diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 1b6bcd11e..641da5339 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2025-01-13") + +Annotation(owl:versionInfo "2025-01-15") Declaration(Class()) Declaration(Class()) @@ -10706,7 +10706,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -13106,7 +13106,7 @@ AnnotationAssertion(rdfs:label "has_broad_synonym") AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") -# Annotation Property: (has cross-reference) +# Annotation Property: (database_cross_reference) AnnotationAssertion( "disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) \"NCIT:C41009\"^^xsd:string") AnnotationAssertion( "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.") @@ -151940,11 +151940,11 @@ AnnotationAssertion(Annotation( "IEDB:BP") "native protein") AnnotationAssertion( "protein") AnnotationAssertion( "PR:000000001") -AnnotationAssertion(rdfs:comment "The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB].") +AnnotationAssertion(rdfs:comment "The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB).") AnnotationAssertion(rdfs:label "protein") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -152577,7 +152577,6 @@ SubClassOf( (prominin) AnnotationAssertion(Annotation( "InterPro:IPR008795") Annotation( "PMID:11467842") "A protein with core architecture consisting of one Prominin (Pfam:PF05478) domain. The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and human prominin and prominin-like 1 are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain.") -AnnotationAssertion( "PANTHER:PTHR22730") AnnotationAssertion( "PIRSF:PIRSF017831") AnnotationAssertion( "protein") AnnotationAssertion( "PR:000001785") @@ -154006,20 +154005,20 @@ AnnotationAssertion(rdfs:comment " AnnotationAssertion(rdfs:label "receptor-type tyrosine-protein phosphatase C isoform CD45R") SubClassOf( ) -# Class: (protein-containing material entity) - -AnnotationAssertion(Annotation( "PRO:DAN") "A material entity that minimally consists of a protein.") -AnnotationAssertion(Annotation( "PRO:DAN") "protein") -AnnotationAssertion(Annotation( "PRO:DAN") "protein aggregate") -AnnotationAssertion(Annotation( "PRO:DAN") "protein complex") -AnnotationAssertion(Annotation( "PRO:DAN") "protein-containing complex") -AnnotationAssertion( "protein") -AnnotationAssertion( "PR:000050567") -AnnotationAssertion(rdfs:comment "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566).") -AnnotationAssertion(rdfs:label "protein-containing material entity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) +# Class: (protein-containing molecular entity) + +AnnotationAssertion(Annotation( "PRO:DAN") "A molecular entity that minimally consists of a protein.") +AnnotationAssertion(Annotation( "PRO:DAN") "protein") +AnnotationAssertion(Annotation( "PRO:DAN") "protein aggregate") +AnnotationAssertion(Annotation( "PRO:DAN") "protein complex") +AnnotationAssertion(Annotation( "PRO:DAN") "protein-containing complex") +AnnotationAssertion( "protein") +AnnotationAssertion( "PR:000064867") +AnnotationAssertion(rdfs:comment "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565).") +AnnotationAssertion(rdfs:label "protein-containing molecular entity") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (interleukin-7 receptor alpha chain (chicken)) @@ -154088,6 +154087,7 @@ AnnotationAssertion(Annotation( "UniProtKB:E1C9E2") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "chick-PROM1") AnnotationAssertion( "protein") +AnnotationAssertion(Annotation( "PRO:DAN") Annotation( ) "PROM1") AnnotationAssertion( "PR:E1C9E2") AnnotationAssertion(rdfs:comment "Category=organism-gene.") AnnotationAssertion(rdfs:label "uncharacterized protein, PROM1 translation product (chicken)") @@ -155367,7 +155367,7 @@ SubClassOf( ObjectSomeValuesFrom( (prolactin (chicken)) -AnnotationAssertion(Annotation( "OMA:P14676") Annotation( "PANTHER:PTHR11417:SF4") Annotation( "PRO:DNx") "A prolactin that is encoded in the genome of chicken.") +AnnotationAssertion(Annotation( "OMA:P14676") Annotation( "PRO:DNx") "A prolactin that is encoded in the genome of chicken.") AnnotationAssertion( "UniProtKB:P14676") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "chick-PRL") AnnotationAssertion( "protein") @@ -155473,7 +155473,7 @@ SubClassOf( ObjectSomeValuesFrom( (myelin basic protein (chicken)) -AnnotationAssertion(Annotation( "PANTHER:PTHR11429:SF0") Annotation( "PRO:DNx") "A myelin basic protein that is encoded in the genome of chicken.") +AnnotationAssertion(Annotation( "PRO:DNx") "A myelin basic protein that is encoded in the genome of chicken.") AnnotationAssertion( "UniProtKB:P15720") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "chick-MBP") AnnotationAssertion( "protein") @@ -156090,7 +156090,7 @@ SubClassOf( ObjectSomeValuesFrom( (GATA-binding factor 2 (chicken)) -AnnotationAssertion(Annotation( "OMA:P23824") Annotation( "PANTHER:PTHR10071:SF107") Annotation( "PRO:DNx") "An endothelial transcription factor GATA-2 that is encoded in the genome of