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Merge pull request #22 from cancerDHC/add-pilot-examples
Adds the CCDH Pilots to the Example Data Repository. Some of these don't work, probably because of bugs in LinkML Runtime (#39). Others either can't be set up with the Python Data Classes or cannot be validated when they are (#40).
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| name: Test with pytest and flake8 | ||
| name: Test with pytest and black | ||
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| on: [push] | ||
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| This folder contains content created for the CCDH Pilot in September 2021. | ||
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| It includes the two demonstrated developed for this Pilot as well as converters | ||
| that translate imported node data into the CRDC-H model as YAML, then validate | ||
| those transformed files using JSON Schema as well as LinkML Python data classes. |
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| Files in this directory were copied here from | ||
| https://github.com/cancerDHC/data-model-harmonization/tree/d83c2853ea6cdd8dfbb9204c2cd4c335969660c6/data-examples/f2f-2021-09-data-examples |
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ccdh-pilot/demonstrator-1/d1_harmonized_gdc_specimen_cc.yaml
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ccdh-pilot/demonstrator-1/d1_harmonized_icdc_specimen_cc.yaml
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| icdc_specimen: | ||
| Title: ICDC Specimen Example - Sept 2021 F2F Demonstrator 1 | ||
| Schema: ccdh.0713cc.Specimen | ||
| Description: | ||
| - "CRDC-H-compliant representation of the 'aggregate' ICDC source data example described here: https://docs.google.com/spreadsheets/d/14lWLDD7iyJG0G57m6BgWYIeqrxK04P3qQRwxziqEz1A/edit#gid=0" | ||
| - "**FOR EASIEST VIEWING TURN WORD WRAP OFF SO THAT COMMENTS DON'T RUN ONTO A NEW LINE**" | ||
| - "In this example enumerated values are captured using a CodeableConcept object which bundles one or more Coding objects, each holding a single concept code and supporting metadata." | ||
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| Example: # type = Specimen | ||
| id: "f2f:052c671d-118a-11e9-afb9-0a9c39d33490" # Local uuid for the Specimen a assigned by the system in which this record lives (here, the CCDH F2F Demonstrator, hence the 'f2f' prefix). | ||
| # identifier: # type = Identifier (Identifier is a complex data type, but we are only showing a single field from this type) | ||
| # - value: "ncats-cop:NCATS-COP01-CCB050227 0103" # ICDC.Sample.sample_id (specified here as a CURIE, where the prefix indicates the system that assigned it) | ||
| # - value: "icdc-sample:30502" # ICDC.Sample._id (specified here as a CURIE, where the prefix indicates the system that assigned it) | ||
| # - value: "biosample:SAMEA1652206" # Proposed globally unique identifier format, per recommendation of the CRDC-DST (specified here as a CURIE, where the prefix indicates the system that assigned it) | ||
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| specimen_type: # type = CodeableConcept | ||
| coding: # type = Coding | ||
| - code: C84517 # The first Coding holds the harmonized code for this concept - the code for an NCIT term. | ||
| label: Fresh Specimen # The preferred label of the term from NCIT. | ||
| system: http://ncithesaurus.nci.nih.gov # A URL for the NCIT system (this is likely not the url we would ultimately use) | ||
| tag: # A tag indicating this to be the harmonized code for this concept | ||
| - harmonized | ||
| - code: Sample # The second Coding holds the original code used by the source node. Here, this is the 'type' of the entity in ICDC (Sample). | ||
| label: Sample # The human-readable label (implicitly the same as the code, which is human-readable) | ||
