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Merge pull request #65 from FlyBase/release_2022-06-08
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release files 2022-06-08
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@Clare72
Clare72 authored Jun 8, 2022
2 parents d71747f + 4861302 commit 5bbdf05
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Showing 22 changed files with 173 additions and 222 deletions.
6 changes: 3 additions & 3 deletions fbdv-base.json
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Expand Up @@ -3218,7 +3218,7 @@
},
{
"pred": "http://www.geneontology.org/formats/oboInOwl#date",
"val": "12:04:2022 10:28"
"val": "08:06:2022 14:58"
},
{
"pred": "http://www.geneontology.org/formats/oboInOwl#default-namespace",
Expand All @@ -3230,11 +3230,11 @@
},
{
"pred": "http://www.w3.org/2002/07/owl#versionInfo",
"val": "2022-04-12"
"val": "2022-06-08"
}
],
"subsets": [],
"version": "http://purl.obolibrary.org/obo/fbdv/releases/2022-04-12/fbdv-base.json",
"version": "http://purl.obolibrary.org/obo/fbdv/releases/2022-06-08/fbdv-base.json",
"xrefs": []
},
"nodes": [
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6 changes: 3 additions & 3 deletions fbdv-base.obo
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@@ -1,6 +1,6 @@
format-version: 1.2
data-version: fbdv/releases/2022-04-12/fbdv-base.owl
date: 12:04:2022 10:28
data-version: fbdv/releases/2022-06-08/fbdv-base.owl
date: 08:06:2022 14:58
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 @@ -30,7 +30,7 @@ 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 "2022-04-12" xsd:string
property_value: owl:versionInfo "2022-06-08" xsd:string

[Term]
id: FBdv:00000000
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6 changes: 3 additions & 3 deletions fbdv-base.owl
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Expand Up @@ -12,7 +12,7 @@
xmlns:terms="http://purl.org/dc/terms/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/fbdv/fbdv-base.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/fbdv/releases/2022-04-12/fbdv-base.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/fbdv/releases/2022-06-08/fbdv-base.owl"/>
<obo:IAO_0000700 rdf:resource="http://purl.obolibrary.org/obo/FBdv_00000000"/>
<obo:IAO_0000700 rdf:resource="http://purl.obolibrary.org/obo/FBdv_00005259"/>
<obo:IAO_0000700 rdf:resource="http://purl.obolibrary.org/obo/FBdv_00007013"/>
Expand All @@ -26,10 +26,10 @@
<dc:type rdf:resource="http://purl.obolibrary.org/obo/IAO_8000001"/>
<terms:license rdf:datatype="http://www.w3.org/2001/XMLSchema#string">https://creativecommons.org/licenses/by/4.0/</terms:license>
<oboInOwl:NamespaceIdRule rdf:datatype="http://www.w3.org/2001/XMLSchema#string">* FBdv:$sequence(8,7000,10000)$</oboInOwl:NamespaceIdRule>
<oboInOwl:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string">12:04:2022 10:28</oboInOwl:date>
<oboInOwl:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string">08:06:2022 14:58</oboInOwl:date>
<oboInOwl:default-namespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase_development_CV</oboInOwl:default-namespace>
<oboInOwl:hasOBOFormatVersion rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1.2</oboInOwl:hasOBOFormatVersion>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-04-12</owl:versionInfo>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-06-08</owl:versionInfo>
</owl:Ontology>


