Merge pull request #30 from FlyBase/release_2020-10-15

release files 2020-10-15
FlyBase · Oct 15, 2020 · e52775f · e52775f
2 parents a826c8c + 2fdf8fd
commit e52775f
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diff --git a/fbdv-base.json b/fbdv-base.json
diff --git a/fbdv-base.obo b/fbdv-base.obo
@@ -1,6 +1,6 @@
 format-version: 1.2
-data-version: fbdv/releases/2020-08-12/fbdv-base.owl
-date: 12:08:2020 14:09
+data-version: fbdv/releases/2020-10-15/fbdv-base.owl
+date: 15:10:2020 11:31
 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"

diff --git a/fbdv-base.owl b/fbdv-base.owl
@@ -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/2020-08-12/fbdv-base.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/fbdv/releases/2020-10-15/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"/>
@@ -25,7 +25,7 @@
         <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/3.0/</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">12:08:2020 14:09</oboInOwl:date>
+        <oboInOwl:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string">15:10:2020 11:31</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:Ontology>

diff --git a/fbdv-full.json b/fbdv-full.json
diff --git a/fbdv-full.obo b/fbdv-full.obo
@@ -1,6 +1,6 @@
 format-version: 1.2
-data-version: fbdv/releases/2020-08-12/fbdv-full.owl
-date: 12:08:2020 14:08
+data-version: fbdv/releases/2020-10-15/fbdv-full.owl
+date: 15:10:2020 11:31
 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_agr "AGR slim"
@@ -2106,6 +2106,7 @@ name: mitotic cell cycle
 namespace: biological_process
 alt_id: GO:0007067
 def: "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." [GOC:mah, ISBN:0815316194, Reactome:69278]
+comment: Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle.
 subset: goslim_chembl
 subset: goslim_drosophila
 subset: goslim_generic
@@ -2425,7 +2426,6 @@ synonym: "regulation of embryonic mitotic cell cycle" EXACT [GOC:dph, GOC:tb]
 synonym: "regulation of embryonic mitotic cell cycle progression" EXACT []
 synonym: "regulation of progression through embryonic mitotic cell cycle" EXACT []
 is_a: GO:0007346 ! regulation of mitotic cell cycle
-is_a: GO:0045995 ! regulation of embryonic development
 intersection_of: GO:0008150 ! biological_process
 intersection_of: regulates GO:0045448 ! mitotic cell cycle, embryonic
 relationship: regulates GO:0045448 ! mitotic cell cycle, embryonic
@@ -2780,6 +2780,7 @@ id: GO:0022403
 name: cell cycle phase
 namespace: biological_process
 def: "One of the distinct periods or stages into which the cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events." [GOC:mtg_cell_cycle]
+comment: Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during).
 subset: gocheck_do_not_annotate
 is_a: GO:0044848 ! biological phase
 
@@ -3289,7 +3290,6 @@ synonym: "up regulation of mitosis" EXACT []
 synonym: "up-regulation of mitosis" EXACT []
 synonym: "upregulation of mitosis" EXACT []
 is_a: GO:0007088 ! regulation of mitotic nuclear division
-is_a: GO:0045931 ! positive regulation of mitotic cell cycle
 is_a: GO:0051785 ! positive regulation of nuclear division
 is_a: GO:0090068 ! positive regulation of cell cycle process
 intersection_of: GO:0008150 ! biological_process
@@ -3378,7 +3378,6 @@ synonym: "negative regulation of embryonic mitotic cell cycle progression" EXACT
 synonym: "negative regulation of progression through embryonic mitotic cell cycle" EXACT [GOC:dph, GOC:tb]
 is_a: GO:0009794 ! regulation of mitotic cell cycle, embryonic
 is_a: GO:0045930 ! negative regulation of mitotic cell cycle
-is_a: GO:0045992 ! negative regulation of embryonic development
 intersection_of: GO:0008150 ! biological_process
 intersection_of: negatively_regulates GO:0045448 ! mitotic cell cycle, embryonic
 relationship: negatively_regulates GO:0045448 ! mitotic cell cycle, embryonic
@@ -3397,7 +3396,6 @@ synonym: "up regulation of mitotic cell cycle, embryonic" EXACT []
 synonym: "up-regulation of mitotic cell cycle, embryonic" EXACT []
 synonym: "upregulation of mitotic cell cycle, embryonic" EXACT []
 is_a: GO:0009794 ! regulation of mitotic cell cycle, embryonic
-is_a: GO:0040019 ! positive regulation of embryonic development
 is_a: GO:0045931 ! positive regulation of mitotic cell cycle
 intersection_of: GO:0008150 ! biological_process
 intersection_of: positively_regulates GO:0045448 ! mitotic cell cycle, embryonic
@@ -4060,10 +4058,12 @@ namespace: biological_process
 def: "A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell." [ISBN:0198547684]
 subset: goslim_chembl
 subset: goslim_generic
+synonym: "mitosis" EXACT []
 is_a: GO:0000280 ! nuclear division
 is_a: GO:1903047 ! mitotic cell cycle process
 intersection_of: GO:0000280 ! nuclear division
 intersection_of: part_of GO:0000278 ! mitotic cell cycle
+property_value: term_tracker_item https://github.com/geneontology/go-ontology/issues/19910 xsd:anyURI
 created_by: pg
 creation_date: 2017-03-23T14:44:23Z
 
