G(1)),xs=O(...ae("consent").map(e=>En(e,{target$:Lt})),...ae("dialog").map(e=>qn(e,{alert$:ro})),...ae("header").map(e=>Yn(e,{viewport$:Oe,header$:rt,main$:Ft})),...ae("palette").map(e=>Jn(e)),...ae("progress").map(e=>Xn(e,{progress$:oo})),...ae("search").map(e=>ui(e,{index$:Ai,keyboard$:to})),...ae("source").map(e=>gi(e))),Es=C(()=>O(...ae("announce").map(e=>xn(e)),...ae("content").map(e=>zn(e,{viewport$:Oe,target$:Lt,print$:_i})),...ae("content").map(e=>B("search.highlight")?di(e,{index$:Ai,location$:Ut}):S),...ae("header-title").map(e=>Bn(e,{viewport$:Oe,header$:rt})),...ae("sidebar").map(e=>e.getAttribute("data-md-type")==="navigation"?Nr(Mi,()=>Zr(e,{viewport$:Oe,header$:rt,main$:Ft})):Nr(hr,()=>Zr(e,{viewport$:Oe,header$:rt,main$:Ft}))),...ae("tabs").map(e=>yi(e,{viewport$:Oe,header$:rt})),...ae("toc").map(e=>xi(e,{viewport$:Oe,header$:rt,main$:Ft,target$:Lt})),...ae("top").map(e=>Ei(e,{viewport$:Oe,header$:rt,main$:Ft,target$:Lt})))),Ci=ot.pipe(v(()=>Es),Re(xs),G(1));Ci.subscribe();window.document$=ot;window.location$=Ut;window.target$=Lt;window.keyboard$=to;window.viewport$=Oe;window.tablet$=hr;window.screen$=Mi;window.print$=_i;window.alert$=ro;window.progress$=oo;window.component$=Ci;})(); +//# sourceMappingURL=bundle.525ec568.min.js.map + diff --git a/assets/javascripts/bundle.525ec568.min.js.map b/assets/javascripts/bundle.525ec568.min.js.map new file mode 100644 index 00000000..ef5d8d34 --- /dev/null +++ b/assets/javascripts/bundle.525ec568.min.js.map @@ -0,0 +1,7 @@ +{ + "version": 3, + "sources": ["node_modules/focus-visible/dist/focus-visible.js", "node_modules/escape-html/index.js", "node_modules/clipboard/dist/clipboard.js", "src/templates/assets/javascripts/bundle.ts", "node_modules/tslib/tslib.es6.mjs", "node_modules/rxjs/src/internal/util/isFunction.ts", "node_modules/rxjs/src/internal/util/createErrorClass.ts", "node_modules/rxjs/src/internal/util/UnsubscriptionError.ts", "node_modules/rxjs/src/internal/util/arrRemove.ts", "node_modules/rxjs/src/internal/Subscription.ts", "node_modules/rxjs/src/internal/config.ts", "node_modules/rxjs/src/internal/scheduler/timeoutProvider.ts", "node_modules/rxjs/src/internal/util/reportUnhandledError.ts", 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"src/templates/assets/javascripts/components/search/suggest/index.ts", "src/templates/assets/javascripts/components/search/_/index.ts", "src/templates/assets/javascripts/components/search/highlight/index.ts", "src/templates/assets/javascripts/components/sidebar/index.ts", "src/templates/assets/javascripts/components/source/facts/github/index.ts", "src/templates/assets/javascripts/components/source/facts/gitlab/index.ts", "src/templates/assets/javascripts/components/source/facts/_/index.ts", "src/templates/assets/javascripts/components/source/_/index.ts", "src/templates/assets/javascripts/components/tabs/index.ts", "src/templates/assets/javascripts/components/toc/index.ts", "src/templates/assets/javascripts/components/top/index.ts", "src/templates/assets/javascripts/patches/ellipsis/index.ts", "src/templates/assets/javascripts/patches/indeterminate/index.ts", "src/templates/assets/javascripts/patches/scrollfix/index.ts", "src/templates/assets/javascripts/patches/scrolllock/index.ts", "src/templates/assets/javascripts/polyfills/index.ts"], + "sourcesContent": ["(function (global, factory) {\n typeof exports === 'object' && typeof module !== 'undefined' ? factory() :\n typeof define === 'function' && define.amd ? define(factory) :\n (factory());\n}(this, (function () { 'use strict';\n\n /**\n * Applies the :focus-visible polyfill at the given scope.\n * A scope in this case is either the top-level Document or a Shadow Root.\n *\n * @param {(Document|ShadowRoot)} scope\n * @see https://github.com/WICG/focus-visible\n */\n function applyFocusVisiblePolyfill(scope) {\n var hadKeyboardEvent = true;\n var hadFocusVisibleRecently = false;\n var hadFocusVisibleRecentlyTimeout = null;\n\n var inputTypesAllowlist = {\n text: true,\n search: true,\n url: true,\n tel: true,\n email: true,\n password: true,\n number: true,\n date: true,\n month: true,\n week: true,\n time: true,\n datetime: true,\n 'datetime-local': true\n };\n\n /**\n * Helper function for legacy browsers and iframes which sometimes focus\n * elements like document, body, and non-interactive SVG.\n * @param {Element} el\n */\n function isValidFocusTarget(el) {\n if (\n el &&\n el !== document &&\n el.nodeName !== 'HTML' &&\n el.nodeName !== 'BODY' &&\n 'classList' in el &&\n 'contains' in el.classList\n ) {\n return true;\n }\n return false;\n }\n\n /**\n * Computes whether the given element should automatically trigger the\n * `focus-visible` class being added, i.e. whether it should always match\n * `:focus-visible` when focused.\n * @param {Element} el\n * @return {boolean}\n */\n function focusTriggersKeyboardModality(el) {\n var type = el.type;\n var tagName = el.tagName;\n\n if (tagName === 'INPUT' && inputTypesAllowlist[type] && !el.readOnly) {\n return true;\n }\n\n if (tagName === 'TEXTAREA' && !el.readOnly) {\n return true;\n }\n\n if (el.isContentEditable) {\n return true;\n }\n\n return false;\n }\n\n /**\n * Add the `focus-visible` class to the given element if it was not added by\n * the author.\n * @param {Element} el\n */\n function addFocusVisibleClass(el) {\n if (el.classList.contains('focus-visible')) {\n return;\n }\n el.classList.add('focus-visible');\n el.setAttribute('data-focus-visible-added', '');\n }\n\n /**\n * Remove the `focus-visible` class from the given element if it was not\n * originally added by the author.\n * @param {Element} el\n */\n function removeFocusVisibleClass(el) {\n if (!el.hasAttribute('data-focus-visible-added')) {\n return;\n }\n el.classList.remove('focus-visible');\n el.removeAttribute('data-focus-visible-added');\n }\n\n /**\n * If the most recent user interaction was via the keyboard;\n * and the key press did not include a meta, alt/option, or control key;\n * then the modality is keyboard. Otherwise, the modality is not keyboard.\n * Apply `focus-visible` to any current active element and keep track\n * of our keyboard modality state with `hadKeyboardEvent`.\n * @param {KeyboardEvent} e\n */\n function onKeyDown(e) {\n if (e.metaKey || e.altKey || e.ctrlKey) {\n return;\n }\n\n if (isValidFocusTarget(scope.activeElement)) {\n addFocusVisibleClass(scope.activeElement);\n }\n\n hadKeyboardEvent = true;\n }\n\n /**\n * If at any point a user clicks with a pointing device, ensure that we change\n * the modality away from keyboard.\n * This avoids the situation where a user presses a key on an already focused\n * element, and then clicks on a different element, focusing it with a\n * pointing device, while we still think we're in keyboard modality.\n * @param {Event} e\n */\n function onPointerDown(e) {\n hadKeyboardEvent = false;\n }\n\n /**\n * On `focus`, add the `focus-visible` class to the target if:\n * - the target received focus as a result of keyboard navigation, or\n * - the event target is an element that will likely require interaction\n * via the keyboard (e.g. a text box)\n * @param {Event} e\n */\n function onFocus(e) {\n // Prevent IE from focusing the document or HTML element.\n if (!isValidFocusTarget(e.target)) {\n return;\n }\n\n if (hadKeyboardEvent || focusTriggersKeyboardModality(e.target)) {\n addFocusVisibleClass(e.target);\n }\n }\n\n /**\n * On `blur`, remove the `focus-visible` class from the target.\n * @param {Event} e\n */\n function onBlur(e) {\n if (!isValidFocusTarget(e.target)) {\n return;\n }\n\n if (\n e.target.classList.contains('focus-visible') ||\n e.target.hasAttribute('data-focus-visible-added')\n ) {\n // To detect a tab/window switch, we look for a blur event followed\n // rapidly by a visibility change.\n // If we don't see a visibility change within 100ms, it's probably a\n // regular focus change.\n hadFocusVisibleRecently = true;\n window.clearTimeout(hadFocusVisibleRecentlyTimeout);\n hadFocusVisibleRecentlyTimeout = window.setTimeout(function() {\n hadFocusVisibleRecently = false;\n }, 100);\n removeFocusVisibleClass(e.target);\n }\n }\n\n /**\n * If the user changes tabs, keep track of whether or not the previously\n * focused element had .focus-visible.\n * @param {Event} e\n */\n function onVisibilityChange(e) {\n if (document.visibilityState === 'hidden') {\n // If the tab becomes active again, the browser will handle calling focus\n // on the element (Safari actually calls it twice).\n // If this tab change caused a blur on an element with focus-visible,\n // re-apply the class when the user switches back to the tab.\n if (hadFocusVisibleRecently) {\n hadKeyboardEvent = true;\n }\n addInitialPointerMoveListeners();\n }\n }\n\n /**\n * Add a group of listeners to detect usage of any pointing devices.\n * These listeners will be added when the polyfill first loads, and anytime\n * the window is blurred, so that they are active when the window regains\n * focus.\n */\n function addInitialPointerMoveListeners() {\n document.addEventListener('mousemove', onInitialPointerMove);\n document.addEventListener('mousedown', onInitialPointerMove);\n document.addEventListener('mouseup', onInitialPointerMove);\n document.addEventListener('pointermove', onInitialPointerMove);\n document.addEventListener('pointerdown', onInitialPointerMove);\n document.addEventListener('pointerup', onInitialPointerMove);\n document.addEventListener('touchmove', onInitialPointerMove);\n document.addEventListener('touchstart', onInitialPointerMove);\n document.addEventListener('touchend', onInitialPointerMove);\n }\n\n function removeInitialPointerMoveListeners() {\n document.removeEventListener('mousemove', onInitialPointerMove);\n document.removeEventListener('mousedown', onInitialPointerMove);\n document.removeEventListener('mouseup', onInitialPointerMove);\n document.removeEventListener('pointermove', onInitialPointerMove);\n document.removeEventListener('pointerdown', onInitialPointerMove);\n document.removeEventListener('pointerup', onInitialPointerMove);\n document.removeEventListener('touchmove', onInitialPointerMove);\n document.removeEventListener('touchstart', onInitialPointerMove);\n document.removeEventListener('touchend', onInitialPointerMove);\n }\n\n /**\n * When the polfyill first loads, assume the user is in keyboard modality.\n * If any event is received from a pointing device (e.g. mouse, pointer,\n * touch), turn off keyboard modality.\n * This accounts for situations where focus enters the page from the URL bar.\n * @param {Event} e\n */\n function onInitialPointerMove(e) {\n // Work around a Safari quirk that fires a mousemove on whenever the\n // window blurs, even if you're tabbing out of the page. \u00AF\\_(\u30C4)_/\u00AF\n if (e.target.nodeName && e.target.nodeName.toLowerCase() === 'html') {\n return;\n }\n\n hadKeyboardEvent = false;\n removeInitialPointerMoveListeners();\n }\n\n // For some kinds of state, we are interested in changes at the global scope\n // only. For example, global pointer input, global key presses and global\n // visibility change should affect the state at every scope:\n document.addEventListener('keydown', onKeyDown, true);\n document.addEventListener('mousedown', onPointerDown, true);\n document.addEventListener('pointerdown', onPointerDown, true);\n document.addEventListener('touchstart', onPointerDown, true);\n document.addEventListener('visibilitychange', onVisibilityChange, true);\n\n addInitialPointerMoveListeners();\n\n // For focus and blur, we specifically care about state changes in the local\n // scope. This is because focus / blur events that originate from within a\n // shadow root are not re-dispatched from the host element if it was already\n // the active element in its own scope:\n scope.addEventListener('focus', onFocus, true);\n scope.addEventListener('blur', onBlur, true);\n\n // We detect that a node is a ShadowRoot by ensuring that it is a\n // DocumentFragment and also has a host property. This check covers native\n // implementation and polyfill implementation transparently. If we only cared\n // about the native implementation, we could just check if the scope was\n // an instance of a ShadowRoot.\n if (scope.nodeType === Node.DOCUMENT_FRAGMENT_NODE && scope.host) {\n // Since a ShadowRoot is a special kind of DocumentFragment, it does not\n // have a root element to add a class to. So, we add this attribute to the\n // host element instead:\n scope.host.setAttribute('data-js-focus-visible', '');\n } else if (scope.nodeType === Node.DOCUMENT_NODE) {\n document.documentElement.classList.add('js-focus-visible');\n document.documentElement.setAttribute('data-js-focus-visible', '');\n }\n }\n\n // It is important to wrap all references to global window and document in\n // these checks to support server-side rendering use cases\n // @see https://github.com/WICG/focus-visible/issues/199\n if (typeof window !== 'undefined' && typeof document !== 'undefined') {\n // Make the polyfill helper globally available. This can be used as a signal\n // to interested libraries that wish to coordinate with the polyfill for e.g.,\n // applying the polyfill to a shadow root:\n window.applyFocusVisiblePolyfill = applyFocusVisiblePolyfill;\n\n // Notify interested libraries of the polyfill's presence, in case the\n // polyfill was loaded lazily:\n var event;\n\n try {\n event = new CustomEvent('focus-visible-polyfill-ready');\n } catch (error) {\n // IE11 does not support using CustomEvent as a constructor directly:\n event = document.createEvent('CustomEvent');\n event.initCustomEvent('focus-visible-polyfill-ready', false, false, {});\n }\n\n window.dispatchEvent(event);\n }\n\n if (typeof document !== 'undefined') {\n // Apply the polyfill to the global document, so that no JavaScript\n // coordination is required to use the polyfill in the top-level document:\n applyFocusVisiblePolyfill(document);\n }\n\n})));\n", "/*!\n * escape-html\n * Copyright(c) 2012-2013 TJ Holowaychuk\n * Copyright(c) 2015 Andreas Lubbe\n * Copyright(c) 2015 Tiancheng \"Timothy\" Gu\n * MIT Licensed\n */\n\n'use strict';\n\n/**\n * Module variables.\n * @private\n */\n\nvar matchHtmlRegExp = /[\"'&<>]/;\n\n/**\n * Module exports.\n * @public\n */\n\nmodule.exports = escapeHtml;\n\n/**\n * Escape special characters in the given string of html.\n *\n * @param {string} string The string to escape for inserting into HTML\n * @return {string}\n * @public\n */\n\nfunction escapeHtml(string) {\n var str = '' + string;\n var match = matchHtmlRegExp.exec(str);\n\n if (!match) {\n return str;\n }\n\n var escape;\n var html = '';\n var index = 0;\n var lastIndex = 0;\n\n for (index = match.index; index < str.length; index++) {\n switch (str.charCodeAt(index)) {\n case 34: // \"\n escape = '"';\n break;\n case 38: // &\n escape = '&';\n break;\n case 39: // '\n escape = ''';\n break;\n case 60: // <\n escape = '<';\n break;\n case 62: // >\n escape = '>';\n break;\n default:\n continue;\n }\n\n if (lastIndex !== index) {\n html += str.substring(lastIndex, index);\n }\n\n lastIndex = index + 1;\n html += escape;\n }\n\n return lastIndex !== index\n ? html + str.substring(lastIndex, index)\n : html;\n}\n", "/*!\n * clipboard.js v2.0.11\n * https://clipboardjs.com/\n *\n * Licensed MIT \u00A9 Zeno Rocha\n */\n(function webpackUniversalModuleDefinition(root, factory) {\n\tif(typeof exports === 'object' && typeof module === 'object')\n\t\tmodule.exports = factory();\n\telse if(typeof define === 'function' && define.amd)\n\t\tdefine([], factory);\n\telse if(typeof exports === 'object')\n\t\texports[\"ClipboardJS\"] = factory();\n\telse\n\t\troot[\"ClipboardJS\"] = factory();\n})(this, function() {\nreturn /******/ (function() { // webpackBootstrap\n/******/ \tvar __webpack_modules__ = ({\n\n/***/ 686:\n/***/ (function(__unused_webpack_module, __webpack_exports__, __webpack_require__) {\n\n\"use strict\";\n\n// EXPORTS\n__webpack_require__.d(__webpack_exports__, {\n \"default\": function() { return /* binding */ clipboard; }\n});\n\n// EXTERNAL MODULE: ./node_modules/tiny-emitter/index.js\nvar tiny_emitter = __webpack_require__(279);\nvar tiny_emitter_default = /*#__PURE__*/__webpack_require__.n(tiny_emitter);\n// EXTERNAL MODULE: ./node_modules/good-listener/src/listen.js\nvar listen = __webpack_require__(370);\nvar listen_default = /*#__PURE__*/__webpack_require__.n(listen);\n// EXTERNAL MODULE: ./node_modules/select/src/select.js\nvar src_select = __webpack_require__(817);\nvar select_default = /*#__PURE__*/__webpack_require__.n(src_select);\n;// CONCATENATED MODULE: ./src/common/command.js\n/**\n * Executes a given operation type.\n * @param {String} type\n * @return {Boolean}\n */\nfunction command(type) {\n try {\n return document.execCommand(type);\n } catch (err) {\n return false;\n }\n}\n;// CONCATENATED MODULE: ./src/actions/cut.js\n\n\n/**\n * Cut action wrapper.\n * @param {String|HTMLElement} target\n * @return {String}\n */\n\nvar ClipboardActionCut = function ClipboardActionCut(target) {\n var selectedText = select_default()(target);\n command('cut');\n return selectedText;\n};\n\n/* harmony default export */ var actions_cut = (ClipboardActionCut);\n;// CONCATENATED MODULE: ./src/common/create-fake-element.js\n/**\n * Creates a fake textarea element with a value.\n * @param {String} value\n * @return {HTMLElement}\n */\nfunction createFakeElement(value) {\n var isRTL = document.documentElement.getAttribute('dir') === 'rtl';\n var fakeElement = document.createElement('textarea'); // Prevent zooming on iOS\n\n fakeElement.style.fontSize = '12pt'; // Reset box model\n\n fakeElement.style.border = '0';\n fakeElement.style.padding = '0';\n fakeElement.style.margin = '0'; // Move element out of screen horizontally\n\n fakeElement.style.position = 'absolute';\n fakeElement.style[isRTL ? 'right' : 'left'] = '-9999px'; // Move element to the same position vertically\n\n var yPosition = window.pageYOffset || document.documentElement.scrollTop;\n fakeElement.style.top = \"\".concat(yPosition, \"px\");\n fakeElement.setAttribute('readonly', '');\n fakeElement.value = value;\n return fakeElement;\n}\n;// CONCATENATED MODULE: ./src/actions/copy.js\n\n\n\n/**\n * Create fake copy action wrapper using a fake element.\n * @param {String} target\n * @param {Object} options\n * @return {String}\n */\n\nvar fakeCopyAction = function fakeCopyAction(value, options) {\n var fakeElement = createFakeElement(value);\n options.container.appendChild(fakeElement);\n var selectedText = select_default()(fakeElement);\n command('copy');\n fakeElement.remove();\n return selectedText;\n};\n/**\n * Copy action wrapper.\n * @param {String|HTMLElement} target\n * @param {Object} options\n * @return {String}\n */\n\n\nvar ClipboardActionCopy = function ClipboardActionCopy(target) {\n var options = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {\n container: document.body\n };\n var selectedText = '';\n\n if (typeof target === 'string') {\n selectedText = fakeCopyAction(target, options);\n } else if (target instanceof HTMLInputElement && !['text', 'search', 'url', 'tel', 'password'].includes(target === null || target === void 0 ? void 0 : target.type)) {\n // If input type doesn't support `setSelectionRange`. Simulate it. https://developer.mozilla.org/en-US/docs/Web/API/HTMLInputElement/setSelectionRange\n selectedText = fakeCopyAction(target.value, options);\n } else {\n selectedText = select_default()(target);\n command('copy');\n }\n\n return selectedText;\n};\n\n/* harmony default export */ var actions_copy = (ClipboardActionCopy);\n;// CONCATENATED MODULE: ./src/actions/default.js\nfunction _typeof(obj) { \"@babel/helpers - typeof\"; if (typeof Symbol === \"function\" && typeof Symbol.iterator === \"symbol\") { _typeof = function _typeof(obj) { return typeof obj; }; } else { _typeof = function _typeof(obj) { return obj && typeof Symbol === \"function\" && obj.constructor === Symbol && obj !