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29 changes: 16 additions & 13 deletions fbdv-full.json
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Expand Up @@ -4705,7 +4705,7 @@
},
{
"pred": "http://www.geneontology.org/formats/oboInOwl#date",
"val": "12:04:2022 10:28"
"val": "08:06:2022 14:58"
},
{
"pred": "http://www.geneontology.org/formats/oboInOwl#default-namespace",
Expand All @@ -4717,11 +4717,11 @@
},
{
"pred": "http://www.w3.org/2002/07/owl#versionInfo",
"val": "2022-04-12"
"val": "2022-06-08"
}
],
"subsets": [],
"version": "http://purl.obolibrary.org/obo/fbdv/releases/2022-04-12/fbdv-full.json",
"version": "http://purl.obolibrary.org/obo/fbdv/releases/2022-06-08/fbdv-full.json",
"xrefs": []
},
"nodes": [
Expand Down Expand Up @@ -10535,7 +10535,6 @@
]
},
"subsets": [
"http://purl.obolibrary.org/obo/go#goslim_aspergillus",
"http://purl.obolibrary.org/obo/go#goslim_candida",
"http://purl.obolibrary.org/obo/go#goslim_pir"
],
Expand Down Expand Up @@ -10590,7 +10589,6 @@
"subsets": [
"http://purl.obolibrary.org/obo/go#gocheck_do_not_manually_annotate",
"http://purl.obolibrary.org/obo/go#goslim_agr",
"http://purl.obolibrary.org/obo/go#goslim_aspergillus",
"http://purl.obolibrary.org/obo/go#goslim_candida",
"http://purl.obolibrary.org/obo/go#goslim_chembl",
"http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon",
Expand Down Expand Up @@ -10686,7 +10684,6 @@
]
},
"subsets": [
"http://purl.obolibrary.org/obo/go#goslim_aspergillus",
"http://purl.obolibrary.org/obo/go#goslim_candida",
"http://purl.obolibrary.org/obo/go#goslim_chembl",
"http://purl.obolibrary.org/obo/go#goslim_metagenomics",
Expand Down Expand Up @@ -11064,7 +11061,6 @@
},
"subsets": [
"http://purl.obolibrary.org/obo/go#goslim_agr",
"http://purl.obolibrary.org/obo/go#goslim_aspergillus",
"http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon",
"http://purl.obolibrary.org/obo/go#goslim_pir"
],
Expand Down Expand Up @@ -14349,7 +14345,7 @@
},
{
"id": "http://purl.obolibrary.org/obo/RO_0017001",
"lbl": "utilizes",
"lbl": "device utilizes material",
"meta": {
"basicPropertyValues": [
{
Expand All @@ -14358,11 +14354,11 @@
},
{
"pred": "http://purl.obolibrary.org/obo/IAO_0000117",
"val": "Asiyah Lin"
"val": "https://orcid.org/0000-0001-9625-1899"
},
{
"pred": "http://purl.obolibrary.org/obo/IAO_0000117",
"val": "https://orcid.org/0000-0001-9625-1899 Bill Duncan"
"val": "https://orcid.org/0000-0003-2620-0345"
},
{
"pred": "http://purl.obolibrary.org/obo/IAO_0000232",
Expand All @@ -14374,13 +14370,20 @@
},
{
"pred": "http://www.geneontology.org/formats/oboInOwl#creation_date",
"val": "2021-11-08"
"val": "2021-11-08T12:00:00Z"
}
],
"definition": {
"val": "X utilizes Y means X and Y are material entities, and X is capable of some process P that has input Y.",
"val": "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.",
"xrefs": []
}
},
"synonyms": [
{
"pred": "hasBroadSynonym",
"val": "utilizes",
"xrefs": []
}
]
},
"type": "PROPERTY"
},
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23 changes: 10 additions & 13 deletions fbdv-full.obo
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@@ -1,12 +1,11 @@
format-version: 1.2
data-version: fbdv/releases/2022-04-12/fbdv-full.owl
date: 12:04:2022 10:28
data-version: fbdv/releases/2022-06-08/fbdv-full.owl
date: 08:06:2022 14:58
subsetdef: gocheck_do_not_annotate ""
subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
subsetdef: gocheck_do_not_manually_annotate ""
subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation"
subsetdef: goslim_agr ""
subsetdef: goslim_aspergillus ""
subsetdef: goslim_aspergillus "Aspergillus GO slim"
subsetdef: goslim_candida ""
subsetdef: goslim_candida "Candida GO slim"
Expand Down Expand Up @@ -50,7 +49,7 @@ 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 "2022-04-12" xsd:string
property_value: owl:versionInfo "2022-06-08" xsd:string

