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release files 2024-08-08 #184

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Aug 8, 2024
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release files 2024-08-08 #184

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8 changes: 4 additions & 4 deletions dpo.obo
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@@ -1,6 +1,6 @@
format-version: 1.2
data-version: dpo/releases/2024-06-13
date: 13:06:2024 12:35
data-version: dpo/releases/2024-08-08
date: 08:08:2024 12:59
subsetdef: abnormal_slim "Abnormal/normal slim"
subsetdef: absent_slim "Absent/present slim"
subsetdef: attribute_slim "Attribute slim"
Expand Down Expand Up @@ -47,7 +47,7 @@ property_value: dc:description "An ontology for the description of Drosophila me
property_value: dc:title "Drosophila Phenotype Ontology (DPO)" xsd:string
property_value: IAO:0000700 FBcv:0000347
property_value: ns:attributionURL "http://dx.doi.org/10.1186/2041-1480-4-30" xsd:string
property_value: owl:versionInfo "2024-06-13" xsd:string
property_value: owl:versionInfo "2024-08-08" xsd:string
property_value: terms:license "https://creativecommons.org/licenses/by/4.0/" xsd:string

[Term]
Expand Down Expand Up @@ -857,7 +857,7 @@ is_a: FBcv:0000671 ! abnormal cell cycle
id: FBcv:0000432
name: abnormal mitotic cell cycle
namespace: phenotypic_class
def: "Phenotype that is any abnormality in mitotic cell cycle (GO:0000278). 'mitotic cell cycle' is defined as: 'Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.'" [FBC:DOS, GOC:mah, ISBN:0815316194, Reactome:69278]
def: "Phenotype that is any abnormality in mitotic cell cycle (GO:0000278). 'mitotic cell cycle' is defined as: 'Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.'" [FBC:DOS, GOC:mah, ISBN:0815316194]
synonym: "mitotic" RELATED []
synonym: "mitotic cell cycle defective" EXACT []
is_a: FBcv:0000671 ! abnormal cell cycle
Expand Down
693 changes: 241 additions & 452 deletions src/ontology/imports/merged_import.owl
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124 changes: 54 additions & 70 deletions src/ontology/reports/basic-report.tsv
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2 changes: 1 addition & 1 deletion src/ontology/reports/chado_load_check_simple.txt
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FBcv:0007533 ! increased rate of proboscis extension reflex has unnapproved def_dbxref type: FB:FBrf0044924
FBcv:0000680 ! abnormal proboscis extension reflex has unnapproved def_dbxref type: FB:FBrf0044924
FBcv:0007545 ! decreased rate of proboscis extension reflex has unnapproved def_dbxref type: FB:FBrf0044924
FBcv:0000680 ! abnormal proboscis extension reflex has unnapproved def_dbxref type: FB:FBrf0044924
4 changes: 2 additions & 2 deletions src/ontology/reports/class-count-by-prefix.tsv
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?prefix ?numberOfClasses
"ENVO" 206
"OBI" 1
"FBbt" 230
"FBbt" 216
"CARO" 19
"FBdv" 125
"BFO" 16
Expand All @@ -10,7 +10,7 @@
"NBO" 17
"PCO" 7
"" 2
"GO" 239
"GO" 237
"CL" 4
"PATO" 134
"CHEBI" 139
2,082 changes: 1,024 additions & 1,058 deletions src/ontology/reports/edges.tsv
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10 changes: 0 additions & 10 deletions src/ontology/reports/obo_qc_dpo.owl.txt
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Expand Up @@ -11,15 +11,8 @@ WARN duplicate_definition FBbt:00005306 IAO:0000115 Nuclear division 10-13. Pola
WARN duplicate_definition FBdv:00005306 IAO:0000115 Nuclear division 10-13. Polar buds divide twice and become tightly grouped at the posterior pole by the end of this stage. Nuclei visible at the rim of the embryo. Stage 4 ends with the beginning of cellularization. Duration at 25 degrees C: approximately 50 minutes (80-130 minutes after egg laying).
WARN duplicate_definition FBbt:00014201 IAO:0000115 A collective term for stages 9 and 10.
WARN duplicate_definition FBdv:00014201 IAO:0000115 A collective term for stages 9 and 10.
WARN duplicate_definition FBbt:00005331 IAO:0000115 A collective term for stages 13-15.
WARN duplicate_definition FBdv:00005331 IAO:0000115 A collective term for stages 13-15.
WARN duplicate_definition FBbt:00004450 IAO:0000115 A collective term for stages 11 and 12.
WARN duplicate_definition FBdv:00004450 IAO:0000115 A collective term for stages 11 and 12.
WARN duplicate_definition FBbt:00000054 IAO:0000115 A collective term for stages 1-4.
WARN duplicate_definition FBdv:00000054 IAO:0000115 A collective term for stages 1-4.
WARN duplicate_definition FBbt:00000052 IAO:0000115 .
WARN duplicate_definition FBbt:00003004 IAO:0000115 .
WARN duplicate_definition FBbt:00105220 IAO:0000115 .
WARN duplicate_exact_synonym GO:0007632 oboInOwl:hasExactSynonym
WARN duplicate_exact_synonym NBO:0000314 oboInOwl:hasExactSynonym
WARN duplicate_exact_synonym GO:0007610 oboInOwl:hasExactSynonym
Expand Down Expand Up @@ -158,7 +151,6 @@ WARN missing_definition CHEBI:52625 IAO:0000115
WARN missing_definition ENVO:00000344 IAO:0000115
WARN missing_definition ENVO:01001782 IAO:0000115
WARN missing_definition FBbt:00001727 IAO:0000115
WARN missing_definition FBbt:00005290 IAO:0000115
WARN missing_definition FBbt:00007006 IAO:0000115
WARN missing_definition FBbt:00007013 IAO:0000115
WARN missing_definition FBbt:00007016 IAO:0000115
Expand Down Expand Up @@ -239,9 +231,7 @@ INFO lowercase_definition BFO:0000062 IAO:0000115 x is preceded by y if and only
INFO lowercase_definition BFO:0000063 IAO:0000115 x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.@en
INFO lowercase_definition BFO:0000066 IAO:0000115 b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t@en
INFO lowercase_definition BFO:0000067 IAO:0000115 [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t@en
INFO lowercase_definition FBbt:00000052 IAO:0000115 .
INFO lowercase_definition FBbt:00003004 IAO:0000115 .
INFO lowercase_definition FBbt:00105220 IAO:0000115 .
INFO lowercase_definition NBO:0000016 IAO:0000115 "\""Behavior relate to the usually upward movement off the ground or other surface through sudden muscular effort in the legs.\"" [GO:0007630]"
INFO lowercase_definition NBO:0000313 IAO:0000115 "\""The action, reaction, or performance of an organism in response to external or internal stimuli.\"" [GO:GO\:0007610]"
INFO lowercase_definition NBO:0000314 IAO:0000115 "\""Behavior related to the actions or reactions of an organism in response to a visual stimulus.\"" [GO:0007632]"
Expand Down
16 changes: 8 additions & 8 deletions src/ontology/reports/robot_simple_diff.txt
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4 axioms in left ontology but not in right ontology:
- Annotation(<http://creativecommons.org/ns#attributionURL> "http://dx.doi.org/10.1186/2041-1480-4-30"^^xsd:string)
- Annotation(<http://www.geneontology.org/formats/oboInOwl#date> "13:06:2024 12:35"^^xsd:string)
- Annotation(owl:versionInfo "2024-06-13"^^xsd:string)
- OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/dpo/dpo-simple.owl>) VersionIRI(<http://purl.obolibrary.org/obo/dpo/dpo-simple/dpo/releases/2024-06-13/dpo-simple.owl/dpo/dpo-simple.owl>))
- Annotation(<http://www.geneontology.org/formats/oboInOwl#date> "08:08:2024 12:59"^^xsd:string)
- Annotation(owl:versionInfo "2024-08-08"^^xsd:string)
- AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "FBC:DOS"^^xsd:string) Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "GOC:mah"^^xsd:string) Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "ISBN:0815316194"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FBcv_0000432> "Phenotype that is any abnormality in mitotic cell cycle (GO:0000278). 'mitotic cell cycle' is defined as: 'Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.'"^^xsd:string)
- OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/dpo/dpo-simple.owl>) VersionIRI(<http://purl.obolibrary.org/obo/dpo/dpo-simple/dpo/releases/2024-08-08/dpo-simple.owl/dpo/dpo-simple.owl>))