== Symbol.prototype ? \"symbol\" : typeof obj; }; } return _typeof(obj); }\n\n\n\n/**\n * Inner function which performs selection from either `text` or `target`\n * properties and then executes copy or cut operations.\n * @param {Object} options\n */\n\nvar ClipboardActionDefault = function ClipboardActionDefault() {\n var options = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};\n // Defines base properties passed from constructor.\n var _options$action = options.action,\n action = _options$action === void 0 ? 'copy' : _options$action,\n container = options.container,\n target = options.target,\n text = options.text; // Sets the `action` to be performed which can be either 'copy' or 'cut'.\n\n if (action !== 'copy' && action !== 'cut') {\n throw new Error('Invalid \"action\" value, use either \"copy\" or \"cut\"');\n } // Sets the `target` property using an element that will be have its content copied.\n\n\n if (target !== undefined) {\n if (target && _typeof(target) === 'object' && target.nodeType === 1) {\n if (action === 'copy' && target.hasAttribute('disabled')) {\n throw new Error('Invalid \"target\" attribute. Please use \"readonly\" instead of \"disabled\" attribute');\n }\n\n if (action === 'cut' && (target.hasAttribute('readonly') || target.hasAttribute('disabled'))) {\n throw new Error('Invalid \"target\" attribute. You can\\'t cut text from elements with \"readonly\" or \"disabled\" attributes');\n }\n } else {\n throw new Error('Invalid \"target\" value, use a valid Element');\n }\n } // Define selection strategy based on `text` property.\n\n\n if (text) {\n return actions_copy(text, {\n container: container\n });\n } // Defines which selection strategy based on `target` property.\n\n\n if (target) {\n return action === 'cut' ? actions_cut(target) : actions_copy(target, {\n container: container\n });\n }\n};\n\n/* harmony default export */ var actions_default = (ClipboardActionDefault);\n;// CONCATENATED MODULE: ./src/clipboard.js\nfunction clipboard_typeof(obj) { \"@babel/helpers - typeof\"; if (typeof Symbol === \"function\" && typeof Symbol.iterator === \"symbol\") { clipboard_typeof = function _typeof(obj) { return typeof obj; }; } else { clipboard_typeof = function _typeof(obj) { return obj && typeof Symbol === \"function\" && obj.constructor === Symbol && obj !== Symbol.prototype ? \"symbol\" : typeof obj; }; } return clipboard_typeof(obj); }\n\nfunction _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError(\"Cannot call a class as a function\"); } }\n\nfunction _defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if (\"value\" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } }\n\nfunction _createClass(Constructor, protoProps, staticProps) { if (protoProps) _defineProperties(Constructor.prototype, protoProps); if (staticProps) _defineProperties(Constructor, staticProps); return Constructor; }\n\nfunction _inherits(subClass, superClass) { if (typeof superClass !== \"function\" && superClass !== null) { throw new TypeError(\"Super expression must either be null or a function\"); } subClass.prototype = Object.create(superClass && superClass.prototype, { constructor: { value: subClass, writable: true, configurable: true } }); if (superClass) _setPrototypeOf(subClass, superClass); }\n\nfunction _setPrototypeOf(o, p) { _setPrototypeOf = Object.setPrototypeOf || function _setPrototypeOf(o, p) { o.__proto__ = p; return o; }; return _setPrototypeOf(o, p); }\n\nfunction _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = _getPrototypeOf(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = _getPrototypeOf(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return _possibleConstructorReturn(this, result); }; }\n\nfunction _possibleConstructorReturn(self, call) { if (call && (clipboard_typeof(call) === \"object\" || typeof call === \"function\")) { return call; } return _assertThisInitialized(self); }\n\nfunction _assertThisInitialized(self) { if (self === void 0) { throw new ReferenceError(\"this hasn't been initialised - super() hasn't been called\"); } return self; }\n\nfunction _isNativeReflectConstruct() { if (typeof Reflect === \"undefined\" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === \"function\") return true; try { Date.prototype.toString.call(Reflect.construct(Date, [], function () {})); return true; } catch (e) { return false; } }\n\nfunction _getPrototypeOf(o) { _getPrototypeOf = Object.setPrototypeOf ? Object.getPrototypeOf : function _getPrototypeOf(o) { return o.__proto__ || Object.getPrototypeOf(o); }; return _getPrototypeOf(o); }\n\n\n\n\n\n\n/**\n * Helper function to retrieve attribute value.\n * @param {String} suffix\n * @param {Element} element\n */\n\nfunction getAttributeValue(suffix, element) {\n var attribute = \"data-clipboard-\".concat(suffix);\n\n if (!element.hasAttribute(attribute)) {\n return;\n }\n\n return element.getAttribute(attribute);\n}\n/**\n * Base class which takes one or more elements, adds event listeners to them,\n * and instantiates a new `ClipboardAction` on each click.\n */\n\n\nvar Clipboard = /*#__PURE__*/function (_Emitter) {\n _inherits(Clipboard, _Emitter);\n\n var _super = _createSuper(Clipboard);\n\n /**\n * @param {String|HTMLElement|HTMLCollection|NodeList} trigger\n * @param {Object} options\n */\n function Clipboard(trigger, options) {\n var _this;\n\n _classCallCheck(this, Clipboard);\n\n _this = _super.call(this);\n\n _this.resolveOptions(options);\n\n _this.listenClick(trigger);\n\n return _this;\n }\n /**\n * Defines if attributes would be resolved using internal setter functions\n * or custom functions that were passed in the constructor.\n * @param {Object} options\n */\n\n\n _createClass(Clipboard, [{\n key: \"resolveOptions\",\n value: function resolveOptions() {\n var options = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};\n this.action = typeof options.action === 'function' ? options.action : this.defaultAction;\n this.target = typeof options.target === 'function' ? options.target : this.defaultTarget;\n this.text = typeof options.text === 'function' ? options.text : this.defaultText;\n this.container = clipboard_typeof(options.container) === 'object' ? options.container : document.body;\n }\n /**\n * Adds a click event listener to the passed trigger.\n * @param {String|HTMLElement|HTMLCollection|NodeList} trigger\n */\n\n }, {\n key: \"listenClick\",\n value: function listenClick(trigger) {\n var _this2 = this;\n\n this.listener = listen_default()(trigger, 'click', function (e) {\n return _this2.onClick(e);\n });\n }\n /**\n * Defines a new `ClipboardAction` on each click event.\n * @param {Event} e\n */\n\n }, {\n key: \"onClick\",\n value: function onClick(e) {\n var trigger = e.delegateTarget || e.currentTarget;\n var action = this.action(trigger) || 'copy';\n var text = actions_default({\n action: action,\n container: this.container,\n target: this.target(trigger),\n text: this.text(trigger)\n }); // Fires an event based on the copy operation result.\n\n this.emit(text ? 'success' : 'error', {\n action: action,\n text: text,\n trigger: trigger,\n clearSelection: function clearSelection() {\n if (trigger) {\n trigger.focus();\n }\n\n window.getSelection().removeAllRanges();\n }\n });\n }\n /**\n * Default `action` lookup function.\n * @param {Element} trigger\n */\n\n }, {\n key: \"defaultAction\",\n value: function defaultAction(trigger) {\n return getAttributeValue('action', trigger);\n }\n /**\n * Default `target` lookup function.\n * @param {Element} trigger\n */\n\n }, {\n key: \"defaultTarget\",\n value: function defaultTarget(trigger) {\n var selector = getAttributeValue('target', trigger);\n\n if (selector) {\n return document.querySelector(selector);\n }\n }\n /**\n * Allow fire programmatically a copy action\n * @param {String|HTMLElement} target\n * @param {Object} options\n * @returns Text copied.\n */\n\n }, {\n key: \"defaultText\",\n\n /**\n * Default `text` lookup function.\n * @param {Element} trigger\n */\n value: function defaultText(trigger) {\n return getAttributeValue('text', trigger);\n }\n /**\n * Destroy lifecycle.\n */\n\n }, {\n key: \"destroy\",\n value: function destroy() {\n this.listener.destroy();\n }\n }], [{\n key: \"copy\",\n value: function copy(target) {\n var options = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {\n container: document.body\n };\n return actions_copy(target, options);\n }\n /**\n * Allow fire programmatically a cut action\n * @param {String|HTMLElement} target\n * @returns Text cutted.\n */\n\n }, {\n key: \"cut\",\n value: function cut(target) {\n return actions_cut(target);\n }\n /**\n * Returns the support of the given action, or all actions if no action is\n * given.\n * @param {String} [action]\n */\n\n }, {\n key: \"isSupported\",\n value: function isSupported() {\n var action = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : ['copy', 'cut'];\n var actions = typeof action === 'string' ? [action] : action;\n var support = !!document.queryCommandSupported;\n actions.forEach(function (action) {\n support = support && !!document.queryCommandSupported(action);\n });\n return support;\n }\n }]);\n\n return Clipboard;\n}((tiny_emitter_default()));\n\n/* harmony default export */ var clipboard = (Clipboard);\n\n/***/ }),\n\n/***/ 828:\n/***/ (function(module) {\n\nvar DOCUMENT_NODE_TYPE = 9;\n\n/**\n * A polyfill for Element.matches()\n */\nif (typeof Element !== 'undefined' && !Element.prototype.matches) {\n var proto = Element.prototype;\n\n proto.matches = proto.matchesSelector ||\n proto.mozMatchesSelector ||\n proto.msMatchesSelector ||\n proto.oMatchesSelector ||\n proto.webkitMatchesSelector;\n}\n\n/**\n * Finds the closest parent that matches a selector.\n *\n * @param {Element} element\n * @param {String} selector\n * @return {Function}\n */\nfunction closest (element, selector) {\n while (element && element.nodeType !== DOCUMENT_NODE_TYPE) {\n if (typeof element.matches === 'function' &&\n element.matches(selector)) {\n return element;\n }\n element = element.parentNode;\n }\n}\n\nmodule.exports = closest;\n\n\n/***/ }),\n\n/***/ 438:\n/***/ (function(module, __unused_webpack_exports, __webpack_require__) {\n\nvar closest = __webpack_require__(828);\n\n/**\n * Delegates event to a selector.\n *\n * @param {Element} element\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @param {Boolean} useCapture\n * @return {Object}\n */\nfunction _delegate(element, selector, type, callback, useCapture) {\n var listenerFn = listener.apply(this, arguments);\n\n element.addEventListener(type, listenerFn, useCapture);\n\n return {\n destroy: function() {\n element.removeEventListener(type, listenerFn, useCapture);\n }\n }\n}\n\n/**\n * Delegates event to a selector.\n *\n * @param {Element|String|Array} [elements]\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @param {Boolean} useCapture\n * @return {Object}\n */\nfunction delegate(elements, selector, type, callback, useCapture) {\n // Handle the regular Element usage\n if (typeof elements.addEventListener === 'function') {\n return _delegate.apply(null, arguments);\n }\n\n // Handle Element-less usage, it defaults to global delegation\n if (typeof type === 'function') {\n // Use `document` as the first parameter, then apply arguments\n // This is a short way to .unshift `arguments` without running into deoptimizations\n return _delegate.bind(null, document).apply(null, arguments);\n }\n\n // Handle Selector-based usage\n if (typeof elements === 'string') {\n elements = document.querySelectorAll(elements);\n }\n\n // Handle Array-like based usage\n return Array.prototype.map.call(elements, function (element) {\n return _delegate(element, selector, type, callback, useCapture);\n });\n}\n\n/**\n * Finds closest match and invokes callback.\n *\n * @param {Element} element\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @return {Function}\n */\nfunction listener(element, selector, type, callback) {\n return function(e) {\n e.delegateTarget = closest(e.target, selector);\n\n if (e.delegateTarget) {\n callback.call(element, e);\n }\n }\n}\n\nmodule.exports = delegate;\n\n\n/***/ }),\n\n/***/ 879:\n/***/ (function(__unused_webpack_module, exports) {\n\n/**\n * Check if argument is a HTML element.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.node = function(value) {\n return value !== undefined\n && value instanceof HTMLElement\n && value.nodeType === 1;\n};\n\n/**\n * Check if argument is a list of HTML elements.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.nodeList = function(value) {\n var type = Object.prototype.toString.call(value);\n\n return value !== undefined\n && (type === '[object NodeList]' || type === '[object HTMLCollection]')\n && ('length' in value)\n && (value.length === 0 || exports.node(value[0]));\n};\n\n/**\n * Check if argument is a string.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.string = function(value) {\n return typeof value === 'string'\n || value instanceof String;\n};\n\n/**\n * Check if argument is a function.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.fn = function(value) {\n var type = Object.prototype.toString.call(value);\n\n return type === '[object Function]';\n};\n\n\n/***/ }),\n\n/***/ 370:\n/***/ (function(module, __unused_webpack_exports, __webpack_require__) {\n\nvar is = __webpack_require__(879);\nvar delegate = __webpack_require__(438);\n\n/**\n * Validates all params and calls the right\n * listener function based on its target type.\n *\n * @param {String|HTMLElement|HTMLCollection|NodeList} target\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listen(target, type, callback) {\n if (!target && !type && !callback) {\n throw new Error('Missing required arguments');\n }\n\n if (!is.string(type)) {\n throw new TypeError('Second argument must be a String');\n }\n\n if (!is.fn(callback)) {\n throw new TypeError('Third argument must be a Function');\n }\n\n if (is.node(target)) {\n return listenNode(target, type, callback);\n }\n else if (is.nodeList(target)) {\n return listenNodeList(target, type, callback);\n }\n else if (is.string(target)) {\n return listenSelector(target, type, callback);\n }\n else {\n throw new TypeError('First argument must be a String, HTMLElement, HTMLCollection, or NodeList');\n }\n}\n\n/**\n * Adds an event listener to a HTML element\n * and returns a remove listener function.\n *\n * @param {HTMLElement} node\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listenNode(node, type, callback) {\n node.addEventListener(type, callback);\n\n return {\n destroy: function() {\n node.removeEventListener(type, callback);\n }\n }\n}\n\n/**\n * Add an event listener to a list of HTML elements\n * and returns a remove listener function.\n *\n * @param {NodeList|HTMLCollection} nodeList\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listenNodeList(nodeList, type, callback) {\n Array.prototype.forEach.call(nodeList, function(node) {\n node.addEventListener(type, callback);\n });\n\n return {\n destroy: function() {\n Array.prototype.forEach.call(nodeList, function(node) {\n node.removeEventListener(type, callback);\n });\n }\n }\n}\n\n/**\n * Add an event listener to a selector\n * and returns a remove listener function.\n *\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listenSelector(selector, type, callback) {\n return delegate(document.body, selector, type, callback);\n}\n\nmodule.exports = listen;\n\n\n/***/ }),\n\n/***/ 817:\n/***/ (function(module) {\n\nfunction select(element) {\n var selectedText;\n\n if (element.nodeName === 'SELECT') {\n element.focus();\n\n selectedText = element.value;\n }\n else if (element.nodeName === 'INPUT' || element.nodeName === 'TEXTAREA') {\n var isReadOnly = element.hasAttribute('readonly');\n\n if (!isReadOnly) {\n element.setAttribute('readonly', '');\n }\n\n element.select();\n element.setSelectionRange(0, element.value.length);\n\n if (!isReadOnly) {\n element.removeAttribute('readonly');\n }\n\n selectedText = element.value;\n }\n else {\n if (element.hasAttribute('contenteditable')) {\n element.focus();\n }\n\n var selection = window.getSelection();\n var range = document.createRange();\n\n range.selectNodeContents(element);\n selection.removeAllRanges();\n selection.addRange(range);\n\n selectedText = selection.toString();\n }\n\n return selectedText;\n}\n\nmodule.exports = select;\n\n\n/***/ }),\n\n/***/ 279:\n/***/ (function(module) {\n\nfunction E () {\n // Keep this empty so it's easier to inherit from\n // (via https://github.com/lipsmack from https://github.com/scottcorgan/tiny-emitter/issues/3)\n}\n\nE.prototype = {\n on: function (name, callback, ctx) {\n var e = this.e || (this.e = {});\n\n (e[name] || (e[name] = [])).push({\n fn: callback,\n ctx: ctx\n });\n\n return this;\n },\n\n once: function (name, callback, ctx) {\n var self = this;\n function listener () {\n self.off(name, listener);\n callback.apply(ctx, arguments);\n };\n\n listener._ = callback\n return this.on(name, listener, ctx);\n },\n\n emit: function (name) {\n var data = [].slice.call(arguments, 1);\n var evtArr = ((this.e || (this.e = {}))[name] || []).slice();\n var i = 0;\n var len = evtArr.length;\n\n for (i; i < len; i++) {\n evtArr[i].fn.apply(evtArr[i].ctx, data);\n }\n\n return this;\n },\n\n off: function (name, callback) {\n var e = this.e || (this.e = {});\n var evts = e[name];\n var liveEvents = [];\n\n if (evts && callback) {\n for (var i = 0, len = evts.length; i < len; i++) {\n if (evts[i].fn !== callback && evts[i].fn._ !== callback)\n liveEvents.push(evts[i]);\n }\n }\n\n // Remove event from queue to prevent memory leak\n // Suggested by https://github.com/lazd\n // Ref: https://github.com/scottcorgan/tiny-emitter/commit/c6ebfaa9bc973b33d110a84a307742b7cf94c953#commitcomment-5024910\n\n (liveEvents.length)\n ? e[name] = liveEvents\n : delete e[name];\n\n return this;\n }\n};\n\nmodule.exports = E;\nmodule.exports.TinyEmitter = E;\n\n\n/***/ })\n\n/******/ \t});\n/************************************************************************/\n/******/ \t// The module cache\n/******/ \tvar __webpack_module_cache__ = {};\n/******/ \t\n/******/ \t// The require function\n/******/ \tfunction __webpack_require__(moduleId) {\n/******/ \t\t// Check if module is in cache\n/******/ \t\tif(__webpack_module_cache__[moduleId]) {\n/******/ \t\t\treturn __webpack_module_cache__[moduleId].exports;\n/******/ \t\t}\n/******/ \t\t// Create a new module (and put it into the cache)\n/******/ \t\tvar module = __webpack_module_cache__[moduleId] = {\n/******/ \t\t\t// no module.id needed\n/******/ \t\t\t// no module.loaded needed\n/******/ \t\t\texports: {}\n/******/ \t\t};\n/******/ \t\n/******/ \t\t// Execute the module function\n/******/ \t\t__webpack_modules__[moduleId](module, module.exports, __webpack_require__);\n/******/ \t\n/******/ \t\t// Return the exports of the module\n/******/ \t\treturn module.exports;\n/******/ \t}\n/******/ \t\n/************************************************************************/\n/******/ \t/* webpack/runtime/compat get default export */\n/******/ \t!function() {\n/******/ \t\t// getDefaultExport function for compatibility with non-harmony modules\n/******/ \t\t__webpack_require__.n = function(module) {\n/******/ \t\t\tvar getter = module && module.__esModule ?\n/******/ \t\t\t\tfunction() { return module['default']; } :\n/******/ \t\t\t\tfunction() { return module; };\n/******/ \t\t\t__webpack_require__.d(getter, { a: getter });\n/******/ \t\t\treturn getter;\n/******/ \t\t};\n/******/ \t}();\n/******/ \t\n/******/ \t/* webpack/runtime/define property getters */\n/******/ \t!function() {\n/******/ \t\t// define getter functions for harmony exports\n/******/ \t\t__webpack_require__.d = function(exports, definition) {\n/******/ \t\t\tfor(var key in definition) {\n/******/ \t\t\t\tif(__webpack_require__.o(definition, key) && !