[Term]
id: BFO:0000002
Expand Down Expand Up @@ -2182,7 +2181,6 @@ name: organelle organization
namespace: biological_process
alt_id: GO:1902589
def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:mah]
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_pir
synonym: "organelle organisation" EXACT []
Expand All @@ -2200,7 +2198,6 @@ namespace: biological_process
def: "The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division." [GOC:go_curators, GOC:mtg_cell_cycle]
subset: gocheck_do_not_manually_annotate
subset: goslim_agr
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_flybase_ribbon
Expand Down Expand Up @@ -2232,7 +2229,6 @@ alt_id: GO:0007582
alt_id: GO:0044699
def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [GOC:pdt]
comment: 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.
subset: goslim_aspergillus
subset: goslim_candida
subset: goslim_chembl
subset: goslim_metagenomics
Expand Down Expand Up @@ -2364,7 +2360,6 @@ namespace: biological_process
alt_id: GO:0044767
def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." [GOC:isa_complete]
subset: goslim_agr
subset: goslim_aspergillus
subset: goslim_flybase_ribbon
subset: goslim_pir
synonym: "development" NARROW []
Expand Down Expand Up @@ -2831,6 +2826,7 @@ property_value: RO:0001900 RO:0001901
holds_over_chain: has_part part_of {http://purl.obolibrary.org/obo/RO_0002582="true"}
holds_over_chain: has_part RO:0002131
holds_over_chain: part_of part_of
is_symmetric: true
is_a: RO:0002323 ! mereotopologically related to
transitive_over: part_of ! part of
expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" []
Expand Down Expand Up @@ -3677,15 +3673,16 @@ is_a: RO:0002566 ! causally influences

[Typedef]
id: RO:0017001
name: utilizes
def: "X utilizes Y means X and Y are material entities, and X is capable of some process P that has input Y." []
name: device utilizes material
def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." []
synonym: "utilizes" BROAD []
property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string
property_value: IAO:0000117 "Asiyah Lin" xsd:string
property_value: IAO:0000117 "https://orcid.org/0000-0001-9625-1899 Bill Duncan" xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 xsd:string
property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string
property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string
holds_over_chain: RO:0002215 RO:0002233
creation_date: 2021-11-08
creation_date: 2021-11-08T12:00:00Z

[Typedef]
id: RO:0019000
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30 changes: 10 additions & 20 deletions fbdv-full.owl
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Expand Up @@ -18,7 +18,7 @@
xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/fbdv/fbdv-full.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/fbdv/releases/2022-04-12/fbdv-full.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/fbdv/releases/2022-06-08/fbdv-full.owl"/>
<obo:IAO_0000700 rdf:resource="http://purl.obolibrary.org/obo/FBdv_00000000"/>
<obo:IAO_0000700 rdf:resource="http://purl.obolibrary.org/obo/FBdv_00005259"/>
<obo:IAO_0000700 rdf:resource="http://purl.obolibrary.org/obo/FBdv_00007013"/>
Expand All @@ -31,10 +31,10 @@
<dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase Developmental Ontology (FBdv)</dc:title>
<terms:license rdf:datatype="http://www.w3.org/2001/XMLSchema#string">https://creativecommons.org/licenses/by/4.0/</terms:license>
<oboInOwl:NamespaceIdRule rdf:datatype="http://www.w3.org/2001/XMLSchema#string">* FBdv:$sequence(8,7000,10000)$</oboInOwl:NamespaceIdRule>
<oboInOwl:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string">12:04:2022 10:28</oboInOwl:date>
<oboInOwl:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string">08:06:2022 14:58</oboInOwl:date>
<oboInOwl:default-namespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">FlyBase_development_CV</oboInOwl:default-namespace>
<oboInOwl:hasOBOFormatVersion rdf:datatype="http://www.w3.org/2001/XMLSchema#string">1.2</oboInOwl:hasOBOFormatVersion>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-04-12</owl:versionInfo>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-06-08</owl:versionInfo>
</owl:Ontology>


Expand Down Expand Up @@ -398,14 +398,6 @@



<!-- http://purl.obolibrary.org/obo/go#goslim_aspergillus -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/go#goslim_aspergillus">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
</owl:AnnotationProperty>



<!-- http://purl.obolibrary.org/obo/go#goslim_candida -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/go#goslim_candida">
Expand Down Expand Up @@ -1351,6 +1343,7 @@ A continuant cannot have an occurrent as part: use &apos;participates in&apos;.