| system: http://crdc.nci.nih.gov/icdc # A URL for the ICDC system (we made this up - t.b.d. what an official URL would look like) | ||
| tag: # A 'tag' indicating this to be the code for this concept in the original source data. | ||
| - original | ||
| source_subject: # type = Subject | ||
| id: "f2f:01b2691b-63d8-11e8-bcf1-0a2705229b82" # Local uuid assigned by this system for the Subject. The Subject instance is represented separately later in this document. | ||
| source_material_type: # type = CodeableConcept (see comments on the 'specimen_type' field above for a detailed explanation of this data object's content) | ||
| coding: # type = Coding | ||
| - code: C12801 # The first Coding holds the harmonized code for this concept - the code for an NCIT term. | ||
| label: Tissue # The preferred label of the term from NCIT. | ||
| system: http://ncithesaurus.nci.nih.gov # A URL for the NCIT system (this is likely not the url we would ultimately use) | ||
| tag: # A tag indicating this to be the harmonized code for this concept | ||
| - harmonized | ||
| - code: Tissue # The second Coding holds the original code used by the source node. ICDC uses a readable strings for their codes. | ||
| label: Tissue # The human-readable label (implicitly the same as the code, which are human-readable in ICDC) | ||
| system: http://crdc.nci.nih.gov/icdc # A URL for the ICDC system (we made this up - t.b.d. what an official URL would look like) | ||
| tag: # A 'tag' indicating this to be the code for this concept in the original source data. | ||
| - original | ||
| general_tissue_pathology: # type = CodeableConcept | ||
| coding: # type = Coding | ||
| - code: C14143 | ||
| label: Malignant | ||
| system: http://ncithesaurus.nci.nih.gov | ||
| tag: | ||
| - harmonized | ||
| - code: Malignant | ||
| label: Malignant | ||
| system: http://crdc.nci.nih.gov/icdc | ||
| tag: | ||
| - original | ||
| specific_tissue_pathology: # type = CodeableConcept | ||
| coding: # type = Coding | ||
| - code: C9145 | ||
| label: Osteosarcoma | ||
| system: http://ncithesaurus.nci.nih.gov | ||
| tag: | ||
| - harmonized | ||
| - code: Osteosarcoma | ||
| label: Osteosarcoma | ||
| system: http://crdc.nci.nih.gov/icdc | ||
| tag: | ||
| - original | ||
| tumor_status_at_collection: # type = CodeableConcept | ||
| coding: # type = Coding | ||
| - code: C3261 | ||
| label: Metastatic Neoplasm | ||
| system: http://ncithesaurus.nci.nih.gov | ||
| tag: | ||
| - harmonized | ||
| - code: Metastatic | ||
| label: Metastatic | ||
| system: http://crdc.nci.nih.gov/icdc | ||
| tag: | ||
| - original | ||
| creation_activity: # type = SpecimenCreationActivity. This object encapsulates data related to how a specimen was created. It is inlined because this is not a stand-alone, identified entity. | ||
| activity_type: # type = CodeableConcept. This field indicates that the activity instance here represents the initial collection from a source, rather than derivation from an existing specimen (e.g via portioning or aliquoting). | ||
| coding: # type = Coding | ||
| - code: C93435 | ||
| label: Performed Specimen Collection | ||
| system: http://ncithesaurus.nci.nih.gov | ||
| tag: | ||
| - harmonized | ||
| date_ended: # type = TimePoint | ||
| date_time: "2010-07-23" | ||
| collection_site: # type = BodySite | ||
| site: # type = CodeableConcept | ||
| coding: # type = Coding | ||
| - code: C12468 | ||
| label: Lung | ||
| system: http://ncithesaurus.nci.nih.gov | ||
| tag: | ||
| - harmonized | ||
| - code: Lung | ||
| label: Lung | ||
| system: http://crdc.nci.nih.gov/icdc | ||
| tag: | ||
| - original | ||
| processing_activity: # type = SpecimenProcessingActivity. This object encapsulates data related to how a specimen was processed. It is inlined because this is not a stand-alone, identified entity. | ||
| - activity_type: # type = CodeableConcept | ||
| coding: # type = Coding | ||
| - code: CC63521 | ||