__webpack_require__.o(exports, key)) {\n/******/ \t\t\t\t\tObject.defineProperty(exports, key, { enumerable: true, get: definition[key] });\n/******/ \t\t\t\t}\n/******/ \t\t\t}\n/******/ \t\t};\n/******/ \t}();\n/******/ \t\n/******/ \t/* webpack/runtime/hasOwnProperty shorthand */\n/******/ \t!function() {\n/******/ \t\t__webpack_require__.o = function(obj, prop) { return Object.prototype.hasOwnProperty.call(obj, prop); }\n/******/ \t}();\n/******/ \t\n/************************************************************************/\n/******/ \t// module exports must be returned from runtime so entry inlining is disabled\n/******/ \t// startup\n/******/ \t// Load entry module and return exports\n/******/ \treturn __webpack_require__(686);\n/******/ })()\n.default;\n});", "/*\n * Copyright (c) 2016-2024 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport \"focus-visible\"\n\nimport {\n EMPTY,\n NEVER,\n Observable,\n Subject,\n defer,\n delay,\n filter,\n map,\n merge,\n mergeWith,\n shareReplay,\n switchMap\n} from \"rxjs\"\n\nimport { configuration, feature } from \"./_\"\nimport {\n at,\n getActiveElement,\n getOptionalElement,\n requestJSON,\n setLocation,\n setToggle,\n watchDocument,\n watchKeyboard,\n watchLocation,\n watchLocationTarget,\n watchMedia,\n watchPrint,\n watchScript,\n watchViewport\n} from \"./browser\"\nimport {\n getComponentElement,\n getComponentElements,\n mountAnnounce,\n mountBackToTop,\n mountConsent,\n mountContent,\n mountDialog,\n mountHeader,\n mountHeaderTitle,\n mountPalette,\n mountProgress,\n mountSearch,\n mountSearchHiglight,\n mountSidebar,\n mountSource,\n mountTableOfContents,\n mountTabs,\n watchHeader,\n watchMain\n} from \"./components\"\nimport {\n SearchIndex,\n setupClipboardJS,\n setupInstantNavigation,\n setupVersionSelector\n} from \"./integrations\"\nimport {\n patchEllipsis,\n patchIndeterminate,\n patchScrollfix,\n patchScrolllock\n} from \"./patches\"\nimport \"./polyfills\"\n\n/* ----------------------------------------------------------------------------\n * Functions - @todo refactor\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch search index\n *\n * @returns Search index observable\n */\nfunction fetchSearchIndex(): Observable {\n if (location.protocol === \"file:\") {\n return watchScript(\n `${new URL(\"search/search_index.js\", config.base)}`\n )\n .pipe(\n // @ts-ignore - @todo fix typings\n map(() => __index),\n shareReplay(1)\n )\n } else {\n return requestJSON(\n new URL(\"search/search_index.json\", config.base)\n )\n }\n}\n\n/* ----------------------------------------------------------------------------\n * Application\n * ------------------------------------------------------------------------- */\n\n/* Yay, JavaScript is available */\ndocument.documentElement.classList.remove(\"no-js\")\ndocument.documentElement.classList.add(\"js\")\n\n/* Set up navigation observables and subjects */\nconst document$ = watchDocument()\nconst location$ = watchLocation()\nconst target$ = watchLocationTarget(location$)\nconst keyboard$ = watchKeyboard()\n\n/* Set up media observables */\nconst viewport$ = watchViewport()\nconst tablet$ = watchMedia(\"(min-width: 960px)\")\nconst screen$ = watchMedia(\"(min-width: 1220px)\")\nconst print$ = watchPrint()\n\n/* Retrieve search index, if search is enabled */\nconst config = configuration()\nconst index$ = document.forms.namedItem(\"search\")\n ? fetchSearchIndex()\n : NEVER\n\n/* Set up Clipboard.js integration */\nconst alert$ = new Subject()\nsetupClipboardJS({ alert$ })\n\n/* Set up progress indicator */\nconst progress$ = new Subject()\n\n/* Set up instant navigation, if enabled */\nif (feature(\"navigation.instant\"))\n setupInstantNavigation({ location$, viewport$, progress$ })\n .subscribe(document$)\n\n/* Set up version selector */\nif (config.version?.provider === \"mike\")\n setupVersionSelector({ document$ })\n\n/* Always close drawer and search on navigation */\nmerge(location$, target$)\n .pipe(\n delay(125)\n )\n .subscribe(() => {\n setToggle(\"drawer\", false)\n setToggle(\"search\", false)\n })\n\n/* Set up global keyboard handlers */\nkeyboard$\n .pipe(\n filter(({ mode }) => mode === \"global\")\n )\n .subscribe(key => {\n switch (key.type) {\n\n /* Go to previous page */\n case \"p\":\n case \",\":\n const prev = getOptionalElement(\"link[rel=prev]\")\n if (typeof prev !== \"undefined\")\n setLocation(prev)\n break\n\n /* Go to next page */\n case \"n\":\n case \".\":\n const next = getOptionalElement(\"link[rel=next]\")\n if (typeof next !== \"undefined\")\n setLocation(next)\n break\n\n /* Expand navigation, see https://bit.ly/3ZjG5io */\n case \"Enter\":\n const active = getActiveElement()\n if (active instanceof HTMLLabelElement)\n active.click()\n }\n })\n\n/* Set up patches */\npatchEllipsis({ viewport$, document$ })\npatchIndeterminate({ document$, tablet$ })\npatchScrollfix({ document$ })\npatchScrolllock({ viewport$, tablet$ })\n\n/* Set up header and main area observable */\nconst header$ = watchHeader(getComponentElement(\"header\"), { viewport$ })\nconst main$ = document$\n .pipe(\n map(() => getComponentElement(\"main\")),\n switchMap(el => watchMain(el, { viewport$, header$ })),\n shareReplay(1)\n )\n\n/* Set up control component observables */\nconst control$ = merge(\n\n /* Consent */\n ...getComponentElements(\"consent\")\n .map(el => mountConsent(el, { target$ })),\n\n /* Dialog */\n ...getComponentElements(\"dialog\")\n .map(el => mountDialog(el, { alert$ })),\n\n /* Header */\n ...getComponentElements(\"header\")\n .map(el => mountHeader(el, { viewport$, header$, main$ })),\n\n /* Color palette */\n ...getComponentElements(\"palette\")\n .map(el => mountPalette(el)),\n\n /* Progress bar */\n ...getComponentElements(\"progress\")\n .map(el => mountProgress(el, { progress$ })),\n\n /* Search */\n ...getComponentElements(\"search\")\n .map(el => mountSearch(el, { index$, keyboard$ })),\n\n /* Repository information */\n ...getComponentElements(\"source\")\n .map(el => mountSource(el))\n)\n\n/* Set up content component observables */\nconst content$ = defer(() => merge(\n\n /* Announcement bar */\n ...getComponentElements(\"announce\")\n .map(el => mountAnnounce(el)),\n\n /* Content */\n ...getComponentElements(\"content\")\n .map(el => mountContent(el, { viewport$, target$, print$ })),\n\n /* Search highlighting */\n ...getComponentElements(\"content\")\n .map(el => feature(\"search.highlight\")\n ? mountSearchHiglight(el, { index$, location$ })\n : EMPTY\n ),\n\n /* Header title */\n ...getComponentElements(\"header-title\")\n .map(el => mountHeaderTitle(el, { viewport$, header$ })),\n\n /* Sidebar */\n ...getComponentElements(\"sidebar\")\n .map(el => el.getAttribute(\"data-md-type\") === \"navigation\"\n ? at(screen$, () => mountSidebar(el, { viewport$, header$, main$ }))\n : at(tablet$, () => mountSidebar(el, { viewport$, header$, main$ }))\n ),\n\n /* Navigation tabs */\n ...getComponentElements(\"tabs\")\n .map(el => mountTabs(el, { viewport$, header$ })),\n\n /* Table of contents */\n ...getComponentElements(\"toc\")\n .map(el => mountTableOfContents(el, {\n viewport$, header$, main$, target$\n })),\n\n /* Back-to-top button */\n ...getComponentElements(\"top\")\n .map(el => mountBackToTop(el, { viewport$, header$, main$, target$ }))\n))\n\n/* Set up component observables */\nconst component$ = document$\n .pipe(\n switchMap(() => content$),\n mergeWith(control$),\n shareReplay(1)\n )\n\n/* Subscribe to all components */\ncomponent$.subscribe()\n\n/* ----------------------------------------------------------------------------\n * Exports\n * ------------------------------------------------------------------------- */\n\nwindow.document$ = document$ /* Document observable */\nwindow.location$ = location$ /* Location subject */\nwindow.target$ = target$ /* Location target observable */\nwindow.keyboard$ = keyboard$ /* Keyboard observable */\nwindow.viewport$ = viewport$ /* Viewport observable */\nwindow.tablet$ = tablet$ /* Media tablet observable */\nwindow.screen$ = screen$ /* Media screen observable */\nwindow.print$ = print$ /* Media print observable */\nwindow.alert$ = alert$ /* Alert subject */\nwindow.progress$ = progress$ /* Progress indicator subject */\nwindow.component$ = component$ /* Component observable */\n", "/******************************************************************************\nCopyright (c) Microsoft Corporation.\n\nPermission to use, copy, modify, and/or distribute this software for any\npurpose with or without fee is hereby granted.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH\nREGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY\nAND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,\nINDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM\nLOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR\nOTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR\nPERFORMANCE OF THIS SOFTWARE.\n***************************************************************************** */\n/* global Reflect, Promise, SuppressedError, Symbol, Iterator */\n\nvar extendStatics = function(d, b) {\n extendStatics = Object.setPrototypeOf ||\n ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||\n function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };\n return extendStatics(d, b);\n};\n\nexport function __extends(d, b) {\n if (typeof b !== \"function\" && b !== null)\n throw new TypeError(\"Class extends value \" + String(b) + \" is not a constructor or null\");\n extendStatics(d, b);\n function __() { this.constructor = d; }\n d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());\n}\n\nexport var __assign = function() {\n __assign = Object.assign || function __assign(t) {\n for (var s, i = 1, n = arguments.length; i < n; i++) {\n s = arguments[i];\n for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p)) t[p] = s[p];\n }\n return t;\n }\n return __assign.apply(this, arguments);\n}\n\nexport function __rest(s, e) {\n var t = {};\n for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p) && e.indexOf(p) < 0)\n t[p] = s[p];\n if (s != null && typeof Object.getOwnPropertySymbols === \"function\")\n for (var i = 0, p = Object.getOwnPropertySymbols(s); i < p.length; i++) {\n if (e.indexOf(p[i]) < 0 && Object.prototype.propertyIsEnumerable.call(s, p[i]))\n t[p[i]] = s[p[i]];\n }\n return t;\n}\n\nexport function __decorate(decorators, target, key, desc) {\n var c = arguments.length, r = c < 3 ? target : desc === null ? desc = Object.getOwnPropertyDescriptor(target, key) : desc, d;\n if (typeof Reflect === \"object\" && typeof Reflect.decorate === \"function\") r = Reflect.decorate(decorators, target, key, desc);\n else for (var i = decorators.length - 1; i >= 0; i--) if (d = decorators[i]) r = (c < 3 ? d(r) : c > 3 ? d(target, key, r) : d(target, key)) || r;\n return c > 3 && r && Object.defineProperty(target, key, r), r;\n}\n\nexport function __param(paramIndex, decorator) {\n return function (target, key) { decorator(target, key, paramIndex); }\n}\n\nexport function __esDecorate(ctor, descriptorIn, decorators, contextIn, initializers, extraInitializers) {\n function accept(f) { if (f !== void 0 && typeof f !== \"function\") throw new TypeError(\"Function expected\"); return f; }\n var kind = contextIn.kind, key = kind === \"getter\" ? \"get\" : kind === \"setter\" ? \"set\" : \"value\";\n var target = !descriptorIn && ctor ? contextIn[\"static\"] ? ctor : ctor.prototype : null;\n var descriptor = descriptorIn || (target ? Object.getOwnPropertyDescriptor(target, contextIn.name) : {});\n var _, done = false;\n for (var i = decorators.length - 1; i >= 0; i--) {\n var context = {};\n for (var p in contextIn) context[p] = p === \"access\" ? {} : contextIn[p];\n for (var p in contextIn.access) context.access[p] = contextIn.access[p];\n context.addInitializer = function (f) { if (done) throw new TypeError(\"Cannot add initializers after decoration has completed\"); extraInitializers.push(accept(f || null)); };\n var result = (0, decorators[i])(kind === \"accessor\" ? { get: descriptor.get, set: descriptor.set } : descriptor[key], context);\n if (kind === \"accessor\") {\n if (result === void 0) continue;\n if (result === null || typeof result !== \"object\") throw new TypeError(\"Object expected\");\n if (_ = accept(result.get)) descriptor.get = _;\n if (_ = accept(result.set)) descriptor.set = _;\n if (_ = accept(result.init)) initializers.unshift(_);\n }\n else if (_ = accept(result)) {\n if (kind === \"field\") initializers.unshift(_);\n else descriptor[key] = _;\n }\n }\n if (target) Object.defineProperty(target, contextIn.name, descriptor);\n done = true;\n};\n\nexport function __runInitializers(thisArg, initializers, value) {\n var useValue = arguments.length > 2;\n for (var i = 0; i < initializers.length; i++) {\n value = useValue ? initializers[i].call(thisArg, value) : initializers[i].call(thisArg);\n }\n return useValue ? value : void 0;\n};\n\nexport function __propKey(x) {\n return typeof x === \"symbol\" ? x : \"\".concat(x);\n};\n\nexport function __setFunctionName(f, name, prefix) {\n if (typeof name === \"symbol\") name = name.description ? \"[\".concat(name.description, \"]\") : \"\";\n return Object.defineProperty(f, \"name\", { configurable: true, value: prefix ? \"\".concat(prefix, \" \", name) : name });\n};\n\nexport function __metadata(metadataKey, metadataValue) {\n if (typeof Reflect === \"object\" && typeof Reflect.metadata === \"function\") return Reflect.metadata(metadataKey, metadataValue);\n}\n\nexport function __awaiter(thisArg, _arguments, P, generator) {\n function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }\n return new (P || (P = Promise))(function (resolve, reject) {\n function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }\n function rejected(value) { try { step(generator[\"throw\"](value)); } catch (e) { reject(e); } }\n function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }\n step((generator = generator.apply(thisArg, _arguments || [])).next());\n });\n}\n\nexport function __generator(thisArg, body) {\n var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g = Object.create((typeof Iterator === \"function\" ? Iterator : Object).prototype);\n return g.next = verb(0), g[\"throw\"] = verb(1), g[\"return\"] = verb(2), typeof Symbol === \"function\" && (g[Symbol.iterator] = function() { return this; }), g;\n function verb(n) { return function (v) { return step([n, v]); }; }\n function step(op) {\n if (f) throw new TypeError(\"Generator is already executing.\");\n while (g && (g = 0, op[0] && (_ = 0)), _) try {\n if (f = 1, y && (t = op[0] & 2 ? y[\"return\"] : op[0] ? y[\"throw\"] || ((t = y[\"return\"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;\n if (y = 0, t) op = [op[0] & 2, t.value];\n switch (op[0]) {\n case 0: case 1: t = op; break;\n case 4: _.label++; return { value: op[1], done: false };\n case 5: _.label++; y = op[1]; op = [0]; continue;\n case 7: op = _.ops.pop(); _.trys.pop(); continue;\n default:\n if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }\n if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }\n if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }\n if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }\n if (t[2]) _.ops.pop();\n _.trys.pop(); continue;\n }\n op = body.call(thisArg, _);\n } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }\n if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };\n }\n}\n\nexport var __createBinding = Object.create ? (function(o, m, k, k2) {\n if (k2 === undefined) k2 = k;\n var desc = Object.getOwnPropertyDescriptor(m, k);\n if (!desc || (\"get\" in desc ? !m.__esModule : desc.writable || desc.configurable)) {\n desc = { enumerable: true, get: function() { return m[k]; } };\n }\n Object.defineProperty(o, k2, desc);\n}) : (function(o, m, k, k2) {\n if (k2 === undefined) k2 = k;\n o[k2] = m[k];\n});\n\nexport function __exportStar(m, o) {\n for (var p in m) if (p !== \"default\" && !Object.prototype.hasOwnProperty.call(o, p)) __createBinding(o, m, p);\n}\n\nexport function __values(o) {\n var s = typeof Symbol === \"function\" && Symbol.iterator, m = s && o[s], i = 0;\n if (m) return m.call(o);\n if (o && typeof o.length === \"number\") return {\n next: function () {\n if (o && i >= o.length) o = void 0;\n return { value: o && o[i++], done: !o };\n }\n };\n throw new TypeError(s ? \"Object is not iterable.\" : \"Symbol.iterator is not defined.\");\n}\n\nexport function __read(o, n) {\n var m = typeof Symbol === \"function\" && o[Symbol.iterator];\n if (!m) return o;\n var i = m.call(o), r, ar = [], e;\n try {\n while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);\n }\n catch (error) { e = { error: error }; }\n finally {\n try {\n if (r && !r.done && (m = i[\"return\"])) m.call(i);\n }\n finally { if (e) throw e.error; }\n }\n return ar;\n}\n\n/** @deprecated */\nexport function __spread() {\n for (var ar = [], i = 0; i < arguments.length; i++)\n ar = ar.concat(__read(arguments[i]));\n return ar;\n}\n\n/** @deprecated */\nexport function __spreadArrays() {\n for (var s = 0, i = 0, il = arguments.length; i < il; i++) s += arguments[i].length;\n for (var r = Array(s), k = 0, i = 0; i < il; i++)\n for (var a = arguments[i], j = 0, jl = a.length; j < jl; j++, k++)\n r[k] = a[j];\n return r;\n}\n\nexport function __spreadArray(to, from, pack) {\n if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {\n if (ar || !(i in from)) {\n if (!ar) ar = Array.prototype.slice.call(from, 0, i);\n ar[i] = from[i];\n }\n }\n return to.concat(ar || Array.prototype.slice.call(from));\n}\n\nexport function __await(v) {\n return this instanceof __await ? (this.v = v, this) : new __await(v);\n}\n\nexport function __asyncGenerator(thisArg, _arguments, generator) {\n if (!Symbol.asyncIterator) throw new TypeError(\"Symbol.asyncIterator is not defined.\");\n var g = generator.apply(thisArg, _arguments || []), i, q = [];\n return i = Object.create((typeof AsyncIterator === \"function\" ? AsyncIterator : Object).prototype), verb(\"next\"), verb(\"throw\"), verb(\"return\", awaitReturn), i[Symbol.asyncIterator] = function () { return this; }, i;\n function awaitReturn(f) { return function (v) { return Promise.resolve(v).then(f, reject); }; }\n function verb(n, f) { if (g[n]) { i[n] = function (v) { return new Promise(function (a, b) { q.push([n, v, a, b]) > 1 || resume(n, v); }); }; if (f) i[n] = f(i[n]); } }\n function resume(n, v) { try { step(g[n](v)); } catch (e) { settle(q[0][3], e); } }\n function step(r) { r.value instanceof __await ? Promise.resolve(r.value.v).then(fulfill, reject) : settle(q[0][2], r); }\n function fulfill(value) { resume(\"next\", value); }\n function reject(value) { resume(\"throw\", value); }\n function settle(f, v) { if (f(v), q.shift(), q.length) resume(q[0][0], q[0][1]); }\n}\n\nexport function __asyncDelegator(o) {\n var i, p;\n return i = {}, verb(\"next\"), verb(\"throw\", function (e) { throw e; }), verb(\"return\"), i[Symbol.iterator] = function () { return this; }, i;\n function verb(n, f) { i[n] = o[n] ? function (v) { return (p = !p) ? { value: __await(o[n](v)), done: false } : f ? f(v) : v; } : f; }\n}\n\nexport function __asyncValues(o) {\n if (!Symbol.asyncIterator) throw new TypeError(\"Symbol.asyncIterator is not defined.\");\n var m = o[Symbol.asyncIterator], i;\n return m ? m.call(o) : (o = typeof __values === \"function\" ? __values(o) : o[Symbol.iterator](), i = {}, verb(\"next\"), verb(\"throw\"), verb(\"return\"), i[Symbol.asyncIterator] = function () { return this; }, i);\n function verb(n) { i[n] = o[n] && function (v) { return new Promise(function (resolve, reject) { v = o[n](v), settle(resolve, reject, v.done, v.value); }); }; }\n function settle(resolve, reject, d, v) { Promise.resolve(v).then(function(v) { resolve({ value: v, done: d }); }, reject); }\n}\n\nexport function __makeTemplateObject(cooked, raw) {\n if (Object.defineProperty) { Object.defineProperty(cooked, \"raw\", { value: raw }); } else { cooked.raw = raw; }\n return cooked;\n};\n\nvar __setModuleDefault = Object.create ? (function(o, v) {\n Object.defineProperty(o, \"default\", { enumerable: true, value: v });\n}) : function(o, v) {\n o[\"default\"] = v;\n};\n\nexport function __importStar(mod) {\n if (mod && mod.