<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0002131">
<rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/RO_0002323"/>
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#SymmetricProperty"/>
<owl:propertyChainAxiom rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
Expand Down Expand Up @@ -2708,13 +2701,14 @@ For example, A and B may be gene products and binding of B by A positively regul
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/RO_0002233"/>
</owl:propertyChainAxiom>
<obo:IAO_0000112>A diagnostic testing device utilizes a specimen.</obo:IAO_0000112>
<obo:IAO_0000115>X utilizes Y means X and Y are material entities, and X is capable of some process P that has input Y.</obo:IAO_0000115>
<obo:IAO_0000117>Asiyah Lin</obo:IAO_0000117>
<obo:IAO_0000117>https://orcid.org/0000-0001-9625-1899 Bill Duncan</obo:IAO_0000117>
<obo:IAO_0000115>X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y.</obo:IAO_0000115>
<obo:IAO_0000117>https://orcid.org/0000-0001-9625-1899</obo:IAO_0000117>
<obo:IAO_0000117>https://orcid.org/0000-0003-2620-0345</obo:IAO_0000117>
<obo:IAO_0000232>A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.</obo:IAO_0000232>
<obo:IAO_0000232>See github ticket https://github.com/oborel/obo-relations/issues/497</obo:IAO_0000232>
<oboInOwl:creation_date>2021-11-08</oboInOwl:creation_date>
<rdfs:label xml:lang="en">utilizes</rdfs:label>
<oboInOwl:creation_date>2021-11-08T12:00:00Z</oboInOwl:creation_date>
<oboInOwl:hasBroadSynonym>utilizes</oboInOwl:hasBroadSynonym>
<rdfs:label xml:lang="en">device utilizes material</rdfs:label>
</owl:ObjectProperty>


Expand Down Expand Up @@ -9947,7 +9941,6 @@ For example, A and B may be gene products and binding of B by A positively regul
<oboInOwl:hasRelatedSynonym>organelle organization and biogenesis</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>single-organism organelle organization</oboInOwl:hasRelatedSynonym>
<oboInOwl:id>GO:0006996</oboInOwl:id>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_aspergillus"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_candida"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_pir"/>
<rdfs:label>organelle organization</rdfs:label>
Expand Down Expand Up @@ -9986,7 +9979,6 @@ For example, A and B may be gene products and binding of B by A positively regul
<oboInOwl:id>GO:0007049</oboInOwl:id>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#gocheck_do_not_manually_annotate"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_agr"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_aspergillus"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_candida"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_chembl"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon"/>
Expand Down Expand Up @@ -10048,7 +10040,6 @@ For example, A and B may be gene products and binding of B by A positively regul
<oboInOwl:hasRelatedSynonym>single organism process</oboInOwl:hasRelatedSynonym>
<oboInOwl:hasRelatedSynonym>single-organism process</oboInOwl:hasRelatedSynonym>
<oboInOwl:id>GO:0008150</oboInOwl:id>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_aspergillus"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_candida"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_chembl"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_metagenomics"/>
Expand Down Expand Up @@ -10315,7 +10306,6 @@ For example, A and B may be gene products and binding of B by A positively regul
<oboInOwl:hasRelatedSynonym>single-organism developmental process</oboInOwl:hasRelatedSynonym>
<oboInOwl:id>GO:0032502</oboInOwl:id>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_agr"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_aspergillus"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_flybase_ribbon"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_pir"/>
<rdfs:label>developmental process</rdfs:label>
Expand Down
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