| label: Quick Freeze | ||
| system: http://ncithesaurus.nci.nih.gov | ||
| tag: | ||
| - harmonized | ||
| - code: Snap Frozen | ||
| label: Snap Frozen | ||
| system: http://crdc.nci.nih.gov/icdc | ||
| tag: | ||
| - original | ||
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| --- | ||
| icdc_subject: | ||
| Title: ICDC Subject Example - Sept 2021 F2F Demonstrator 1 | ||
| Schema: ccdh.0713.Subject | ||
| Description: | ||
| - "This is a minimal example showing only id and identifiers. For a richer Subject record, see the examples in Demonstrator 2." | ||
| Example: # type: Subject | ||
| id: "f2f:17029fd8-cd05-4089-8da3-52795823a647" # Local uuid assigned by this system for the Subject | ||
| # identifier: # type: Identifier | ||
| # - value: "icdc-case:30196" # ICDC.Cases.case_id | ||
| # - value: "crdc:su0000003" # Proposed globally unique identifier per recommendation of the CRDC-DST | ||
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| --- | ||
| icdc_diagnosis: | ||
| Title: ICDC Diagnosis Example - Sept 2021 F2F Demonstrator 1 | ||
| Schema: "ccdh.0713cc.Diagnosis" | ||
| Description: | ||
| - "CRDC-H-compliant representation of the synthetic source data example described here: https://docs.google.com/spreadsheets/d/14lWLDD7iyJG0G57m6BgWYIeqrxK04P3qQRwxziqEz1A/edit#gid=0" | ||
| - "For easiest viewing, **TURN WORD WRAP OFF** so that comments don't run onto a new line." | ||
| Example: # type = Diagnosis | ||
| id: "f2f:de3468e83-4c86-4258-98d1-a986445cce73" # Local uuid assigned by this system for the Diagnosis | ||
| # identifier: # type = Identifier | ||
| # - value: "icdc-diagnosis:30279" # ICDC.Diagnosis._id | ||
| subject: # type = Subject | ||
| id: "f2f:01b2691b-63d8-11e8-bcf1-0a2705229b82" | ||
| condition: # type = CodeableConcept | ||
| coding: # type = Coding | ||
| - code: C9145 | ||
| label: Osteosarcoma | ||
| system: http://ncithesaurus.nci.nih.gov | ||
| tag: | ||
| - harmonized | ||
| - code: Osteosarcoma (OS) | ||
| label: Osteosarcoma (OS) | ||
| system: http://crdc.nci.nih.gov/icdc | ||
| tag: | ||
| - original | ||
| # primary_site: # type = BodySite | ||
| # - site: # type = CodeableConcept | ||
| # coding: # type = Coding | ||
| # - code: C12366 | ||
| # label: Bone | ||
| # system: http://ncithesaurus.nci.nih.gov | ||
| # tag: | ||
| # - harmonized | ||
| # - code: Bone | ||
| # label: Bone | ||
| # system: http://crdc.nci.nih.gov/icdc | ||
| # tag: | ||
| # - original | ||
| # stage: # type = CancerStageObservationSet | ||
| # - observations: # type = CancerStageObservation - one of many individual Stage determinations (e.g. T, N, M, Overall) about the same tumor that can comprise a single CancerStageObservationSet (here just an 'Overall' assessment, but may also include T, N, and M assessments). | ||
| # - observation_type: # type = CodeableConcept (This Codeable Concept does not contain a second Coding for the original source code because the staging level semantic is captured in an explicit property in the source PDC model, not a key-value pair as shown here) | ||
| # coding: # type = Coding | ||
| # - code: C25605 | ||
| # label: Overall | ||
| # system: http://ncithesaurus.nci.nih.gov | ||
| # tag: | ||
| # - harmonized | ||
| # value_codeable_concept: # type = CodeableConcept | ||
| # coding: # type = Coding | ||
| # - code: C27971 | ||
| # label: Stage IV | ||
| # system: http://ncithesaurus.nci.nih.gov | ||
| # tag: | ||
| # - harmonized | ||
| # - code: IV | ||
| # label: IV | ||
| # system: http://crdc.nci.nih.gov/icdc | ||
| # tag: | ||
| # - original | ||
| diagnosis_date: # type = TimePoint | ||
| date_time: "2013-06-14" | ||
| related_specimen: # type = Specimen | ||
| - id: "f2f:052c671d-118a-11e9-afb9-0a9c39d33490" # A reference to a specimen that was used to generate this Diagnosis (the Specimen instance above). | ||
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