__esModule) return mod;\n var result = {};\n if (mod != null) for (var k in mod) if (k !== \"default\" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);\n __setModuleDefault(result, mod);\n return result;\n}\n\nexport function __importDefault(mod) {\n return (mod && mod.__esModule) ? mod : { default: mod };\n}\n\nexport function __classPrivateFieldGet(receiver, state, kind, f) {\n if (kind === \"a\" && !f) throw new TypeError(\"Private accessor was defined without a getter\");\n if (typeof state === \"function\" ? receiver !== state || !f : !state.has(receiver)) throw new TypeError(\"Cannot read private member from an object whose class did not declare it\");\n return kind === \"m\" ? f : kind === \"a\" ? f.call(receiver) : f ? f.value : state.get(receiver);\n}\n\nexport function __classPrivateFieldSet(receiver, state, value, kind, f) {\n if (kind === \"m\") throw new TypeError(\"Private method is not writable\");\n if (kind === \"a\" && !f) throw new TypeError(\"Private accessor was defined without a setter\");\n if (typeof state === \"function\" ? receiver !== state || !f : !state.has(receiver)) throw new TypeError(\"Cannot write private member to an object whose class did not declare it\");\n return (kind === \"a\" ? f.call(receiver, value) : f ? f.value = value : state.set(receiver, value)), value;\n}\n\nexport function __classPrivateFieldIn(state, receiver) {\n if (receiver === null || (typeof receiver !== \"object\" && typeof receiver !== \"function\")) throw new TypeError(\"Cannot use 'in' operator on non-object\");\n return typeof state === \"function\" ? receiver === state : state.has(receiver);\n}\n\nexport function __addDisposableResource(env, value, async) {\n if (value !== null && value !== void 0) {\n if (typeof value !== \"object\" && typeof value !== \"function\") throw new TypeError(\"Object expected.\");\n var dispose, inner;\n if (async) {\n if (!Symbol.asyncDispose) throw new TypeError(\"Symbol.asyncDispose is not defined.\");\n dispose = value[Symbol.asyncDispose];\n }\n if (dispose === void 0) {\n if (!Symbol.dispose) throw new TypeError(\"Symbol.dispose is not defined.\");\n dispose = value[Symbol.dispose];\n if (async) inner = dispose;\n }\n if (typeof dispose !== \"function\") throw new TypeError(\"Object not disposable.\");\n if (inner) dispose = function() { try { inner.call(this); } catch (e) { return Promise.reject(e); } };\n env.stack.push({ value: value, dispose: dispose, async: async });\n }\n else if (async) {\n env.stack.push({ async: true });\n }\n return value;\n}\n\nvar _SuppressedError = typeof SuppressedError === \"function\" ? SuppressedError : function (error, suppressed, message) {\n var e = new Error(message);\n return e.name = \"SuppressedError\", e.error = error, e.suppressed = suppressed, e;\n};\n\nexport function __disposeResources(env) {\n function fail(e) {\n env.error = env.hasError ? new _SuppressedError(e, env.error, \"An error was suppressed during disposal.\") : e;\n env.hasError = true;\n }\n var r, s = 0;\n function next() {\n while (r = env.stack.pop()) {\n try {\n if (!r.async && s === 1) return s = 0, env.stack.push(r), Promise.resolve().then(next);\n if (r.dispose) {\n var result = r.dispose.call(r.value);\n if (r.async) return s |= 2, Promise.resolve(result).then(next, function(e) { fail(e); return next(); });\n }\n else s |= 1;\n }\n catch (e) {\n fail(e);\n }\n }\n if (s === 1) return env.hasError ? Promise.reject(env.error) : Promise.resolve();\n if (env.hasError) throw env.error;\n }\n return next();\n}\n\nexport default {\n __extends,\n __assign,\n __rest,\n __decorate,\n __param,\n __metadata,\n __awaiter,\n __generator,\n __createBinding,\n __exportStar,\n __values,\n __read,\n __spread,\n __spreadArrays,\n __spreadArray,\n __await,\n __asyncGenerator,\n __asyncDelegator,\n __asyncValues,\n __makeTemplateObject,\n __importStar,\n __importDefault,\n __classPrivateFieldGet,\n __classPrivateFieldSet,\n __classPrivateFieldIn,\n __addDisposableResource,\n __disposeResources,\n};\n", "/**\n * Returns true if the object is a function.\n * @param value The value to check\n */\nexport function isFunction(value: any): value is (...args: any[]) => any {\n return typeof value === 'function';\n}\n", "/**\n * Used to create Error subclasses until the community moves away from ES5.\n *\n * This is because compiling from TypeScript down to ES5 has issues with subclassing Errors\n * as well as other built-in types: https://github.com/Microsoft/TypeScript/issues/12123\n *\n * @param createImpl A factory function to create the actual constructor implementation. The returned\n * function should be a named function that calls `_super` internally.\n */\nexport function createErrorClass(createImpl: (_super: any) => any): T {\n const _super = (instance: any) => {\n Error.call(instance);\n instance.stack = new Error().stack;\n };\n\n const ctorFunc = createImpl(_super);\n ctorFunc.prototype = Object.create(Error.prototype);\n ctorFunc.prototype.constructor = ctorFunc;\n return ctorFunc;\n}\n", "import { createErrorClass } from './createErrorClass';\n\nexport interface UnsubscriptionError extends Error {\n readonly errors: any[];\n}\n\nexport interface UnsubscriptionErrorCtor {\n /**\n * @deprecated Internal implementation detail. Do not construct error instances.\n * Cannot be tagged as internal: https://github.com/ReactiveX/rxjs/issues/6269\n */\n new (errors: any[]): UnsubscriptionError;\n}\n\n/**\n * An error thrown when one or more errors have occurred during the\n * `unsubscribe` of a {@link Subscription}.\n */\nexport const UnsubscriptionError: UnsubscriptionErrorCtor = createErrorClass(\n (_super) =>\n function UnsubscriptionErrorImpl(this: any, errors: (Error | string)[]) {\n _super(this);\n this.message = errors\n ? `${errors.length} errors occurred during unsubscription:\n${errors.map((err, i) => `${i + 1}) ${err.toString()}`).join('\\n ')}`\n : '';\n this.name = 'UnsubscriptionError';\n this.errors = errors;\n }\n);\n", "/**\n * Removes an item from an array, mutating it.\n * @param arr The array to remove the item from\n * @param item The item to remove\n */\nexport function arrRemove(arr: T[] | undefined | null, item: T) {\n if (arr) {\n const index = arr.indexOf(item);\n 0 <= index && arr.splice(index, 1);\n }\n}\n", "import { isFunction } from './util/isFunction';\nimport { UnsubscriptionError } from './util/UnsubscriptionError';\nimport { SubscriptionLike, TeardownLogic, Unsubscribable } from './types';\nimport { arrRemove } from './util/arrRemove';\n\n/**\n * Represents a disposable resource, such as the execution of an Observable. A\n * Subscription has one important method, `unsubscribe`, that takes no argument\n * and just disposes the resource held by the subscription.\n *\n * Additionally, subscriptions may be grouped together through the `add()`\n * method, which will attach a child Subscription to the current Subscription.\n * When a Subscription is unsubscribed, all its children (and its grandchildren)\n * will be unsubscribed as well.\n *\n * @class Subscription\n */\nexport class Subscription implements SubscriptionLike {\n /** @nocollapse */\n public static EMPTY = (() => {\n const empty = new Subscription();\n empty.closed = true;\n return empty;\n })();\n\n /**\n * A flag to indicate whether this Subscription has already been unsubscribed.\n */\n public closed = false;\n\n private _parentage: Subscription[] | Subscription | null = null;\n\n /**\n * The list of registered finalizers to execute upon unsubscription. Adding and removing from this\n * list occurs in the {@link #add} and {@link #remove} methods.\n */\n private _finalizers: Exclude[] | null = null;\n\n /**\n * @param initialTeardown A function executed first as part of the finalization\n * process that is kicked off when {@link #unsubscribe} is called.\n */\n constructor(private initialTeardown?: () => void) {}\n\n /**\n * Disposes the resources held by the subscription. May, for instance, cancel\n * an ongoing Observable execution or cancel any other type of work that\n * started when the Subscription was created.\n * @return {void}\n */\n unsubscribe(): void {\n let errors: any[] | undefined;\n\n if (!this.closed) {\n this.closed = true;\n\n // Remove this from it's parents.\n const { _parentage } = this;\n if (_parentage) {\n this._parentage = null;\n if (Array.isArray(_parentage)) {\n for (const parent of _parentage) {\n parent.remove(this);\n }\n } else {\n _parentage.remove(this);\n }\n }\n\n const { initialTeardown: initialFinalizer } = this;\n if (isFunction(initialFinalizer)) {\n try {\n initialFinalizer();\n } catch (e) {\n errors = e instanceof UnsubscriptionError ? e.errors : [e];\n }\n }\n\n const { _finalizers } = this;\n if (_finalizers) {\n this._finalizers = null;\n for (const finalizer of _finalizers) {\n try {\n execFinalizer(finalizer);\n } catch (err) {\n errors = errors ?? [];\n if (err instanceof UnsubscriptionError) {\n errors = [...errors, ...err.errors];\n } else {\n errors.push(err);\n }\n }\n }\n }\n\n if (errors) {\n throw new UnsubscriptionError(errors);\n }\n }\n }\n\n /**\n * Adds a finalizer to this subscription, so that finalization will be unsubscribed/called\n * when this subscription is unsubscribed. If this subscription is already {@link #closed},\n * because it has already been unsubscribed, then whatever finalizer is passed to it\n * will automatically be executed (unless the finalizer itself is also a closed subscription).\n *\n * Closed Subscriptions cannot be added as finalizers to any subscription. Adding a closed\n * subscription to a any subscription will result in no operation. (A noop).\n *\n * Adding a subscription to itself, or adding `null` or `undefined` will not perform any\n * operation at all. (A noop).\n *\n * `Subscription` instances that are added to this instance will automatically remove themselves\n * if they are unsubscribed. Functions and {@link Unsubscribable} objects that you wish to remove\n * will need to be removed manually with {@link #remove}\n *\n * @param teardown The finalization logic to add to this subscription.\n */\n add(teardown: TeardownLogic): void {\n // Only add the finalizer if it's not undefined\n // and don't add a subscription to itself.\n if (teardown && teardown !== this) {\n if (this.closed) {\n // If this subscription is already closed,\n // execute whatever finalizer is handed to it automatically.\n execFinalizer(teardown);\n } else {\n if (teardown instanceof Subscription) {\n // We don't add closed subscriptions, and we don't add the same subscription\n // twice. Subscription unsubscribe is idempotent.\n if (teardown.closed || teardown._hasParent(this)) {\n return;\n }\n teardown._addParent(this);\n }\n (this._finalizers = this._finalizers ?? []).push(teardown);\n }\n }\n }\n\n /**\n * Checks to see if a this subscription already has a particular parent.\n * This will signal that this subscription has already been added to the parent in question.\n * @param parent the parent to check for\n */\n private _hasParent(parent: Subscription) {\n const { _parentage } = this;\n return _parentage === parent || (Array.isArray(_parentage) && _parentage.includes(parent));\n }\n\n /**\n * Adds a parent to this subscription so it can be removed from the parent if it\n * unsubscribes on it's own.\n *\n * NOTE: THIS ASSUMES THAT {@link _hasParent} HAS ALREADY BEEN CHECKED.\n * @param parent The parent subscription to add\n */\n private _addParent(parent: Subscription) {\n const { _parentage } = this;\n this._parentage = Array.isArray(_parentage) ? (_parentage.push(parent), _parentage) : _parentage ? [_parentage, parent] : parent;\n }\n\n /**\n * Called on a child when it is removed via {@link #remove}.\n * @param parent The parent to remove\n */\n private _removeParent(parent: Subscription) {\n const { _parentage } = this;\n if (_parentage === parent) {\n this._parentage = null;\n } else if (Array.isArray(_parentage)) {\n arrRemove(_parentage, parent);\n }\n }\n\n /**\n * Removes a finalizer from this subscription that was previously added with the {@link #add} method.\n *\n * Note that `Subscription` instances, when unsubscribed, will automatically remove themselves\n * from every other `Subscription` they have been added to. This means that using the `remove` method\n * is not a common thing and should be used thoughtfully.\n *\n * If you add the same finalizer instance of a function or an unsubscribable object to a `Subscription` instance\n * more than once, you will need to call `remove` the same number of times to remove all instances.\n *\n * All finalizer instances are removed to free up memory upon unsubscription.\n *\n * @param teardown The finalizer to remove from this subscription\n */\n remove(teardown: Exclude): void {\n const { _finalizers } = this;\n _finalizers && arrRemove(_finalizers, teardown);\n\n if (teardown instanceof Subscription) {\n teardown._removeParent(this);\n }\n }\n}\n\nexport const EMPTY_SUBSCRIPTION = Subscription.EMPTY;\n\nexport function isSubscription(value: any): value is Subscription {\n return (\n value instanceof Subscription ||\n (value && 'closed' in value && isFunction(value.remove) && isFunction(value.add) && isFunction(value.unsubscribe))\n );\n}\n\nfunction execFinalizer(finalizer: Unsubscribable | (() => void)) {\n if (isFunction(finalizer)) {\n finalizer();\n } else {\n finalizer.unsubscribe();\n }\n}\n", "import { Subscriber } from './Subscriber';\nimport { ObservableNotification } from './types';\n\n/**\n * The {@link GlobalConfig} object for RxJS. It is used to configure things\n * like how to react on unhandled errors.\n */\nexport const config: GlobalConfig = {\n onUnhandledError: null,\n onStoppedNotification: null,\n Promise: undefined,\n useDeprecatedSynchronousErrorHandling: false,\n useDeprecatedNextContext: false,\n};\n\n/**\n * The global configuration object for RxJS, used to configure things\n * like how to react on unhandled errors. Accessible via {@link config}\n * object.\n */\nexport interface GlobalConfig {\n /**\n * A registration point for unhandled errors from RxJS. These are errors that\n * cannot were not handled by consuming code in the usual subscription path. For\n * example, if you have this configured, and you subscribe to an observable without\n * providing an error handler, errors from that subscription will end up here. This\n * will _always_ be called asynchronously on another job in the runtime. This is because\n * we do not want errors thrown in this user-configured handler to interfere with the\n * behavior of the library.\n */\n onUnhandledError: ((err: any) => void) | null;\n\n /**\n * A registration point for notifications that cannot be sent to subscribers because they\n * have completed, errored or have been explicitly unsubscribed. By default, next, complete\n * and error notifications sent to stopped subscribers are noops. However, sometimes callers\n * might want a different behavior. For example, with sources that attempt to report errors\n * to stopped subscribers, a caller can configure RxJS to throw an unhandled error instead.\n * This will _always_ be called asynchronously on another job in the runtime. This is because\n * we do not want errors thrown in this user-configured handler to interfere with the\n * behavior of the library.\n */\n onStoppedNotification: ((notification: ObservableNotification, subscriber: Subscriber) => void) | null;\n\n /**\n * The promise constructor used by default for {@link Observable#toPromise toPromise} and {@link Observable#forEach forEach}\n * methods.\n *\n * @deprecated As of version 8, RxJS will no longer support this sort of injection of a\n * Promise constructor. If you need a Promise implementation other than native promises,\n * please polyfill/patch Promise as you see appropriate. Will be removed in v8.\n */\n Promise?: PromiseConstructorLike;\n\n /**\n * If true, turns on synchronous error rethrowing, which is a deprecated behavior\n * in v6 and higher. This behavior enables bad patterns like wrapping a subscribe\n * call in a try/catch block. It also enables producer interference, a nasty bug\n * where a multicast can be broken for all observers by a downstream consumer with\n * an unhandled error. DO NOT USE THIS FLAG UNLESS IT'S NEEDED TO BUY TIME\n * FOR MIGRATION REASONS.\n *\n * @deprecated As of version 8, RxJS will no longer support synchronous throwing\n * of unhandled errors. All errors will be thrown on a separate call stack to prevent bad\n * behaviors described above. Will be removed in v8.\n */\n useDeprecatedSynchronousErrorHandling: boolean;\n\n /**\n * If true, enables an as-of-yet undocumented feature from v5: The ability to access\n * `unsubscribe()` via `this` context in `next` functions created in observers passed\n * to `subscribe`.\n *\n * This is being removed because the performance was severely problematic, and it could also cause\n * issues when types other than POJOs are passed to subscribe as subscribers, as they will likely have\n * their `this` context overwritten.\n *\n * @deprecated As of version 8, RxJS will no longer support altering the\n * context of next functions provided as part of an observer to Subscribe. Instead,\n * you will have access to a subscription or a signal or token that will allow you to do things like\n * unsubscribe and test closed status. Will be removed in v8.\n */\n useDeprecatedNextContext: boolean;\n}\n", "import type { TimerHandle } from './timerHandle';\ntype SetTimeoutFunction = (handler: () => void, timeout?: number, ...args: any[]) => TimerHandle;\ntype ClearTimeoutFunction = (handle: TimerHandle) => void;\n\ninterface TimeoutProvider {\n setTimeout: SetTimeoutFunction;\n clearTimeout: ClearTimeoutFunction;\n delegate:\n | {\n setTimeout: SetTimeoutFunction;\n clearTimeout: ClearTimeoutFunction;\n }\n | undefined;\n}\n\nexport const timeoutProvider: TimeoutProvider = {\n // When accessing the delegate, use the variable rather than `this` so that\n // the functions can be called without being bound to the provider.\n setTimeout(handler: () => void, timeout?: number, ...args) {\n const { delegate } = timeoutProvider;\n if (delegate?.setTimeout) {\n return delegate.setTimeout(handler, timeout, ...args);\n }\n return setTimeout(handler, timeout, ...args);\n },\n clearTimeout(handle) {\n const { delegate } = timeoutProvider;\n return (delegate?.clearTimeout || clearTimeout)(handle as any);\n },\n delegate: undefined,\n};\n", "import { config } from '../config';\nimport { timeoutProvider } from '../scheduler/timeoutProvider';\n\n/**\n * Handles an error on another job either with the user-configured {@link onUnhandledError},\n * or by throwing it on that new job so it can be picked up by `window.onerror`, `process.on('error')`, etc.\n *\n * This should be called whenever there is an error that is out-of-band with the subscription\n * or when an error hits a terminal boundary of the subscription and no error handler was provided.\n *\n * @param err the error to report\n */\nexport function reportUnhandledError(err: any) {\n timeoutProvider.setTimeout(() => {\n const { onUnhandledError } = config;\n if (onUnhandledError) {\n // Execute the user-configured error handler.\n onUnhandledError(err);\n } else {\n // Throw so it is picked up by the runtime's uncaught error mechanism.\n throw err;\n }\n });\n}\n", "/* tslint:disable:no-empty */\nexport function noop() { }\n", "import { CompleteNotification, NextNotification, ErrorNotification } from './types';\n\n/**\n * A completion object optimized for memory use and created to be the\n * same \"shape\" as other notifications in v8.