@@ -5536,7 +5536,7 @@ comment: Creating this relation as a temporary fix, pending adding the axiom occ
 xref: FBdv:00018001
 is_transitive: true
 is_a: happens_during ! happens during
-is_a: occurent_part_of ! occurent part of
+is_a: occurent_part_of ! occurent_part_of
 
 [Typedef]
 id: term_tracker_item

diff --git a/fbdv-full.owl b/fbdv-full.owl
@@ -19,7 +19,7 @@
      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/2020-08-12/fbdv-full.owl"/>
+        <owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/fbdv/releases/2020-10-15/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"/>
@@ -32,7 +32,7 @@
         <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/3.0/</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">12:08:2020 14:08</oboInOwl:date>
+        <oboInOwl:date rdf:datatype="http://www.w3.org/2001/XMLSchema#string">15:10:2020 11:31</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:Ontology>
@@ -10057,6 +10057,7 @@ For example, A and B may be gene products and binding of B by A positively regul
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_drosophila"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_generic"/>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_yeast"/>
+        <rdfs:comment>Note that this term should not be confused with &apos;GO:0140014 ; mitotic nuclear division&apos;. &apos;GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while &apos;GO:0140014 ; mitotic nuclear division&apos; specifically represents the actual nuclear division step of the mitotic cell cycle.</rdfs:comment>
         <rdfs:label>mitotic cell cycle</rdfs:label>
     </owl:Class>
     <owl:Axiom>
@@ -10692,7 +10693,6 @@ For example, A and B may be gene products and binding of B by A positively regul
             </owl:Class>
         </owl:equivalentClass>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0007346"/>
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0045995"/>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002211"/>
@@ -11726,6 +11726,7 @@ For example, A and B may be gene products and binding of B by A positively regul
         <oboInOwl:hasOBONamespace>biological_process</oboInOwl:hasOBONamespace>
         <oboInOwl:id>GO:0022403</oboInOwl:id>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate"/>
+        <rdfs:comment>Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is &apos;regulation of x/y phase transition&apos; or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during).</rdfs:comment>
         <rdfs:label>cell cycle phase</rdfs:label>
     </owl:Class>
     <owl:Axiom>
@@ -13050,7 +13051,6 @@ For example, A and B may be gene products and binding of B by A positively regul
             </owl:Class>
         </owl:equivalentClass>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0007088"/>
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0045931"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0051785"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0090068"/>
         <rdfs:subClassOf>
@@ -13282,7 +13282,6 @@ For example, A and B may be gene products and binding of B by A positively regul
         </owl:equivalentClass>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0009794"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0045930"/>
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0045992"/>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002212"/>
@@ -13341,7 +13340,6 @@ For example, A and B may be gene products and binding of B by A positively regul
             </owl:Class>
         </owl:equivalentClass>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0009794"/>
-        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0040019"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0045931"/>
         <rdfs:subClassOf>
             <owl:Restriction>
@@ -15142,8 +15140,10 @@ For example, A and B may be gene products and binding of B by A positively regul
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0000280"/>
         <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_1903047"/>
         <obo:IAO_0000115>A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell.</obo:IAO_0000115>
+        <obo:IAO_0000233 rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://github.com/geneontology/go-ontology/issues/19910</obo:IAO_0000233>
         <oboInOwl:created_by>pg</oboInOwl:created_by>
         <oboInOwl:creation_date>2017-03-23T14:44:23Z</oboInOwl:creation_date>
+        <oboInOwl:hasExactSynonym>mitosis</oboInOwl:hasExactSynonym>
         <oboInOwl:hasOBONamespace>biological_process</oboInOwl:hasOBONamespace>
         <oboInOwl:id>GO:0140014</oboInOwl:id>
         <oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/go#goslim_chembl"/>