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Merge pull request #87 from FlyBase/release_2023-12-07
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release files 2023-12-07
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@Clare72
Clare72 authored Dec 7, 2023
2 parents 66e28fa + f43d015 commit 09ea359
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Showing 5 changed files with 19 additions and 40 deletions.
6 changes: 3 additions & 3 deletions fbdv.obo
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format-version: 1.2
data-version: fbdv/releases/2023-10-18
date: 18:10:2023 14:12
data-version: fbdv/releases/2023-12-07
date: 07:12:2023 07:29
subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation"
subsetdef: goslim_aspergillus "Aspergillus GO slim"
Expand Down Expand Up @@ -32,7 +32,7 @@ property_value: IAO:0000700 FBdv:00000000
property_value: IAO:0000700 FBdv:00005259
property_value: IAO:0000700 FBdv:00007013
property_value: IAO:0000700 FBdv:00007024
property_value: owl:versionInfo "2023-10-18" xsd:string
property_value: owl:versionInfo "2023-12-07" xsd:string

[Term]
id: FBdv:00000000
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4 changes: 2 additions & 2 deletions fly_development.obo
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format-version: 1.2
data-version: 2023-10-18
date: 18:10:2023 14:12
data-version: 2023-12-07
date: 07:12:2023 07:30
subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation"
subsetdef: goslim_aspergillus "Aspergillus GO slim"
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8 changes: 4 additions & 4 deletions src/ontology/imports/merged_import.owl
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Expand Up @@ -7,8 +7,8 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(<http://purl.obolibrary.org/obo/fbdv/imports/merged_import.owl>
<http://purl.obolibrary.org/obo/fbdv/releases/2023-10-18/imports/merged_import.owl>
Annotation(owl:versionInfo "2023-10-18")
<http://purl.obolibrary.org/obo/fbdv/releases/2023-12-07/imports/merged_import.owl>
Annotation(owl:versionInfo "2023-12-07")

Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))
Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000003>))
Expand Down Expand Up @@ -1860,7 +1860,7 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <htt
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/GO_0003674> <http://purl.obolibrary.org/obo/go#goslim_pir>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/GO_0003674> <http://purl.obolibrary.org/obo/go#goslim_plant>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/GO_0003674> <http://purl.obolibrary.org/obo/go#goslim_yeast>)
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/GO_0003674> "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.")
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/GO_0003674> "Note that, in addition to forming the root of the molecular function ontology, this term is recommended for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/GO_0003674> "molecular_function")

# Class: <http://purl.obolibrary.org/obo/GO_0003824> (catalytic activity)
Expand Down Expand Up @@ -1951,7 +1951,7 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <htt
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/GO_0008150> <http://purl.obolibrary.org/obo/go#goslim_plant>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/GO_0008150> <http://purl.obolibrary.org/obo/go#goslim_pombe>)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/GO_0008150> <http://purl.obolibrary.org/obo/go#goslim_yeast>)
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/GO_0008150> "Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.")
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/GO_0008150> "Note that, in addition to forming the root of the biological process ontology, this term is recommended for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/GO_0008150> "biological_process")

# Class: <http://purl.obolibrary.org/obo/GO_0009790> (embryo development)
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38 changes: 8 additions & 30 deletions src/ontology/reports/robot_simple_diff.txt
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8 axioms in left ontology but not in right ontology:
- Annotation(<oboInOwl:date> "18:10:2023 14:12")
- Annotation(<owl:versionInfo> "2023-10-18")
- AnnotationAssertion(<oboInOwl:id>[id] <FBdv:00018001>[substage of] "FBdv:00018001")
- AnnotationAssertion(<oboInOwl:id>[id] <RO:0002012>[occurrent part of] "RO:0002012")
- AnnotationAssertion(<oboInOwl:id>[id] <RO:0002087>[immediately preceded by] "RO:0002087")
- AnnotationAssertion(<oboInOwl:id>[id] <RO:0002090>[immediately precedes] "RO:0002090")
- AnnotationAssertion(<oboInOwl:id>[id] <RO:0002092>[happens during] "RO:0002092")
- OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/fbdv/fbdv-simple.owl>) VersionIRI(<http://purl.obolibrary.org/obo/fbdv/fbdv-simple/fbdv/releases/2023-10-18/fbdv-simple.owl/fbdv/fbdv-simple.owl>))
3 axioms in left ontology but not in right ontology:
- Annotation(<oboInOwl:date> "07:12:2023 07:29")
- Annotation(<owl:versionInfo> "2023-12-07")
- OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/fbdv/fbdv-simple.owl>) VersionIRI(<http://purl.obolibrary.org/obo/fbdv/fbdv-simple/fbdv/releases/2023-12-07/fbdv-simple.owl/fbdv/fbdv-simple.owl>))