\n * @internal\n */\nexport const COMPLETE_NOTIFICATION = (() => createNotification('C', undefined, undefined) as CompleteNotification)();\n\n/**\n * Internal use only. Creates an optimized error notification that is the same \"shape\"\n * as other notifications.\n * @internal\n */\nexport function errorNotification(error: any): ErrorNotification {\n return createNotification('E', undefined, error) as any;\n}\n\n/**\n * Internal use only. Creates an optimized next notification that is the same \"shape\"\n * as other notifications.\n * @internal\n */\nexport function nextNotification(value: T) {\n return createNotification('N', value, undefined) as NextNotification;\n}\n\n/**\n * Ensures that all notifications created internally have the same \"shape\" in v8.\n *\n * TODO: This is only exported to support a crazy legacy test in `groupBy`.\n * @internal\n */\nexport function createNotification(kind: 'N' | 'E' | 'C', value: any, error: any) {\n return {\n kind,\n value,\n error,\n };\n}\n", "import { config } from '../config';\n\nlet context: { errorThrown: boolean; error: any } | null = null;\n\n/**\n * Handles dealing with errors for super-gross mode. Creates a context, in which\n * any synchronously thrown errors will be passed to {@link captureError}. Which\n * will record the error such that it will be rethrown after the call back is complete.\n * TODO: Remove in v8\n * @param cb An immediately executed function.\n */\nexport function errorContext(cb: () => void) {\n if (config.useDeprecatedSynchronousErrorHandling) {\n const isRoot = !context;\n if (isRoot) {\n context = { errorThrown: false, error: null };\n }\n cb();\n if (isRoot) {\n const { errorThrown, error } = context!;\n context = null;\n if (errorThrown) {\n throw error;\n }\n }\n } else {\n // This is the general non-deprecated path for everyone that\n // isn't crazy enough to use super-gross mode (useDeprecatedSynchronousErrorHandling)\n cb();\n }\n}\n\n/**\n * Captures errors only in super-gross mode.\n * @param err the error to capture\n */\nexport function captureError(err: any) {\n if (config.useDeprecatedSynchronousErrorHandling && context) {\n context.errorThrown = true;\n context.error = err;\n }\n}\n", "import { isFunction } from './util/isFunction';\nimport { Observer, ObservableNotification } from './types';\nimport { isSubscription, Subscription } from './Subscription';\nimport { config } from './config';\nimport { reportUnhandledError } from './util/reportUnhandledError';\nimport { noop } from './util/noop';\nimport { nextNotification, errorNotification, COMPLETE_NOTIFICATION } from './NotificationFactories';\nimport { timeoutProvider } from './scheduler/timeoutProvider';\nimport { captureError } from './util/errorContext';\n\n/**\n * Implements the {@link Observer} interface and extends the\n * {@link Subscription} class. While the {@link Observer} is the public API for\n * consuming the values of an {@link Observable}, all Observers get converted to\n * a Subscriber, in order to provide Subscription-like capabilities such as\n * `unsubscribe`. Subscriber is a common type in RxJS, and crucial for\n * implementing operators, but it is rarely used as a public API.\n *\n * @class Subscriber\n */\nexport class Subscriber extends Subscription implements Observer {\n /**\n * A static factory for a Subscriber, given a (potentially partial) definition\n * of an Observer.\n * @param next The `next` callback of an Observer.\n * @param error The `error` callback of an\n * Observer.\n * @param complete The `complete` callback of an\n * Observer.\n * @return A Subscriber wrapping the (partially defined)\n * Observer represented by the given arguments.\n * @nocollapse\n * @deprecated Do not use. Will be removed in v8. There is no replacement for this\n * method, and there is no reason to be creating instances of `Subscriber` directly.\n * If you have a specific use case, please file an issue.\n */\n static create(next?: (x?: T) => void, error?: (e?: any) => void, complete?: () => void): Subscriber {\n return new SafeSubscriber(next, error, complete);\n }\n\n /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n protected isStopped: boolean = false;\n /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n protected destination: Subscriber | Observer; // this `any` is the escape hatch to erase extra type param (e.g. R)\n\n /**\n * @deprecated Internal implementation detail, do not use directly. Will be made internal in v8.\n * There is no reason to directly create an instance of Subscriber. This type is exported for typings reasons.\n */\n constructor(destination?: Subscriber | Observer) {\n super();\n if (destination) {\n this.destination = destination;\n // Automatically chain subscriptions together here.\n // if destination is a Subscription, then it is a Subscriber.\n if (isSubscription(destination)) {\n destination.add(this);\n }\n } else {\n this.destination = EMPTY_OBSERVER;\n }\n }\n\n /**\n * The {@link Observer} callback to receive notifications of type `next` from\n * the Observable, with a value. The Observable may call this method 0 or more\n * times.\n * @param {T} [value] The `next` value.\n * @return {void}\n */\n next(value?: T): void {\n if (this.isStopped) {\n handleStoppedNotification(nextNotification(value), this);\n } else {\n this._next(value!);\n }\n }\n\n /**\n * The {@link Observer} callback to receive notifications of type `error` from\n * the Observable, with an attached `Error`. Notifies the Observer that\n * the Observable has experienced an error condition.\n * @param {any} [err] The `error` exception.\n * @return {void}\n */\n error(err?: any): void {\n if (this.isStopped) {\n handleStoppedNotification(errorNotification(err), this);\n } else {\n this.isStopped = true;\n this._error(err);\n }\n }\n\n /**\n * The {@link Observer} callback to receive a valueless notification of type\n * `complete` from the Observable. Notifies the Observer that the Observable\n * has finished sending push-based notifications.\n * @return {void}\n */\n complete(): void {\n if (this.isStopped) {\n handleStoppedNotification(COMPLETE_NOTIFICATION, this);\n } else {\n this.isStopped = true;\n this._complete();\n }\n }\n\n unsubscribe(): void {\n if (!this.closed) {\n this.isStopped = true;\n super.unsubscribe();\n this.destination = null!;\n }\n }\n\n protected _next(value: T): void {\n this.destination.next(value);\n }\n\n protected _error(err: any): void {\n try {\n this.destination.error(err);\n } finally {\n this.unsubscribe();\n }\n }\n\n protected _complete(): void {\n try {\n this.destination.complete();\n } finally {\n this.unsubscribe();\n }\n }\n}\n\n/**\n * This bind is captured here because we want to be able to have\n * compatibility with monoid libraries that tend to use a method named\n * `bind`. In particular, a library called Monio requires this.\n */\nconst _bind = Function.prototype.bind;\n\nfunction bind any>(fn: Fn, thisArg: any): Fn {\n return _bind.call(fn, thisArg);\n}\n\n/**\n * Internal optimization only, DO NOT EXPOSE.\n * @internal\n */\nclass ConsumerObserver implements Observer {\n constructor(private partialObserver: Partial>) {}\n\n next(value: T): void {\n const { partialObserver } = this;\n if (partialObserver.next) {\n try {\n partialObserver.next(value);\n } catch (error) {\n handleUnhandledError(error);\n }\n }\n }\n\n error(err: any): void {\n const { partialObserver } = this;\n if (partialObserver.error) {\n try {\n partialObserver.error(err);\n } catch (error) {\n handleUnhandledError(error);\n }\n } else {\n handleUnhandledError(err);\n }\n }\n\n complete(): void {\n const { partialObserver } = this;\n if (partialObserver.complete) {\n try {\n partialObserver.complete();\n } catch (error) {\n handleUnhandledError(error);\n }\n }\n }\n}\n\nexport class SafeSubscriber extends Subscriber {\n constructor(\n observerOrNext?: Partial> | ((value: T) => void) | null,\n error?: ((e?: any) => void) | null,\n complete?: (() => void) | null\n ) {\n super();\n\n let partialObserver: Partial>;\n if (isFunction(observerOrNext) || !observerOrNext) {\n // The first argument is a function, not an observer. The next\n // two arguments *could* be observers, or they could be empty.\n partialObserver = {\n next: (observerOrNext ?? undefined) as (((value: T) => void) | undefined),\n error: error ?? undefined,\n complete: complete ?? undefined,\n };\n } else {\n // The first argument is a partial observer.\n let context: any;\n if (this && config.useDeprecatedNextContext) {\n // This is a deprecated path that made `this.unsubscribe()` available in\n // next handler functions passed to subscribe. This only exists behind a flag\n // now, as it is *very* slow.\n context = Object.create(observerOrNext);\n context.unsubscribe = () => this.unsubscribe();\n partialObserver = {\n next: observerOrNext.next && bind(observerOrNext.next, context),\n error: observerOrNext.error && bind(observerOrNext.error, context),\n complete: observerOrNext.complete && bind(observerOrNext.complete, context),\n };\n } else {\n // The \"normal\" path. Just use the partial observer directly.\n partialObserver = observerOrNext;\n }\n }\n\n // Wrap the partial observer to ensure it's a full observer, and\n // make sure proper error handling is accounted for.\n this.destination = new ConsumerObserver(partialObserver);\n }\n}\n\nfunction handleUnhandledError(error: any) {\n if (config.useDeprecatedSynchronousErrorHandling) {\n captureError(error);\n } else {\n // Ideal path, we report this as an unhandled error,\n // which is thrown on a new call stack.\n reportUnhandledError(error);\n }\n}\n\n/**\n * An error handler used when no error handler was supplied\n * to the SafeSubscriber -- meaning no error handler was supplied\n * do the `subscribe` call on our observable.\n * @param err The error to handle\n */\nfunction defaultErrorHandler(err: any) {\n throw err;\n}\n\n/**\n * A handler for notifications that cannot be sent to a stopped subscriber.\n * @param notification The notification being sent\n * @param subscriber The stopped subscriber\n */\nfunction handleStoppedNotification(notification: ObservableNotification, subscriber: Subscriber) {\n const { onStoppedNotification } = config;\n onStoppedNotification && timeoutProvider.setTimeout(() => onStoppedNotification(notification, subscriber));\n}\n\n/**\n * The observer used as a stub for subscriptions where the user did not\n * pass any arguments to `subscribe`. Comes with the default error handling\n * behavior.\n */\nexport const EMPTY_OBSERVER: Readonly> & { closed: true } = {\n closed: true,\n next: noop,\n error: defaultErrorHandler,\n complete: noop,\n};\n", "/**\n * Symbol.observable or a string \"@@observable\". Used for interop\n *\n * @deprecated We will no longer be exporting this symbol in upcoming versions of RxJS.\n * Instead polyfill and use Symbol.observable directly *or* use https://www.npmjs.com/package/symbol-observable\n */\nexport const observable: string | symbol = (() => (typeof Symbol === 'function' && Symbol.observable) || '@@observable')();\n", "/**\n * This function takes one parameter and just returns it. Simply put,\n * this is like `(x: T): T => x`.\n *\n * ## Examples\n *\n * This is useful in some cases when using things like `mergeMap`\n *\n * ```ts\n * import { interval, take, map, range, mergeMap, identity } from 'rxjs';\n *\n * const source$ = interval(1000).pipe(take(5));\n *\n * const result$ = source$.pipe(\n * map(i => range(i)),\n * mergeMap(identity) // same as mergeMap(x => x)\n * );\n *\n * result$.subscribe({\n * next: console.log\n * });\n * ```\n *\n * Or when you want to selectively apply an operator\n *\n * ```ts\n * import { interval, take, identity } from 'rxjs';\n *\n * const shouldLimit = () => Math.random() < 0.5;\n *\n * const source$ = interval(1000);\n *\n * const result$ = source$.pipe(shouldLimit() ? take(5) : identity);\n *\n * result$.subscribe({\n * next: console.log\n * });\n * ```\n *\n * @param x Any value that is returned by this function\n * @returns The value passed as the first parameter to this function\n */\nexport function identity(x: T): T {\n return x;\n}\n", "import { identity } from './identity';\nimport { UnaryFunction } from '../types';\n\nexport function pipe(): typeof identity;\nexport function pipe(fn1: UnaryFunction): UnaryFunction;\nexport function pipe(fn1: UnaryFunction, fn2: UnaryFunction): UnaryFunction;\nexport function pipe(fn1: UnaryFunction, fn2: UnaryFunction, fn3: UnaryFunction): UnaryFunction;\nexport function pipe(\n fn1: UnaryFunction,\n fn2: UnaryFunction,\n fn3: UnaryFunction,\n fn4: UnaryFunction\n): UnaryFunction;\nexport function pipe(\n fn1: UnaryFunction,\n fn2: UnaryFunction,\n fn3: UnaryFunction,\n fn4: UnaryFunction,\n fn5: UnaryFunction\n): UnaryFunction;\nexport function pipe(\n fn1: UnaryFunction,\n fn2: UnaryFunction,\n fn3: UnaryFunction,\n fn4: UnaryFunction,\n fn5: UnaryFunction,\n fn6: UnaryFunction\n): UnaryFunction;\nexport function pipe(\n fn1: UnaryFunction,\n fn2: UnaryFunction,\n fn3: UnaryFunction,\n fn4: UnaryFunction,\n fn5: UnaryFunction,\n fn6: UnaryFunction,\n fn7: UnaryFunction\n): UnaryFunction;\nexport function pipe(\n fn1: UnaryFunction,\n fn2: UnaryFunction,\n fn3: UnaryFunction,\n fn4: UnaryFunction,\n fn5: UnaryFunction,\n fn6: UnaryFunction,\n fn7: UnaryFunction,\n fn8: UnaryFunction\n): UnaryFunction;\nexport function pipe(\n fn1: UnaryFunction,\n fn2: UnaryFunction,\n fn3: UnaryFunction,\n fn4: UnaryFunction,\n fn5: UnaryFunction,\n fn6: UnaryFunction,\n fn7: UnaryFunction,\n fn8: UnaryFunction,\n fn9: UnaryFunction\n): UnaryFunction;\nexport function pipe(\n fn1: UnaryFunction,\n fn2: UnaryFunction,\n fn3: UnaryFunction,\n fn4: UnaryFunction,\n fn5: UnaryFunction,\n fn6: UnaryFunction,\n fn7: UnaryFunction,\n fn8: UnaryFunction,\n fn9: UnaryFunction,\n ...fns: UnaryFunction[]\n): UnaryFunction;\n\n/**\n * pipe() can be called on one or more functions, each of which can take one argument (\"UnaryFunction\")\n * and uses it to return a value.\n * It returns a function that takes one argument, passes it to the first UnaryFunction, and then\n * passes the result to the next one, passes that result to the next one, and so on. \n */\nexport function pipe(...fns: Array>): UnaryFunction {\n return pipeFromArray(fns);\n}\n\n/** @internal */\nexport function pipeFromArray(fns: Array>): UnaryFunction {\n if (fns.length === 0) {\n return identity as UnaryFunction;\n }\n\n if (fns.length === 1) {\n return fns[0];\n }\n\n return function piped(input: T): R {\n return fns.reduce((prev: any, fn: UnaryFunction) => fn(prev), input as any);\n };\n}\n", "import { Operator } from './Operator';\nimport { SafeSubscriber, Subscriber } from './Subscriber';\nimport { isSubscription, Subscription } from './Subscription';\nimport { TeardownLogic, OperatorFunction, Subscribable, Observer } from './types';\nimport { observable as Symbol_observable } from './symbol/observable';\nimport { pipeFromArray } from './util/pipe';\nimport { config } from './config';\nimport { isFunction } from './util/isFunction';\nimport { errorContext } from './util/errorContext';\n\n/**\n * A representation of any set of values over any amount of time. This is the most basic building block\n * of RxJS.\n *\n * @class Observable\n */\nexport class Observable implements Subscribable {\n /**\n * @deprecated Internal implementation detail, do not use directly. Will be made internal in v8.\n */\n source: Observable | undefined;\n\n /**\n * @deprecated Internal implementation detail, do not use directly. Will be made internal in v8.\n */\n operator: Operator | undefined;\n\n /**\n * @constructor\n * @param {Function} subscribe the function that is called when the Observable is\n * initially subscribed to. This function is given a Subscriber, to which new values\n * can be `next`ed, or an `error` method can be called to raise an error, or\n * `complete` can be called to notify of a successful completion.\n */\n constructor(subscribe?: (this: Observable, subscriber: Subscriber) => TeardownLogic) {\n if (subscribe) {\n this._subscribe = subscribe;\n }\n }\n\n // HACK: Since TypeScript inherits static properties too, we have to\n // fight against TypeScript here so Subject can have a different static create signature\n /**\n * Creates a new Observable by calling the Observable constructor\n * @owner Observable\n * @method create\n * @param {Function} subscribe? the subscriber function to be passed to the Observable constructor\n * @return {Observable} a new observable\n * @nocollapse\n * @deprecated Use `new Observable()` instead. Will be removed in v8.\n */\n static create: (...args: any[]) => any = (subscribe?: (subscriber: Subscriber) => TeardownLogic) => {\n return new Observable(subscribe);\n };\n\n /**\n * Creates a new Observable, with this Observable instance as the source, and the passed\n * operator defined as the new observable's operator.\n * @method lift\n * @param operator the operator defining the operation to take on the observable\n * @return a new observable with the Operator applied\n * @deprecated Internal implementation detail, do not use directly. Will be made internal in v8.\n * If you have implemented an operator using `lift`, it is recommended that you create an\n * operator by simply returning `new Observable()` directly. See \"Creating new operators from\n * scratch\" section here: https://rxjs.dev/guide/operators\n */\n lift(operator?: Operator): Observable {\n const observable = new Observable();\n observable.source = this;\n observable.operator = operator;\n return observable;\n }\n\n subscribe(observerOrNext?: Partial> | ((value: T) => void)): Subscription;\n /** @deprecated Instead of passing separate callback arguments, use an observer argument. Signatures taking separate callback arguments will be removed in v8. Details: https://rxjs.dev/deprecations/subscribe-arguments */\n subscribe(next?: ((value: T) => void) | null, error?: ((error: any) => void) | null, complete?: (() => void) | null): Subscription;\n /**\n * Invokes an execution of an Observable and registers Observer handlers for notifications it will emit.\n *\n * Use it when you have all these Observables, but still nothing is happening.\n *\n * `subscribe` is not a regular operator, but a method that calls Observable's internal `subscribe` function. It\n * might be for example a function that you passed to Observable's constructor, but most of the time it is\n * a library implementation, which defines what will be emitted by an Observable, and when it be will emitted. This means\n * that calling `subscribe` is actually the moment when Observable starts its work, not when it is created, as it is often\n * the thought.\n *\n * Apart from starting the execution of an Observable, this method allows you to listen for values\n * that an Observable emits, as well as for when it completes or errors. You can achieve this in two\n * of the following ways.\n *\n * The first way is creating an object that implements {@link Observer} interface. It should have methods\n * defined by that interface, but note that it should be just a regular JavaScript object, which you can create\n * yourself in any way you want (ES6 class, classic function constructor, object literal etc.). In particular, do\n * not attempt to use any RxJS implementation details to create Observers - you don't need them. Remember also\n * that your object does not have to implement all methods. If you find yourself creating a method that doesn't\n * do anything, you can simply omit it. Note however, if the `error` method is not provided and an error happens,\n * it will be thrown asynchronously. Errors thrown asynchronously cannot be caught using `try`/`catch`. Instead,\n * use the {@link onUnhandledError} configuration option or use a runtime handler (like `window.onerror` or\n * `process.on('error)`) to be notified of unhandled errors. Because of this, it's recommended that you provide\n * an `error` method to avoid missing thrown errors.