4 axioms in right ontology but not in left ontology:
+ Annotation(<http://purl.obolibrary.org/obo/dpo/dpo-simple#attributionURL> "http://dx.doi.org/10.1186/2041-1480-4-30"^^xsd:string)
+ Annotation(<http://www.geneontology.org/formats/oboInOwl#date> "25:04:2024 13:28"^^xsd:string)
+ Annotation(owl:versionInfo "2024-04-25"^^xsd:string)
+ OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/dpo/dpo-simple.owl>) VersionIRI(<http://purl.obolibrary.org/obo/dpo/dpo-simple/dpo/releases/2024-04-25/dpo-simple.owl/dpo/dpo-simple.owl>))
+ Annotation(<http://www.geneontology.org/formats/oboInOwl#date> "13:06:2024 12:35"^^xsd:string)
+ Annotation(owl:versionInfo "2024-06-13"^^xsd:string)
+ AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "FBC:DOS"^^xsd:string) Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "GOC:mah"^^xsd:string) Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "ISBN:0815316194"^^xsd:string) Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "Reactome:69278"^^xsd:string) <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/FBcv_0000432> "Phenotype that is any abnormality in mitotic cell cycle (GO:0000278). 'mitotic cell cycle' is defined as: 'Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.'"^^xsd:string)
+ OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/dpo/dpo-simple.owl>) VersionIRI(<http://purl.obolibrary.org/obo/dpo/dpo-simple/dpo/releases/2024-06-13/dpo-simple.owl/dpo/dpo-simple.owl>))
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