20 axioms in right ontology but not in left ontology:
+ Annotation(<oboInOwl:date> "02:08:2023 12:54")
+ Annotation(<owl:versionInfo> "2023-08-02")
+ AnnotationAssertion(<oboInOwl:hasDbXref>[database_cross_reference] <FBdv:00018001>[substage of] "FBdv:00018001")
+ AnnotationAssertion(<oboInOwl:hasDbXref>[database_cross_reference] <RO:0002012>[occurrent part of] "RO:0002012")
+ AnnotationAssertion(<oboInOwl:hasDbXref>[database_cross_reference] <RO:0002087>[immediately preceded by] "RO:0002087")
+ AnnotationAssertion(<oboInOwl:hasDbXref>[database_cross_reference] <RO:0002090>[immediately precedes] "RO:0002090")
+ AnnotationAssertion(<oboInOwl:hasDbXref>[database_cross_reference] <RO:0002092>[happens during] "RO:0002092")
+ AnnotationAssertion(<oboInOwl:id>[id] <FBdv:00018001>[substage of] "substage_of")
+ AnnotationAssertion(<oboInOwl:id>[id] <RO:0002012>[occurrent part of] "occurrent_part_of")
+ AnnotationAssertion(<oboInOwl:id>[id] <RO:0002087>[immediately preceded by] "immediately_preceded_by")
+ AnnotationAssertion(<oboInOwl:id>[id] <RO:0002090>[immediately precedes] "immediately_precedes")
+ AnnotationAssertion(<oboInOwl:id>[id] <RO:0002092>[happens during] "happens_during")
+ AnnotationAssertion(<oboInOwl:shorthand>[shorthand] <FBdv:00018001>[substage of] "substage_of")
+ AnnotationAssertion(<oboInOwl:shorthand>[shorthand] <RO:0002012>[occurrent part of] "occurrent_part_of")
+ AnnotationAssertion(<oboInOwl:shorthand>[shorthand] <RO:0002087>[immediately preceded by] "immediately_preceded_by")
+ AnnotationAssertion(<oboInOwl:shorthand>[shorthand] <RO:0002090>[immediately precedes] "immediately_precedes")
+ AnnotationAssertion(<oboInOwl:shorthand>[shorthand] <RO:0002092>[happens during] "happens_during")
+ AnnotationAssertion(<rdfs:label> <oboInOwl:shorthand>[shorthand] "shorthand")
+ Declaration(AnnotationProperty(<oboInOwl:shorthand>[shorthand]))
+ OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/fbdv/fbdv-simple.owl>) VersionIRI(<http://purl.obolibrary.org/obo/fbdv/fbdv-simple/fbdv/releases/2023-08-02/fbdv-simple.owl/fbdv/fbdv-simple.owl>))
3 axioms in right ontology but not in left ontology:
+ Annotation(<oboInOwl:date> "18:10:2023 14:12")
+ Annotation(<owl:versionInfo> "2023-10-18")
+ OntologyID(OntologyIRI(<http://purl.obolibrary.org/obo/fbdv/fbdv-simple.owl>) VersionIRI(<http://purl.obolibrary.org/obo/fbdv/fbdv-simple/fbdv/releases/2023-10-18/fbdv-simple.owl/fbdv/fbdv-simple.owl>))
3 changes: 2 additions & 1 deletion src/scripts/chado_load_checks.pl
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Expand Up @@ -19,6 +19,7 @@
FBC:\<curator initials\>;
PMID:\d+;
http://...;
https://...;
ISBN:<legal ISBN13>;
CARO:<CARO curator initials>.
Expand Down Expand Up @@ -133,7 +134,7 @@ sub is_dbxref_legal {
&ISBN_check($1)
}
# If not ISBN, does it follow one of the other legal dbxref syntaxes?
elsif ($_ =~ m/FlyBase\:FBrf\d{7}|VFB_vol\:\d{8}|FBC\:\S+|SO\:ma|FlyBase\:FBim\d{7}|PMID\:\d+|http\:\/\/.+|CARO\:\S+|doi\:\d+\.\d+\/\w+|FlyBrain_NDB\:\d+|FlyPNS\:\S+|DoOR\:\S+|CHEBI\:\d+|GO\:\d+|PATO\:\d+|XCO\:\d+|EFO\:\d+|MeSH\:D\d+|GOC:\S+|GO_REF\:\d+|Reactome\:\d+|SO\:\S+|UniProt\:P\d+|UniProt\:Q\S+|WB_REF\:\S+|FB\:FBrfd{7}|Wikipedia\:\S+/) {
elsif ($_ =~ m/FlyBase\:FBrf\d{7}|VFB_vol\:\d{8}|FBC\:\S+|SO\:ma|FlyBase\:FBim\d{7}|PMID\:\d+|https?\:\/\/.+|CARO\:\S+|doi\:\d+\.\d+\/\w+|FlyBrain_NDB\:\d+|FlyPNS\:\S+|DoOR\:\S+|CHEBI\:\d+|GO\:\d+|PATO\:\d+|XCO\:\d+|EFO\:\d+|MeSH\:D\d+|GOC:\S+|GO_REF\:\d+|Reactome\:\d+|SO\:\S+|UniProt\:P\d+|UniProt\:Q\S+|WB_REF\:\S+|FB\:FBrfd{7}|Wikipedia\:\S+/) {
$legal_stat=1;
} else {
$legal_stat=0
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