\n *\n * The second way is to give up on Observer object altogether and simply provide callback functions in place of its methods.\n * This means you can provide three functions as arguments to `subscribe`, where the first function is equivalent\n * of a `next` method, the second of an `error` method and the third of a `complete` method. Just as in case of an Observer,\n * if you do not need to listen for something, you can omit a function by passing `undefined` or `null`,\n * since `subscribe` recognizes these functions by where they were placed in function call. When it comes\n * to the `error` function, as with an Observer, if not provided, errors emitted by an Observable will be thrown asynchronously.\n *\n * You can, however, subscribe with no parameters at all. This may be the case where you're not interested in terminal events\n * and you also handled emissions internally by using operators (e.g. using `tap`).\n *\n * Whichever style of calling `subscribe` you use, in both cases it returns a Subscription object.\n * This object allows you to call `unsubscribe` on it, which in turn will stop the work that an Observable does and will clean\n * up all resources that an Observable used. Note that cancelling a subscription will not call `complete` callback\n * provided to `subscribe` function, which is reserved for a regular completion signal that comes from an Observable.\n *\n * Remember that callbacks provided to `subscribe` are not guaranteed to be called asynchronously.\n * It is an Observable itself that decides when these functions will be called. For example {@link of}\n * by default emits all its values synchronously. Always check documentation for how given Observable\n * will behave when subscribed and if its default behavior can be modified with a `scheduler`.\n *\n * #### Examples\n *\n * Subscribe with an {@link guide/observer Observer}\n *\n * ```ts\n * import { of } from 'rxjs';\n *\n * const sumObserver = {\n * sum: 0,\n * next(value) {\n * console.log('Adding: ' + value);\n * this.sum = this.sum + value;\n * },\n * error() {\n * // We actually could just remove this method,\n * // since we do not really care about errors right now.\n * },\n * complete() {\n * console.log('Sum equals: ' + this.sum);\n * }\n * };\n *\n * of(1, 2, 3) // Synchronously emits 1, 2, 3 and then completes.\n * .subscribe(sumObserver);\n *\n * // Logs:\n * // 'Adding: 1'\n * // 'Adding: 2'\n * // 'Adding: 3'\n * // 'Sum equals: 6'\n * ```\n *\n * Subscribe with functions ({@link deprecations/subscribe-arguments deprecated})\n *\n * ```ts\n * import { of } from 'rxjs'\n *\n * let sum = 0;\n *\n * of(1, 2, 3).subscribe(\n * value => {\n * console.log('Adding: ' + value);\n * sum = sum + value;\n * },\n * undefined,\n * () => console.log('Sum equals: ' + sum)\n * );\n *\n * // Logs:\n * // 'Adding: 1'\n * // 'Adding: 2'\n * // 'Adding: 3'\n * // 'Sum equals: 6'\n * ```\n *\n * Cancel a subscription\n *\n * ```ts\n * import { interval } from 'rxjs';\n *\n * const subscription = interval(1000).subscribe({\n * next(num) {\n * console.log(num)\n * },\n * complete() {\n * // Will not be called, even when cancelling subscription.\n * console.log('completed!');\n * }\n * });\n *\n * setTimeout(() => {\n * subscription.unsubscribe();\n * console.log('unsubscribed!');\n * }, 2500);\n *\n * // Logs:\n * // 0 after 1s\n * // 1 after 2s\n * // 'unsubscribed!' after 2.5s\n * ```\n *\n * @param {Observer|Function} observerOrNext (optional) Either an observer with methods to be called,\n * or the first of three possible handlers, which is the handler for each value emitted from the subscribed\n * Observable.\n * @param {Function} error (optional) A handler for a terminal event resulting from an error. If no error handler is provided,\n * the error will be thrown asynchronously as unhandled.\n * @param {Function} complete (optional) A handler for a terminal event resulting from successful completion.\n * @return {Subscription} a subscription reference to the registered handlers\n * @method subscribe\n */\n subscribe(\n observerOrNext?: Partial> | ((value: T) => void) | null,\n error?: ((error: any) => void) | null,\n complete?: (() => void) | null\n ): Subscription {\n const subscriber = isSubscriber(observerOrNext) ? observerOrNext : new SafeSubscriber(observerOrNext, error, complete);\n\n errorContext(() => {\n const { operator, source } = this;\n subscriber.add(\n operator\n ? // We're dealing with a subscription in the\n // operator chain to one of our lifted operators.\n operator.call(subscriber, source)\n : source\n ? // If `source` has a value, but `operator` does not, something that\n // had intimate knowledge of our API, like our `Subject`, must have\n // set it. We're going to just call `_subscribe` directly.\n this._subscribe(subscriber)\n : // In all other cases, we're likely wrapping a user-provided initializer\n // function, so we need to catch errors and handle them appropriately.\n this._trySubscribe(subscriber)\n );\n });\n\n return subscriber;\n }\n\n /** @internal */\n protected _trySubscribe(sink: Subscriber): TeardownLogic {\n try {\n return this._subscribe(sink);\n } catch (err) {\n // We don't need to return anything in this case,\n // because it's just going to try to `add()` to a subscription\n // above.\n sink.error(err);\n }\n }\n\n /**\n * Used as a NON-CANCELLABLE means of subscribing to an observable, for use with\n * APIs that expect promises, like `async/await`. You cannot unsubscribe from this.\n *\n * **WARNING**: Only use this with observables you *know* will complete. If the source\n * observable does not complete, you will end up with a promise that is hung up, and\n * potentially all of the state of an async function hanging out in memory. To avoid\n * this situation, look into adding something like {@link timeout}, {@link take},\n * {@link takeWhile}, or {@link takeUntil} amongst others.\n *\n * #### Example\n *\n * ```ts\n * import { interval, take } from 'rxjs';\n *\n * const source$ = interval(1000).pipe(take(4));\n *\n * async function getTotal() {\n * let total = 0;\n *\n * await source$.forEach(value => {\n * total += value;\n * console.log('observable -> ' + value);\n * });\n *\n * return total;\n * }\n *\n * getTotal().then(\n * total => console.log('Total: ' + total)\n * );\n *\n * // Expected:\n * // 'observable -> 0'\n * // 'observable -> 1'\n * // 'observable -> 2'\n * // 'observable -> 3'\n * // 'Total: 6'\n * ```\n *\n * @param next a handler for each value emitted by the observable\n * @return a promise that either resolves on observable completion or\n * rejects with the handled error\n */\n forEach(next: (value: T) => void): Promise;\n\n /**\n * @param next a handler for each value emitted by the observable\n * @param promiseCtor a constructor function used to instantiate the Promise\n * @return a promise that either resolves on observable completion or\n * rejects with the handled error\n * @deprecated Passing a Promise constructor will no longer be available\n * in upcoming versions of RxJS. This is because it adds weight to the library, for very\n * little benefit. If you need this functionality, it is recommended that you either\n * polyfill Promise, or you create an adapter to convert the returned native promise\n * to whatever promise implementation you wanted. Will be removed in v8.\n */\n forEach(next: (value: T) => void, promiseCtor: PromiseConstructorLike): Promise;\n\n forEach(next: (value: T) => void, promiseCtor?: PromiseConstructorLike): Promise {\n promiseCtor = getPromiseCtor(promiseCtor);\n\n return new promiseCtor((resolve, reject) => {\n const subscriber = new SafeSubscriber({\n next: (value) => {\n try {\n next(value);\n } catch (err) {\n reject(err);\n subscriber.unsubscribe();\n }\n },\n error: reject,\n complete: resolve,\n });\n this.subscribe(subscriber);\n }) as Promise;\n }\n\n /** @internal */\n protected _subscribe(subscriber: Subscriber): TeardownLogic {\n return this.source?.subscribe(subscriber);\n }\n\n /**\n * An interop point defined by the es7-observable spec https://github.com/zenparsing/es-observable\n * @method Symbol.observable\n * @return {Observable} this instance of the observable\n */\n [Symbol_observable]() {\n return this;\n }\n\n /* tslint:disable:max-line-length */\n pipe(): Observable;\n pipe(op1: OperatorFunction): Observable;\n pipe(op1: OperatorFunction, op2: OperatorFunction): Observable;\n pipe(op1: OperatorFunction, op2: OperatorFunction, op3: OperatorFunction): Observable;\n pipe(\n op1: OperatorFunction,\n op2: OperatorFunction,\n op3: OperatorFunction,\n op4: OperatorFunction\n ): Observable;\n pipe(\n op1: OperatorFunction,\n op2: OperatorFunction,\n op3: OperatorFunction,\n op4: OperatorFunction,\n op5: OperatorFunction\n ): Observable;\n pipe(\n op1: OperatorFunction,\n op2: OperatorFunction,\n op3: OperatorFunction,\n op4: OperatorFunction,\n op5: OperatorFunction,\n op6: OperatorFunction\n ): Observable;\n pipe(\n op1: OperatorFunction,\n op2: OperatorFunction,\n op3: OperatorFunction,\n op4: OperatorFunction,\n op5: OperatorFunction,\n op6: OperatorFunction,\n op7: OperatorFunction\n ): Observable;\n pipe(\n op1: OperatorFunction,\n op2: OperatorFunction,\n op3: OperatorFunction,\n op4: OperatorFunction,\n op5: OperatorFunction,\n op6: OperatorFunction,\n op7: OperatorFunction,\n op8: OperatorFunction\n ): Observable;\n pipe(\n op1: OperatorFunction,\n op2: OperatorFunction,\n op3: OperatorFunction,\n op4: OperatorFunction,\n op5: OperatorFunction,\n op6: OperatorFunction,\n op7: OperatorFunction,\n op8: OperatorFunction,\n op9: OperatorFunction\n ): Observable;\n pipe(\n op1: OperatorFunction,\n op2: OperatorFunction,\n op3: OperatorFunction,\n op4: OperatorFunction,\n op5: OperatorFunction,\n op6: OperatorFunction,\n op7: OperatorFunction,\n op8: OperatorFunction,\n op9: OperatorFunction,\n ...operations: OperatorFunction[]\n ): Observable;\n /* tslint:enable:max-line-length */\n\n /**\n * Used to stitch together functional operators into a chain.\n * @method pipe\n * @return {Observable} the Observable result of all of the operators having\n * been called in the order they were passed in.\n *\n * ## Example\n *\n * ```ts\n * import { interval, filter, map, scan } from 'rxjs';\n *\n * interval(1000)\n * .pipe(\n * filter(x => x % 2 === 0),\n * map(x => x + x),\n * scan((acc, x) => acc + x)\n * )\n * .subscribe(x => console.log(x));\n * ```\n */\n pipe(...operations: OperatorFunction[]): Observable {\n return pipeFromArray(operations)(this);\n }\n\n /* tslint:disable:max-line-length */\n /** @deprecated Replaced with {@link firstValueFrom} and {@link lastValueFrom}. Will be removed in v8. Details: https://rxjs.dev/deprecations/to-promise */\n toPromise(): Promise;\n /** @deprecated Replaced with {@link firstValueFrom} and {@link lastValueFrom}. Will be removed in v8. Details: https://rxjs.dev/deprecations/to-promise */\n toPromise(PromiseCtor: typeof Promise): Promise;\n /** @deprecated Replaced with {@link firstValueFrom} and {@link lastValueFrom}. Will be removed in v8. Details: https://rxjs.dev/deprecations/to-promise */\n toPromise(PromiseCtor: PromiseConstructorLike): Promise;\n /* tslint:enable:max-line-length */\n\n /**\n * Subscribe to this Observable and get a Promise resolving on\n * `complete` with the last emission (if any).\n *\n * **WARNING**: Only use this with observables you *know* will complete. If the source\n * observable does not complete, you will end up with a promise that is hung up, and\n * potentially all of the state of an async function hanging out in memory. To avoid\n * this situation, look into adding something like {@link timeout}, {@link take},\n * {@link takeWhile}, or {@link takeUntil} amongst others.\n *\n * @method toPromise\n * @param [promiseCtor] a constructor function used to instantiate\n * the Promise\n * @return A Promise that resolves with the last value emit, or\n * rejects on an error. If there were no emissions, Promise\n * resolves with undefined.\n * @deprecated Replaced with {@link firstValueFrom} and {@link lastValueFrom}. Will be removed in v8. Details: https://rxjs.dev/deprecations/to-promise\n */\n toPromise(promiseCtor?: PromiseConstructorLike): Promise {\n promiseCtor = getPromiseCtor(promiseCtor);\n\n return new promiseCtor((resolve, reject) => {\n let value: T | undefined;\n this.subscribe(\n (x: T) => (value = x),\n (err: any) => reject(err),\n () => resolve(value)\n );\n }) as Promise;\n }\n}\n\n/**\n * Decides between a passed promise constructor from consuming code,\n * A default configured promise constructor, and the native promise\n * constructor and returns it. If nothing can be found, it will throw\n * an error.\n * @param promiseCtor The optional promise constructor to passed by consuming code\n */\nfunction getPromiseCtor(promiseCtor: PromiseConstructorLike | undefined) {\n return promiseCtor ?? config.Promise ?? Promise;\n}\n\nfunction isObserver(value: any): value is Observer {\n return value && isFunction(value.next) && isFunction(value.error) && isFunction(value.complete);\n}\n\nfunction isSubscriber(value: any): value is Subscriber {\n return (value && value instanceof Subscriber) || (isObserver(value) && isSubscription(value));\n}\n", "import { Observable } from '../Observable';\nimport { Subscriber } from '../Subscriber';\nimport { OperatorFunction } from '../types';\nimport { isFunction } from './isFunction';\n\n/**\n * Used to determine if an object is an Observable with a lift function.\n */\nexport function hasLift(source: any): source is { lift: InstanceType['lift'] } {\n return isFunction(source?.lift);\n}\n\n/**\n * Creates an `OperatorFunction`. Used to define operators throughout the library in a concise way.\n * @param init The logic to connect the liftedSource to the subscriber at the moment of subscription.\n */\nexport function operate(\n init: (liftedSource: Observable, subscriber: Subscriber) => (() => void) | void\n): OperatorFunction {\n return (source: Observable) => {\n if (hasLift(source)) {\n return source.lift(function (this: Subscriber, liftedSource: Observable) {\n try {\n return init(liftedSource, this);\n } catch (err) {\n this.error(err);\n }\n });\n }\n throw new TypeError('Unable to lift unknown Observable type');\n };\n}\n", "import { Subscriber } from '../Subscriber';\n\n/**\n * Creates an instance of an `OperatorSubscriber`.\n * @param destination The downstream subscriber.\n * @param onNext Handles next values, only called if this subscriber is not stopped or closed. Any\n * error that occurs in this function is caught and sent to the `error` method of this subscriber.\n * @param onError Handles errors from the subscription, any errors that occur in this handler are caught\n * and send to the `destination` error handler.\n * @param onComplete Handles completion notification from the subscription. Any errors that occur in\n * this handler are sent to the `destination` error handler.\n * @param onFinalize Additional teardown logic here. This will only be called on teardown if the\n * subscriber itself is not already closed. This is called after all other teardown logic is executed.\n */\nexport function createOperatorSubscriber(\n destination: Subscriber,\n onNext?: (value: T) => void,\n onComplete?: () => void,\n onError?: (err: any) => void,\n onFinalize?: () => void\n): Subscriber {\n return new OperatorSubscriber(destination, onNext, onComplete, onError, onFinalize);\n}\n\n/**\n * A generic helper for allowing operators to be created with a Subscriber and\n * use closures to capture necessary state from the operator function itself.\n */\nexport class OperatorSubscriber extends Subscriber {\n /**\n * Creates an instance of an `OperatorSubscriber`.\n * @param destination The downstream subscriber.\n * @param onNext Handles next values, only called if this subscriber is not stopped or closed. Any\n * error that occurs in this function is caught and sent to the `error` method of this subscriber.\n * @param onError Handles errors from the subscription, any errors that occur in this handler are caught\n * and send to the `destination` error handler.\n * @param onComplete Handles completion notification from the subscription. Any errors that occur in\n * this handler are sent to the `destination` error handler.\n * @param onFinalize Additional finalization logic here. This will only be called on finalization if the\n * subscriber itself is not already closed. This is called after all other finalization logic is executed.\n * @param shouldUnsubscribe An optional check to see if an unsubscribe call should truly unsubscribe.\n * NOTE: This currently **ONLY** exists to support the strange behavior of {@link groupBy}, where unsubscription\n * to the resulting observable does not actually disconnect from the source if there are active subscriptions\n * to any grouped observable. (DO NOT EXPOSE OR USE EXTERNALLY!!!)\n */\n constructor(\n destination: Subscriber,\n onNext?: (value: T) => void,\n onComplete?: () => void,\n onError?: (err: any) => void,\n private onFinalize?: () => void,\n private shouldUnsubscribe?: () => boolean\n ) {\n // It's important - for performance reasons - that all of this class's\n // members are initialized and that they are always initialized in the same\n // order. This will ensure that all OperatorSubscriber instances have the\n // same hidden class in V8. This, in turn, will help keep the number of\n // hidden classes involved in property accesses within the base class as\n // low as possible. If the number of hidden classes involved exceeds four,\n // the property accesses will become megamorphic and performance penalties\n // will be incurred - i.e. inline caches won't be used.\n //\n // The reasons for ensuring all instances have the same hidden class are\n // further discussed in this blog post from Benedikt Meurer:\n // https://benediktmeurer.de/2018/03/23/impact-of-polymorphism-on-component-based-frameworks-like-react/\n super(destination);\n this._next = onNext\n ? function (this: OperatorSubscriber, value: T) {\n try {\n onNext(value);\n } catch (err) {\n destination.error(err);\n }\n }\n : super._next;\n this._error = onError\n ? function (this: OperatorSubscriber, err: any) {\n try {\n onError(err);\n } catch (err) {\n // Send any errors that occur down stream.\n destination.error(err);\n } finally {\n // Ensure finalization.\n this.unsubscribe();\n }\n }\n : super._error;\n this._complete = onComplete\n ? function (this: OperatorSubscriber) {\n try {\n onComplete();\n } catch (err) {\n // Send any errors that occur down stream.\n destination.error(err);\n } finally {\n // Ensure finalization.\n this.unsubscribe();\n }\n }\n : super._complete;\n }\n\n unsubscribe() {\n if (!this.shouldUnsubscribe || this.shouldUnsubscribe()) {\n const { closed } = this;\n super.unsubscribe();\n // Execute additional teardown if we have any and we didn't already do so.\n !closed && this.onFinalize?.();\n }\n }\n}\n", "import { Subscription } from '../Subscription';\n\ninterface AnimationFrameProvider {\n schedule(callback: FrameRequestCallback): Subscription;\n requestAnimationFrame: typeof requestAnimationFrame;\n cancelAnimationFrame: typeof cancelAnimationFrame;\n delegate:\n | {\n requestAnimationFrame: typeof requestAnimationFrame;\n cancelAnimationFrame: typeof cancelAnimationFrame;\n }\n | undefined;\n}\n\nexport const animationFrameProvider: AnimationFrameProvider = {\n // When accessing the delegate, use the variable rather than `this` so that\n // the functions can be called without being bound to the provider.