chicken.") +AnnotationAssertion(Annotation( "OMA:P23824") Annotation( "PRO:DNx") "An endothelial transcription factor GATA-2 that is encoded in the genome of chicken.") AnnotationAssertion( "UniProtKB:P23824") AnnotationAssertion(Annotation( "UniProtKB:P23824") "GATA-2 (chicken)") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "chick-GATA2") @@ -156312,7 +156312,7 @@ AnnotationAssertion(Annotation( "ADP-ribosyl cyclase 1 (human)") AnnotationAssertion(Annotation( "UniProtKB:P28907") "ADPRC 1 (human)") AnnotationAssertion(Annotation( "UniProtKB:P28907") "T10 (human)") -AnnotationAssertion(Annotation( "UniProtKB:P28907") "cADPr hydrolase 1 (human)") +AnnotationAssertion(Annotation( "UniProtKB:P28907") "cADPR hydrolase 1 (human)") AnnotationAssertion(Annotation( "UniProtKB:P28907") "cyclic ADP-ribose hydrolase 1 (human)") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "hCD38") AnnotationAssertion( "protein") @@ -156782,7 +156782,7 @@ AnnotationAssertion(Annotation( "UniProtKB:P56528") "CD38 (mouse)") AnnotationAssertion(Annotation( "UniProtKB:P56528") "I-19 (mouse)") AnnotationAssertion(Annotation( "UniProtKB:P56528") "NIM-R5 antigen (mouse)") -AnnotationAssertion(Annotation( "UniProtKB:P56528") "cADPr hydrolase 1 (mouse)") +AnnotationAssertion(Annotation( "UniProtKB:P56528") "cADPR hydrolase 1 (mouse)") AnnotationAssertion(Annotation( "UniProtKB:P56528") "cyclic ADP-ribose hydrolase 1 (mouse)") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "mCD38") AnnotationAssertion( "protein") @@ -157021,7 +157021,7 @@ SubClassOf( ObjectSomeValuesFrom( (mast/stem cell growth factor receptor Kit (chicken)) -AnnotationAssertion(Annotation( "OMA:Q08156") Annotation( "PANTHER:PTHR24416:SF238") Annotation( "PRO:DNx") "A mast/stem cell growth factor receptor that is encoded in the genome of chicken.") +AnnotationAssertion(Annotation( "OMA:Q08156") Annotation( "PRO:DNx") "A mast/stem cell growth factor receptor that is encoded in the genome of chicken.") AnnotationAssertion( "UniProtKB:Q08156") AnnotationAssertion(Annotation( "UniProtKB:Q08156") "SCFR (chicken)") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "chick-KIT") @@ -157270,7 +157270,7 @@ SubClassOf( ObjectSomeValuesFrom( (cadherin-5 (chicken)) -AnnotationAssertion(Annotation( "OMA:Q8AYD0") Annotation( "PANTHER:PTHR24027:SF44") Annotation( "PRO:DNx") "A cadherin-5 that is encoded in the genome of chicken.") +AnnotationAssertion(Annotation( "OMA:Q8AYD0") Annotation( "PRO:DNx") "A cadherin-5 that is encoded in the genome of chicken.") AnnotationAssertion( "UniProtKB:Q8AYD0") AnnotationAssertion(Annotation( "UniProtKB:Q8AYD0") "VE-cadherin (chicken)") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "chick-CDH5") @@ -157336,7 +157336,7 @@ SubClassOf( ObjectSomeValuesFrom( (fibroblast growth factor 8 (chicken)) -AnnotationAssertion(Annotation( "OMA:Q90722") Annotation( "PANTHER:PTHR11486:SF2") Annotation( "PRO:DNx") "A fibroblast growth factor 8 that is encoded in the genome of chicken.") +AnnotationAssertion(Annotation( "OMA:Q90722") Annotation( "PRO:DNx") "A fibroblast growth factor 8 that is encoded in the genome of chicken.") AnnotationAssertion( "UniProtKB:Q90722") AnnotationAssertion(Annotation( "UniProtKB:Q90722") "FGF-8 (chicken)") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "chick-FGF8") @@ -157354,7 +157354,7 @@ SubClassOf( ObjectSomeValuesFrom( (transferrin receptor protein 1 (chicken)) -AnnotationAssertion(Annotation( "PANTHER:PTHR10404:SF26") Annotation( "PRO:DNx") "A transferrin receptor protein 1 that is encoded in the genome of chicken.") +AnnotationAssertion(Annotation( "PRO:WCB") "A transferrin receptor protein 1 that is encoded in the genome of chicken.") AnnotationAssertion( "UniProtKB:Q90997") AnnotationAssertion(Annotation( "UniProtKB:Q90997") "TR (chicken)") AnnotationAssertion(Annotation( "UniProtKB:Q90997") "TfR (chicken)") @@ -157373,7 +157373,7 @@ SubClassOf( ObjectSomeValuesFrom( (sonic hedgehog protein (chicken)) -AnnotationAssertion(Annotation( "PANTHER:PTHR11889:SF16") Annotation( "PRO:DNx") "A sonic hedgehog protein that is encoded in the genome of chicken.") +AnnotationAssertion(Annotation( "OMA:Q91035") Annotation( "PRO:DNx") "A sonic hedgehog protein that is encoded in the genome of chicken.") AnnotationAssertion( "UniProtKB:Q91035") AnnotationAssertion(Annotation( "UniProtKB:Q91035") "Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains (chicken)") AnnotationAssertion(Annotation( "UniProtKB:Q91035") "ShhNC (chicken)") @@ -157572,7 +157572,7 @@ SubClassOf( ObjectSomeValuesFrom( (spondin-1 (chicken)) -AnnotationAssertion(Annotation( "PANTHER:PTHR11311:SF2") Annotation( "PRO:DNx") "A spondin-1 that is encoded in the genome of chicken.") +AnnotationAssertion(Annotation( "OMA:Q9W770") Annotation( "PRO:DNx") "A spondin-1 that is encoded in the genome of chicken.") AnnotationAssertion( "UniProtKB:Q9W770") AnnotationAssertion(Annotation( "UniProtKB:Q9W770") "F-spondin (chicken)") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "chick-SPON1")