\n schedule(callback) {\n let request = requestAnimationFrame;\n let cancel: typeof cancelAnimationFrame | undefined = cancelAnimationFrame;\n const { delegate } = animationFrameProvider;\n if (delegate) {\n request = delegate.requestAnimationFrame;\n cancel = delegate.cancelAnimationFrame;\n }\n const handle = request((timestamp) => {\n // Clear the cancel function. The request has been fulfilled, so\n // attempting to cancel the request upon unsubscription would be\n // pointless.\n cancel = undefined;\n callback(timestamp);\n });\n return new Subscription(() => cancel?.(handle));\n },\n requestAnimationFrame(...args) {\n const { delegate } = animationFrameProvider;\n return (delegate?.requestAnimationFrame || requestAnimationFrame)(...args);\n },\n cancelAnimationFrame(...args) {\n const { delegate } = animationFrameProvider;\n return (delegate?.cancelAnimationFrame || cancelAnimationFrame)(...args);\n },\n delegate: undefined,\n};\n", "import { createErrorClass } from './createErrorClass';\n\nexport interface ObjectUnsubscribedError extends Error {}\n\nexport interface ObjectUnsubscribedErrorCtor {\n /**\n * @deprecated Internal implementation detail. Do not construct error instances.\n * Cannot be tagged as internal: https://github.com/ReactiveX/rxjs/issues/6269\n */\n new (): ObjectUnsubscribedError;\n}\n\n/**\n * An error thrown when an action is invalid because the object has been\n * unsubscribed.\n *\n * @see {@link Subject}\n * @see {@link BehaviorSubject}\n *\n * @class ObjectUnsubscribedError\n */\nexport const ObjectUnsubscribedError: ObjectUnsubscribedErrorCtor = createErrorClass(\n (_super) =>\n function ObjectUnsubscribedErrorImpl(this: any) {\n _super(this);\n this.name = 'ObjectUnsubscribedError';\n this.message = 'object unsubscribed';\n }\n);\n", "import { Operator } from './Operator';\nimport { Observable } from './Observable';\nimport { Subscriber } from './Subscriber';\nimport { Subscription, EMPTY_SUBSCRIPTION } from './Subscription';\nimport { Observer, SubscriptionLike, TeardownLogic } from './types';\nimport { ObjectUnsubscribedError } from './util/ObjectUnsubscribedError';\nimport { arrRemove } from './util/arrRemove';\nimport { errorContext } from './util/errorContext';\n\n/**\n * A Subject is a special type of Observable that allows values to be\n * multicasted to many Observers. Subjects are like EventEmitters.\n *\n * Every Subject is an Observable and an Observer. You can subscribe to a\n * Subject, and you can call next to feed values as well as error and complete.\n */\nexport class Subject extends Observable implements SubscriptionLike {\n closed = false;\n\n private currentObservers: Observer[] | null = null;\n\n /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n observers: Observer[] = [];\n /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n isStopped = false;\n /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n hasError = false;\n /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n thrownError: any = null;\n\n /**\n * Creates a \"subject\" by basically gluing an observer to an observable.\n *\n * @nocollapse\n * @deprecated Recommended you do not use. Will be removed at some point in the future. Plans for replacement still under discussion.\n */\n static create: (...args: any[]) => any = (destination: Observer, source: Observable): AnonymousSubject => {\n return new AnonymousSubject(destination, source);\n };\n\n constructor() {\n // NOTE: This must be here to obscure Observable's constructor.\n super();\n }\n\n /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n lift(operator: Operator): Observable {\n const subject = new AnonymousSubject(this, this);\n subject.operator = operator as any;\n return subject as any;\n }\n\n /** @internal */\n protected _throwIfClosed() {\n if (this.closed) {\n throw new ObjectUnsubscribedError();\n }\n }\n\n next(value: T) {\n errorContext(() => {\n this._throwIfClosed();\n if (!this.isStopped) {\n if (!this.currentObservers) {\n this.currentObservers = Array.from(this.observers);\n }\n for (const observer of this.currentObservers) {\n observer.next(value);\n }\n }\n });\n }\n\n error(err: any) {\n errorContext(() => {\n this._throwIfClosed();\n if (!this.isStopped) {\n this.hasError = this.isStopped = true;\n this.thrownError = err;\n const { observers } = this;\n while (observers.length) {\n observers.shift()!.error(err);\n }\n }\n });\n }\n\n complete() {\n errorContext(() => {\n this._throwIfClosed();\n if (!this.isStopped) {\n this.isStopped = true;\n const { observers } = this;\n while (observers.length) {\n observers.shift()!.complete();\n }\n }\n });\n }\n\n unsubscribe() {\n this.isStopped = this.closed = true;\n this.observers = this.currentObservers = null!;\n }\n\n get observed() {\n return this.observers?.length > 0;\n }\n\n /** @internal */\n protected _trySubscribe(subscriber: Subscriber): TeardownLogic {\n this._throwIfClosed();\n return super._trySubscribe(subscriber);\n }\n\n /** @internal */\n protected _subscribe(subscriber: Subscriber): Subscription {\n this._throwIfClosed();\n this._checkFinalizedStatuses(subscriber);\n return this._innerSubscribe(subscriber);\n }\n\n /** @internal */\n protected _innerSubscribe(subscriber: Subscriber) {\n const { hasError, isStopped, observers } = this;\n if (hasError || isStopped) {\n return EMPTY_SUBSCRIPTION;\n }\n this.currentObservers = null;\n observers.push(subscriber);\n return new Subscription(() => {\n this.currentObservers = null;\n arrRemove(observers, subscriber);\n });\n }\n\n /** @internal */\n protected _checkFinalizedStatuses(subscriber: Subscriber) {\n const { hasError, thrownError, isStopped } = this;\n if (hasError) {\n subscriber.error(thrownError);\n } else if (isStopped) {\n subscriber.complete();\n }\n }\n\n /**\n * Creates a new Observable with this Subject as the source. You can do this\n * to create custom Observer-side logic of the Subject and conceal it from\n * code that uses the Observable.\n * @return {Observable} Observable that the Subject casts to\n */\n asObservable(): Observable {\n const observable: any = new Observable();\n observable.source = this;\n return observable;\n }\n}\n\n/**\n * @class AnonymousSubject\n */\nexport class AnonymousSubject extends Subject {\n constructor(\n /** @deprecated Internal implementation detail, do not use directly. Will be made internal in v8. */\n public destination?: Observer,\n source?: Observable\n ) {\n super();\n this.source = source;\n }\n\n next(value: T) {\n this.destination?.next?.(value);\n }\n\n error(err: any) {\n this.destination?.error?.(err);\n }\n\n complete() {\n this.destination?.complete?.();\n }\n\n /** @internal */\n protected _subscribe(subscriber: Subscriber): Subscription {\n return this.source?.subscribe(subscriber) ?? EMPTY_SUBSCRIPTION;\n }\n}\n", "import { Subject } from './Subject';\nimport { Subscriber } from './Subscriber';\nimport { Subscription } from './Subscription';\n\n/**\n * A variant of Subject that requires an initial value and emits its current\n * value whenever it is subscribed to.\n *\n * @class BehaviorSubject\n */\nexport class BehaviorSubject extends Subject {\n constructor(private _value: T) {\n super();\n }\n\n get value(): T {\n return this.getValue();\n }\n\n /** @internal */\n protected _subscribe(subscriber: Subscriber): Subscription {\n const subscription = super._subscribe(subscriber);\n !subscription.closed && subscriber.next(this._value);\n return subscription;\n }\n\n getValue(): T {\n const { hasError, thrownError, _value } = this;\n if (hasError) {\n throw thrownError;\n }\n this._throwIfClosed();\n return _value;\n }\n\n next(value: T): void {\n super.next((this._value = value));\n }\n}\n", "import { TimestampProvider } from '../types';\n\ninterface DateTimestampProvider extends TimestampProvider {\n delegate: TimestampProvider | undefined;\n}\n\nexport const dateTimestampProvider: DateTimestampProvider = {\n now() {\n // Use the variable rather than `this` so that the function can be called\n // without being bound to the provider.\n return (dateTimestampProvider.delegate || Date).now();\n },\n delegate: undefined,\n};\n", "import { Subject } from './Subject';\nimport { TimestampProvider } from './types';\nimport { Subscriber } from './Subscriber';\nimport { Subscription } from './Subscription';\nimport { dateTimestampProvider } from './scheduler/dateTimestampProvider';\n\n/**\n * A variant of {@link Subject} that \"replays\" old values to new subscribers by emitting them when they first subscribe.\n *\n * `ReplaySubject` has an internal buffer that will store a specified number of values that it has observed. Like `Subject`,\n * `ReplaySubject` \"observes\" values by having them passed to its `next` method. When it observes a value, it will store that\n * value for a time determined by the configuration of the `ReplaySubject`, as passed to its constructor.\n *\n * When a new subscriber subscribes to the `ReplaySubject` instance, it will synchronously emit all values in its buffer in\n * a First-In-First-Out (FIFO) manner. The `ReplaySubject` will also complete, if it has observed completion; and it will\n * error if it has observed an error.\n *\n * There are two main configuration items to be concerned with:\n *\n * 1. `bufferSize` - This will determine how many items are stored in the buffer, defaults to infinite.\n * 2. `windowTime` - The amount of time to hold a value in the buffer before removing it from the buffer.\n *\n * Both configurations may exist simultaneously. So if you would like to buffer a maximum of 3 values, as long as the values\n * are less than 2 seconds old, you could do so with a `new ReplaySubject(3, 2000)`.\n *\n * ### Differences with BehaviorSubject\n *\n * `BehaviorSubject` is similar to `new ReplaySubject(1)`, with a couple of exceptions:\n *\n * 1. `BehaviorSubject` comes \"primed\" with a single value upon construction.\n * 2. `ReplaySubject` will replay values, even after observing an error, where `BehaviorSubject` will not.\n *\n * @see {@link Subject}\n * @see {@link BehaviorSubject}\n * @see {@link shareReplay}\n */\nexport class ReplaySubject extends Subject {\n private _buffer: (T | number)[] = [];\n private _infiniteTimeWindow = true;\n\n /**\n * @param bufferSize The size of the buffer to replay on subscription\n * @param windowTime The amount of time the buffered items will stay buffered\n * @param timestampProvider An object with a `now()` method that provides the current timestamp. This is used to\n * calculate the amount of time something has been buffered.\n */\n constructor(\n private _bufferSize = Infinity,\n private _windowTime = Infinity,\n private _timestampProvider: TimestampProvider = dateTimestampProvider\n ) {\n super();\n this._infiniteTimeWindow = _windowTime === Infinity;\n this._bufferSize = Math.max(1, _bufferSize);\n this._windowTime = Math.max(1, _windowTime);\n }\n\n next(value: T): void {\n const { isStopped, _buffer, _infiniteTimeWindow, _timestampProvider, _windowTime } = this;\n if (!isStopped) {\n _buffer.push(value);\n !_infiniteTimeWindow && _buffer.push(_timestampProvider.now() + _windowTime);\n }\n this._trimBuffer();\n super.next(value);\n }\n\n /** @internal */\n protected _subscribe(subscriber: Subscriber): Subscription {\n this._throwIfClosed();\n this._trimBuffer();\n\n const subscription = this._innerSubscribe(subscriber);\n\n const { _infiniteTimeWindow, _buffer } = this;\n // We use a copy here, so reentrant code does not mutate our array while we're\n // emitting it to a new subscriber.\n const copy = _buffer.slice();\n for (let i = 0; i < copy.length && !subscriber.closed; i += _infiniteTimeWindow ? 1 : 2) {\n subscriber.next(copy[i] as T);\n }\n\n this._checkFinalizedStatuses(subscriber);\n\n return subscription;\n }\n\n private _trimBuffer() {\n const { _bufferSize, _timestampProvider, _buffer, _infiniteTimeWindow } = this;\n // If we don't have an infinite buffer size, and we're over the length,\n // use splice to truncate the old buffer values off. Note that we have to\n // double the size for instances where we're not using an infinite time window\n // because we're storing the values and the timestamps in the same array.\n const adjustedBufferSize = (_infiniteTimeWindow ? 1 : 2) * _bufferSize;\n _bufferSize < Infinity && adjustedBufferSize < _buffer.length && _buffer.splice(0, _buffer.length - adjustedBufferSize);\n\n // Now, if we're not in an infinite time window, remove all values where the time is\n // older than what is allowed.\n if (!_infiniteTimeWindow) {\n const now = _timestampProvider.now();\n let last = 0;\n // Search the array for the first timestamp that isn't expired and\n // truncate the buffer up to that point.\n for (let i = 1; i < _buffer.length && (_buffer[i] as number) <= now; i += 2) {\n last = i;\n }\n last && _buffer.splice(0, last + 1);\n }\n }\n}\n", "import { Scheduler } from '../Scheduler';\nimport { Subscription } from '../Subscription';\nimport { SchedulerAction } from '../types';\n\n/**\n * A unit of work to be executed in a `scheduler`. An action is typically\n * created from within a {@link SchedulerLike} and an RxJS user does not need to concern\n * themselves about creating and manipulating an Action.\n *\n * ```ts\n * class Action extends Subscription {\n * new (scheduler: Scheduler, work: (state?: T) => void);\n * schedule(state?: T, delay: number = 0): Subscription;\n * }\n * ```\n *\n * @class Action\n */\nexport class Action extends Subscription {\n constructor(scheduler: Scheduler, work: (this: SchedulerAction, state?: T) => void) {\n super();\n }\n /**\n * Schedules this action on its parent {@link SchedulerLike} for execution. May be passed\n * some context object, `state`. May happen at some point in the future,\n * according to the `delay` parameter, if specified.\n * @param {T} [state] Some contextual data that the `work` function uses when\n * called by the Scheduler.\n * @param {number} [delay] Time to wait before executing the work, where the\n * time unit is implicit and defined by the Scheduler.\n * @return {void}\n */\n public schedule(state?: T, delay: number = 0): Subscription {\n return this;\n }\n}\n", "import type { TimerHandle } from './timerHandle';\ntype SetIntervalFunction = (handler: () => void, timeout?: number, ...args: any[]) => TimerHandle;\ntype ClearIntervalFunction = (handle: TimerHandle) => void;\n\ninterface IntervalProvider {\n setInterval: SetIntervalFunction;\n clearInterval: ClearIntervalFunction;\n delegate:\n | {\n setInterval: SetIntervalFunction;\n clearInterval: ClearIntervalFunction;\n }\n | undefined;\n}\n\nexport const intervalProvider: IntervalProvider = {\n // When accessing the delegate, use the variable rather than `this` so that\n // the functions can be called without being bound to the provider.\n setInterval(handler: () => void, timeout?: number, ...args) {\n const { delegate } = intervalProvider;\n if (delegate?.setInterval) {\n return delegate.setInterval(handler, timeout, ...args);\n }\n return setInterval(handler, timeout, ...args);\n },\n clearInterval(handle) {\n const { delegate } = intervalProvider;\n return (delegate?.clearInterval || clearInterval)(handle as any);\n },\n delegate: undefined,\n};\n", "import { Action } from './Action';\nimport { SchedulerAction } from '../types';\nimport { Subscription } from '../Subscription';\nimport { AsyncScheduler } from './AsyncScheduler';\nimport { intervalProvider } from './intervalProvider';\nimport { arrRemove } from '../util/arrRemove';\nimport { TimerHandle } from './timerHandle';\n\nexport class AsyncAction extends Action {\n public id: TimerHandle | undefined;\n public state?: T;\n // @ts-ignore: Property has no initializer and is not definitely assigned\n public delay: number;\n protected pending: boolean = false;\n\n constructor(protected scheduler: AsyncScheduler, protected work: (this: SchedulerAction, state?: T) => void) {\n super(scheduler, work);\n }\n\n public schedule(state?: T, delay: number = 0): Subscription {\n if (this.closed) {\n return this;\n }\n\n // Always replace the current state with the new state.\n this.state = state;\n\n const id = this.id;\n const scheduler = this.scheduler;\n\n //\n // Important implementation note:\n //\n // Actions only execute once by default, unless rescheduled from within the\n // scheduled callback. This allows us to implement single and repeat\n // actions via the same code path, without adding API surface area, as well\n // as mimic traditional recursion but across asynchronous boundaries.\n //\n // However, JS runtimes and timers distinguish between intervals achieved by\n // serial `setTimeout` calls vs. a single `setInterval` call. An interval of\n // serial `setTimeout` calls can be individually delayed, which delays\n // scheduling the next `setTimeout`, and so on. `setInterval` attempts to\n // guarantee the interval callback will be invoked more precisely to the\n // interval period, regardless of load.\n //\n // Therefore, we use `setInterval` to schedule single and repeat actions.\n // If the action reschedules itself with the same delay, the interval is not\n // canceled. If the action doesn't reschedule, or reschedules with a\n // different delay, the interval will be canceled after scheduled callback\n // execution.\n //\n if (id != null) {\n this.id = this.recycleAsyncId(scheduler, id, delay);\n }\n\n // Set the pending flag indicating that this action has been scheduled, or\n // has recursively rescheduled itself.\n this.pending = true;\n\n this.delay = delay;\n // If this action has already an async Id, don't request a new one.\n this.id = this.id ?? this.requestAsyncId(scheduler, this.id, delay);\n\n return this;\n }\n\n protected requestAsyncId(scheduler: AsyncScheduler, _id?: TimerHandle, delay: number = 0): TimerHandle {\n return intervalProvider.setInterval(scheduler.flush.bind(scheduler, this), delay);\n }\n\n protected recycleAsyncId(_scheduler: AsyncScheduler, id?: TimerHandle, delay: number | null = 0): TimerHandle | undefined {\n // If this action is rescheduled with the same delay time, don't clear the interval id.\n if (delay != null && this.delay === delay && this.pending === false) {\n return id;\n }\n // Otherwise, if the action's delay time is different from the current delay,\n // or the action has been rescheduled before it's executed, clear the interval id\n if (id != null) {\n intervalProvider.clearInterval(id);\n }\n\n return undefined;\n }\n\n /**\n * Immediately executes this action and the `work` it contains.\n * @return {any}\n */\n public execute(state: T, delay: number): any {\n if (this.closed) {\n return new Error('executing a cancelled action');\n }\n\n this.pending = false;\n const error = this._execute(state, delay);\n if (error) {\n return error;\n } else if (this.pending === false && this.id != null) {\n // Dequeue if the action didn't reschedule itself. Don't call\n // unsubscribe(), because the action could reschedule later.\n // For example:\n // ```\n // scheduler.schedule(function doWork(counter) {\n // /* ... I'm a busy worker bee ... */\n // var originalAction = this;\n // /* wait 100ms before rescheduling the action */\n // setTimeout(function () {\n // originalAction.schedule(counter + 1);\n // }, 100);\n // }, 1000);\n // ```\n this.id = this.recycleAsyncId(this.scheduler, this.id, null);\n }\n }\n\n protected _execute(state: T, _delay: number): any {\n let errored: boolean = false;\n let errorValue: any;\n try {\n this.work(state);\n } catch (e) {\n errored = true;\n // HACK: Since code elsewhere is relying on the \"truthiness\" of the\n // return here, we can't have it return \"\" or 0 or false.\n // TODO: Clean this up when we refactor schedulers mid-version-8 or so.\n errorValue = e ? e : new Error('Scheduled action threw falsy error');\n }\n if (errored) {\n this.unsubscribe();\n return errorValue;\n }\n }\n\n unsubscribe() {\n if (!this.closed) {\n const { id, scheduler } = this;\n const { actions } = scheduler;\n\n this.work = this.state = this.scheduler = null!;\n this.pending = false;\n\n arrRemove(actions, this);\n if (id != null) {\n this.id = this.recycleAsyncId(scheduler, id, null);\n }\n\n this.delay = null!;\n super.unsubscribe();\n }\n }\n}\n", "import { Action } from './scheduler/Action';\nimport { Subscription } from './Subscription';\nimport { SchedulerLike, SchedulerAction } from './types';\nimport { dateTimestampProvider } from './scheduler/dateTimestampProvider';\n\n/**\n * An execution context and a data structure to order tasks and schedule their\n * execution. Provides a notion of (potentially virtual) time, through the\n * `now()` getter method.\n *\n * Each unit of work in a Scheduler is called an `Action`.\n *\n * ```ts\n * class Scheduler {\n * now(): number;\n * schedule(work, delay?, state?): Subscription;\n * }\n * ```\n *\n * @class Scheduler\n * @deprecated Scheduler is an internal implementation detail of RxJS, and\n * should not be used directly. Rather, create your own class and implement\n * {@link SchedulerLike}. Will be made internal in v8.\n */\nexport class Scheduler implements SchedulerLike {\n public static now: () => number = dateTimestampProvider.now;\n\n constructor(private schedulerActionCtor: typeof Action, now: () => number = Scheduler.now) {\n this.now = now;\n }\n\n /**\n * A getter method that returns a number representing the current time\n * (at the time this function was called) according to the scheduler's own\n * internal clock.\n * @return {number} A number that represents the current time. May or may not\n * have a relation to wall-clock time. May or may not refer to a time unit\n * (e.g. milliseconds).\n */\n public now: () => number;\n\n /**\n * Schedules a function, `work`, for execution. May happen at some point in\n * the future, according to the `delay` parameter, if specified. May be passed\n * some context object, `state`, which will be passed to the `work` function.\n *\n * The given arguments will be processed an stored as an Action object in a\n * queue of actions.\n *\n * @param {function(state: ?T): ?Subscription} work A function representing a\n * task, or some unit of work to be executed by the Scheduler.\n * @param {number} [delay] Time to wait before executing the work, where the\n * time unit is implicit and defined by the Scheduler itself.\n * @param {T} [state] Some contextual data that the `work` function uses when\n * called by the Scheduler.\n * @return {Subscription} A subscription in order to be able to unsubscribe\n * the scheduled work.\n */\n public schedule(work: (this: SchedulerAction, state?: T) => void, delay: number = 0, state?: T): Subscription {\n return new this.schedulerActionCtor(this, work).schedule(state, delay);\n }\n}\n", "import { Scheduler } from '../Scheduler';\nimport { Action } from './Action';\nimport { AsyncAction } from './AsyncAction';\nimport { TimerHandle } from './timerHandle';\n\nexport class AsyncScheduler extends Scheduler {\n public actions: Array> = [];\n /**\n * A flag to indicate whether the Scheduler is currently executing a batch of\n * queued actions.\n * @type {boolean}\n * @internal\n */\n public _active: boolean = false;\n /**\n * An internal ID used to track the latest asynchronous task such as those\n * coming from `setTimeout`, `setInterval`, `requestAnimationFrame`, and\n * others.\n * @type {any}\n * @internal\n */\n public _scheduled: TimerHandle | undefined;\n\n constructor(SchedulerAction: typeof Action, now: () => number = Scheduler.now) {\n super(SchedulerAction, now);\n }\n\n public flush(action: AsyncAction): void {\n const { actions } = this;\n\n if (this._active) {\n actions.push(action);\n return;\n }\n\n let error: any;\n this._active = true;\n\n do {\n if ((error = action.execute(action.state, action.delay))) {\n break;\n }\n } while ((action = actions.shift()!)); // exhaust the scheduler queue\n\n this._active = false;\n\n if (error) {\n while ((action = actions.shift()!)) {\n action.unsubscribe();\n }\n throw error;\n }\n }\n}\n", "import { AsyncAction } from './AsyncAction';\nimport { AsyncScheduler } from './AsyncScheduler';\n\n/**\n *\n * Async Scheduler\n *\n * Schedule task as if you used setTimeout(task, duration)\n *\n * `async` scheduler schedules tasks asynchronously, by putting them on the JavaScript\n * event loop queue. It is best used to delay tasks in time or to schedule tasks repeating\n * in intervals.\n *\n * If you just want to \"defer\" task, that is to perform it right after currently\n * executing synchronous code ends (commonly achieved by `setTimeout(deferredTask, 0)`),\n * better choice will be the {@link asapScheduler} scheduler.\n *\n * ## Examples\n * Use async scheduler to delay task\n * ```ts\n * import { asyncScheduler } from 'rxjs';\n *\n * const task = () => console.log('it works!');\n *\n * asyncScheduler.schedule(task, 2000);\n *\n * // After 2 seconds logs:\n * // \"it works!\"\n * ```\n *\n * Use async scheduler to repeat task in intervals\n * ```ts\n * import { asyncScheduler } from 'rxjs';\n *\n * function task(state) {\n * console.log(state);\n * this.schedule(state + 1, 1000); // `this` references currently executing Action,\n * // which we reschedule with new state and delay\n * }\n *\n * asyncScheduler.schedule(task, 3000, 0);\n *\n * // Logs:\n * // 0 after 3s\n * // 1 after 4s\n * // 2 after 5s\n * // 3 after 6s\n * ```\n */\n\nexport const asyncScheduler = new AsyncScheduler(AsyncAction);\n\n/**\n * @deprecated Renamed to {@link asyncScheduler}. Will be removed in v8.\n */\nexport const async = asyncScheduler;\n", "import { AsyncAction } from './AsyncAction';\nimport { Subscription } from '../Subscription';\nimport { QueueScheduler } from './QueueScheduler';\nimport { SchedulerAction } from '../types';\nimport { TimerHandle } from './timerHandle';\n\nexport class QueueAction extends AsyncAction {\n constructor(protected scheduler: QueueScheduler, protected work: (this: SchedulerAction, state?: T) => void) {\n super(scheduler, work);\n }\n\n public schedule(state?: T, delay: number = 0): Subscription {\n if (delay > 0) {\n return super.schedule(state, delay);\n }\n this.delay = delay;\n this.state = state;\n this.scheduler.flush(this);\n return this;\n }\n\n public execute(state: T, delay: number): any {\n return delay > 0 || this.closed ? super.execute(state, delay) : this._execute(state, delay);\n }\n\n protected requestAsyncId(scheduler: QueueScheduler, id?: TimerHandle, delay: number = 0): TimerHandle {\n // If delay exists and is greater than 0, or if the delay is null (the\n // action wasn't rescheduled) but was originally scheduled as an async\n // action, then recycle as an async action.\n\n if ((delay != null && delay > 0) || (delay == null && this.delay > 0)) {\n return super.requestAsyncId(scheduler, id, delay);\n }\n\n // Otherwise flush the scheduler starting with this action.\n scheduler.flush(this);\n\n // HACK: In the past, this was returning `void`. However, `void` isn't a valid\n // `TimerHandle`, and generally the return value here isn't really used. So the\n // compromise is to return `0` which is both \"falsy\" and a valid `TimerHandle`,\n // as opposed to refactoring every other instanceo of `requestAsyncId`.\n return 0;\n }\n}\n", "import { AsyncScheduler } from './AsyncScheduler';\n\nexport class QueueScheduler extends AsyncScheduler {\n}\n", "import { QueueAction } from './QueueAction';\nimport { QueueScheduler } from './QueueScheduler';\n\n/**\n *\n * Queue Scheduler\n *\n * Put every next task on a queue, instead of executing it immediately\n *\n * `queue` scheduler, when used with delay, behaves the same as {@link asyncScheduler} scheduler.\n *\n * When used without delay, it schedules given task synchronously - executes it right when\n * it is scheduled. However when called recursively, that is when inside the scheduled task,\n * another task is scheduled with queue scheduler, instead of executing immediately as well,\n * that task will be put on a queue and wait for current one to finish.\n *\n * This means that when you execute task with `queue` scheduler, you are sure it will end\n * before any other task scheduled with that scheduler will start.\n *\n * ## Examples\n * Schedule recursively first, then do something\n * ```ts\n * import { queueScheduler } from 'rxjs';\n *\n * queueScheduler.schedule(() => {\n * queueScheduler.schedule(() => console.log('second')); // will not happen now, but will be put on a queue\n *\n * console.log('first');\n * });\n *\n * // Logs:\n * // \"first\"\n * // \"second\"\n * ```\n *\n * Reschedule itself recursively\n * ```ts\n * import { queueScheduler } from 'rxjs';\n *\n * queueScheduler.schedule(function(state) {\n * if (state !== 0) {\n * console.log('before', state);\n * this.schedule(state - 1); // `this` references currently executing Action,\n * // which we reschedule with new state\n * console.log('after', state);\n * }\n * }, 0, 3);\n *\n * // In scheduler that runs recursively, you would expect:\n * // \"before\", 3\n * // \"before\", 2\n * // \"before\", 1\n * // \"after\", 1\n * // \"after\", 2\n * // \"after\", 3\n *\n * // But with queue it logs:\n * // \"before\", 3\n * // \"after\", 3\n * // \"before\", 2\n * // \"after\", 2\n * // \"before\", 1\n * // \"after\", 1\n * ```\n */\n\nexport const queueScheduler = new QueueScheduler(QueueAction);\n\n/**\n * @deprecated Renamed to {@link queueScheduler}. Will be removed in v8.\n */\nexport const queue = queueScheduler;\n", "import { AsyncAction } from './AsyncAction';\nimport { AnimationFrameScheduler } from './AnimationFrameScheduler';\nimport { SchedulerAction } from '../types';\nimport { animationFrameProvider } from './animationFrameProvider';\nimport { TimerHandle } from './timerHandle';\n\nexport class AnimationFrameAction extends AsyncAction {\n constructor(protected scheduler: AnimationFrameScheduler, protected work: (this: SchedulerAction, state?: T) => void) {\n super(scheduler, work);\n }\n\n protected requestAsyncId(scheduler: AnimationFrameScheduler, id?: TimerHandle, delay: number = 0): TimerHandle {\n // If delay is greater than 0, request as an async action.\n if (delay !== null && delay > 0) {\n return super.requestAsyncId(scheduler, id, delay);\n }\n // Push the action to the end of the scheduler queue.\n scheduler.actions.push(this);\n // If an animation frame has already been requested, don't request another\n // one. If an animation frame hasn't been requested yet, request one. Return\n // the current animation frame request id.\n return scheduler._scheduled || (scheduler._scheduled = animationFrameProvider.requestAnimationFrame(() => scheduler.flush(undefined)));\n }\n\n protected recycleAsyncId(scheduler: AnimationFrameScheduler, id?: TimerHandle, delay: number = 0): TimerHandle | undefined {\n // If delay exists and is greater than 0, or if the delay is null (the\n // action wasn't rescheduled) but was originally scheduled as an async\n // action, then recycle as an async action.\n if (delay != null ? delay > 0 : this.delay > 0) {\n return super.recycleAsyncId(scheduler, id, delay);\n }\n // If the scheduler queue has no remaining actions with the same async id,\n // cancel the requested animation frame and set the scheduled flag to\n // undefined so the next AnimationFrameAction will request its own.\n const { actions } = scheduler;\n if (id != null && actions[actions.length - 1]?.id !== id) {\n animationFrameProvider.cancelAnimationFrame(id as number);\n scheduler._scheduled = undefined;\n }\n // Return undefined so the action knows to request a new async id if it's rescheduled.\n return undefined;\n }\n}\n", "import { AsyncAction } from './AsyncAction';\nimport { AsyncScheduler } from './AsyncScheduler';\n\nexport class AnimationFrameScheduler extends AsyncScheduler {\n public flush(action?: AsyncAction): void {\n this._active = true;\n // The async id that effects a call to flush is stored in _scheduled.\n // Before executing an action, it's necessary to check the action's async\n // id to determine whether it's supposed to be executed in the current\n // flush.\n // Previous implementations of this method used a count to determine this,\n // but that was unsound, as actions that are unsubscribed - i.e. cancelled -\n // are removed from the actions array and that can shift actions that are\n // scheduled to be executed in a subsequent flush into positions at which\n // they are executed within the current flush.\n const flushId = this._scheduled;\n this._scheduled = undefined;\n\n const { actions } = this;\n let error: any;\n action = action || actions.shift()!;\n\n do {\n if ((error = action.execute(action.state, action.delay))) {\n break;\n }\n } while ((action = actions[0]) && action.id === flushId && actions.shift());\n\n this._active = false;\n\n if (error) {\n while ((action = actions[0]) && action.id === flushId && actions.shift()) {\n action.unsubscribe();\n }\n throw error;\n }\n }\n}\n", "import { AnimationFrameAction } from './AnimationFrameAction';\nimport { AnimationFrameScheduler } from './AnimationFrameScheduler';\n\n/**\n *\n * Animation Frame Scheduler\n *\n * Perform task when `window.requestAnimationFrame` would fire\n *\n * When `animationFrame` scheduler is used with delay, it will fall back to {@link asyncScheduler} scheduler\n * behaviour.\n *\n * Without delay, `animationFrame` scheduler can be used to create smooth browser animations.\n * It makes sure scheduled task will happen just before next browser content repaint,\n * thus performing animations as efficiently as possible.\n *\n * ## Example\n * Schedule div height animation\n * ```ts\n * // html:
\n * import { animationFrameScheduler } from 'rxjs';\n *\n * const div = document.querySelector('div');\n *\n * animationFrameScheduler.schedule(function(height) {\n * div.style.height = height + \"px\";\n *\n * this.schedule(height + 1); // `this` references currently executing Action,\n * // which we reschedule with new state\n * }, 0, 0);\n *\n * // You will see a div element growing in height\n * ```\n */\n\nexport const animationFrameScheduler = new AnimationFrameScheduler(AnimationFrameAction);\n\n/**\n * @deprecated Renamed to {@link animationFrameScheduler}. Will be removed in v8.\n */\nexport const animationFrame = animationFrameScheduler;\n", "import { Observable } from '../Observable';\nimport { SchedulerLike } from '../types';\n\n/**\n * A simple Observable that emits no items to the Observer and immediately\n * emits a complete notification.\n *\n * Just emits 'complete', and nothing else.\n *\n * ![](empty.png)\n *\n * A simple Observable that only emits the complete notification. It can be used\n * for composing with other Observables, such as in a {@link mergeMap}.\n *\n * ## Examples\n *\n * Log complete notification\n *\n * ```ts\n * import { EMPTY } from 'rxjs';\n *\n * EMPTY.subscribe({\n * next: () => console.log('Next'),\n * complete: () => console.log('Complete!')\n * });\n *\n * // Outputs\n * // Complete!\n * ```\n *\n * Emit the number 7, then complete\n *\n * ```ts\n * import { EMPTY, startWith } from 'rxjs';\n *\n * const result = EMPTY.pipe(startWith(7));\n * result.subscribe(x => console.log(x));\n *\n * // Outputs\n * // 7\n * ```\n *\n * Map and flatten only odd numbers to the sequence `'a'`, `'b'`, `'c'`\n *\n * ```ts\n * import { interval, mergeMap, of, EMPTY } from 'rxjs';\n *\n * const interval$ = interval(1000);\n * const result = interval$.pipe(\n * mergeMap(x => x % 2 === 1 ? of('a', 'b', 'c') : EMPTY),\n * );\n * result.subscribe(x => console.log(x));\n *\n * // Results in the following to the console:\n * // x is equal to the count on the interval, e.g. (0, 1, 2, 3, ...)\n * // x will occur every 1000ms\n * // if x % 2 is equal to 1, print a, b, c (each on its own)\n * // if x % 2 is not equal to 1, nothing will be output\n * ```\n *\n * @see {@link Observable}\n * @see {@link NEVER}\n * @see {@link of}\n * @see {@link throwError}\n */\nexport const EMPTY = new Observable((subscriber) => subscriber.complete());\n\n/**\n * @param scheduler A {@link SchedulerLike} to use for scheduling\n * the emission of the complete notification.\n * @deprecated Replaced with the {@link EMPTY} constant or {@link scheduled} (e.g. `scheduled([], scheduler)`). Will be removed in v8.\n */\nexport function empty(scheduler?: SchedulerLike) {\n return scheduler ? emptyScheduled(scheduler) : EMPTY;\n}\n\nfunction emptyScheduled(scheduler: SchedulerLike) {\n return new Observable((subscriber) => scheduler.schedule(() => subscriber.complete()));\n}\n", "import { SchedulerLike } from '../types';\nimport { isFunction } from './isFunction';\n\nexport function isScheduler(value: any): value is SchedulerLike {\n return value && isFunction(value.schedule);\n}\n", "import { SchedulerLike } from '../types';\nimport { isFunction } from './isFunction';\nimport { isScheduler } from './isScheduler';\n\nfunction last(arr: T[]): T | undefined {\n return arr[arr.length - 1];\n}\n\nexport function popResultSelector(args: any[]): ((...args: unknown[]) => unknown) | undefined {\n return isFunction(last(args)) ? args.pop() : undefined;\n}\n\nexport function popScheduler(args: any[]): SchedulerLike | undefined {\n return isScheduler(last(args)) ? args.pop() : undefined;\n}\n\nexport function popNumber(args: any[], defaultValue: number): number {\n return typeof last(args) === 'number' ? args.pop()! : defaultValue;\n}\n", "export const isArrayLike = ((x: any): x is ArrayLike => x && typeof x.length === 'number' && typeof x !== 'function');", "import { isFunction } from \"./isFunction\";\n\n/**\n * Tests to see if the object is \"thennable\".\n * @param value the object to test\n */\nexport function isPromise(value: any): value is PromiseLike {\n return isFunction(value?.then);\n}\n", "import { InteropObservable } from '../types';\nimport { observable as Symbol_observable } from '../symbol/observable';\nimport { isFunction } from './isFunction';\n\n/** Identifies an input as being Observable (but not necessary an Rx Observable) */\nexport function isInteropObservable(input: any): input is InteropObservable {\n return isFunction(input[Symbol_observable]);\n}\n", "import { isFunction } from './isFunction';\n\nexport function isAsyncIterable(obj: any): obj is AsyncIterable {\n return Symbol.asyncIterator && isFunction(obj?.[Symbol.asyncIterator]);\n}\n", "/**\n * Creates the TypeError to throw if an invalid object is passed to `from` or `scheduled`.\n * @param input The object that was passed.\n */\nexport function createInvalidObservableTypeError(input: any) {\n // TODO: We should create error codes that can be looked up, so this can be less verbose.\n return new TypeError(\n `You provided ${\n input !== null && typeof input === 'object' ? 'an invalid object' : `'${input}'`\n } where a stream was expected. You can provide an Observable, Promise, ReadableStream, Array, AsyncIterable, or Iterable.`\n );\n}\n", "export function getSymbolIterator(): symbol {\n if (typeof Symbol !== 'function' || !Symbol.iterator) {\n return '@@iterator' as any;\n }\n\n return Symbol.iterator;\n}\n\nexport const iterator = getSymbolIterator();\n", "import { iterator as Symbol_iterator } from '../symbol/iterator';\nimport { isFunction } from './isFunction';\n\n/** Identifies an input as being an Iterable */\nexport function isIterable(input: any): input is Iterable {\n return isFunction(input?.[Symbol_iterator]);\n}\n", "import { ReadableStreamLike } from '../types';\nimport { isFunction } from './isFunction';\n\nexport async function* readableStreamLikeToAsyncGenerator(readableStream: ReadableStreamLike): AsyncGenerator {\n const reader = readableStream.getReader();\n try {\n while (true) {\n const { value, done } = await reader.read();\n if (done) {\n return;\n }\n yield value!;\n }\n } finally {\n reader.releaseLock();\n }\n}\n\nexport function isReadableStreamLike(obj: any): obj is ReadableStreamLike {\n // We don't want to use instanceof checks because they would return\n // false for instances from another Realm, like an