diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 93d221fa3..ae5e3b234 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3066,6 +3066,8 @@ Declaration(Class(obo:CL_4042021)) Declaration(Class(obo:CL_4042022)) Declaration(Class(obo:CL_4042023)) Declaration(Class(obo:CL_4042024)) +Declaration(Class(obo:CL_4042026)) +Declaration(Class(obo:CL_4042027)) Declaration(Class(obo:CL_4047006)) Declaration(Class(obo:CL_4047007)) Declaration(Class(obo:CL_4047011)) @@ -3134,6 +3136,7 @@ Declaration(Class(obo:PR_000001244)) Declaration(Class(obo:PR_000002030)) Declaration(Class(obo:PR_000002123)) Declaration(Class(obo:PR_000003264)) +Declaration(Class(obo:PR_000004691)) Declaration(Class(obo:PR_000004919)) Declaration(Class(obo:PR_000005444)) Declaration(Class(obo:PR_000005460)) @@ -3142,9 +3145,11 @@ Declaration(Class(obo:PR_000007479)) Declaration(Class(obo:PR_000007489)) Declaration(Class(obo:PR_000007785)) Declaration(Class(obo:PR_000009981)) +Declaration(Class(obo:PR_000013047)) Declaration(Class(obo:PR_000010529)) Declaration(Class(obo:PR_000013502)) Declaration(Class(obo:PR_000014419)) +Declaration(Class(obo:PR_000014898)) Declaration(Class(obo:PR_000015325)) Declaration(Class(obo:PR_000015665)) Declaration(Class(obo:PR_000017299)) @@ -32424,6 +32429,28 @@ AnnotationAssertion(rdfs:label obo:CL_4042024 "striatal PTHLH MOXD1 expressing i SubClassOf(obo:CL_4042024 obo:CL_4042023) SubClassOf(obo:CL_4042024 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000010529)) +# Class: obo:CL_4042026 (GABAergic interneuron of the anterior substantia nigra pars reticulata) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:36148148") obo:IAO_0000115 obo:CL_4042026 "A GABAergic interneuron that has its soma in the anterior section of the substantia nigra pars reticulata. This GABAergic interneuron is characterized by the expression of Six3 and Foxp1 and it develops from Nkx6-2 expressing neuronal progenitors in the ventrolateral midbrain-diencephalon region.") +AnnotationAssertion(terms:contributor obo:CL_4042026 ) +AnnotationAssertion(terms:date obo:CL_4042026 "2024-09-23T13:56:01Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:36148148") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasRelatedSynonym obo:CL_4042026 "aSNpr") +AnnotationAssertion(rdfs:label obo:CL_4042026 "GABAergic interneuron of the anterior substantia nigra pars reticulata"@en) +SubClassOf(obo:CL_4042026 obo:CL_0002614) +SubClassOf(obo:CL_4042026 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000007643)) +SubClassOf(obo:CL_4042026 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000013047)) +SubClassOf(obo:CL_4042026 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000014898)) + +# Class: obo:CL_4042027 (GABAergic interneuron of the posterior substantia nigra pars reticulata) + +AnnotationAssertion(terms:contributor obo:CL_4042027 ) +AnnotationAssertion(terms:date obo:CL_4042027 "2024-09-23T14:49:11Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:36148148") oboInOwl:hasRelatedSynonym obo:CL_4042027 "A GABAergic interneuron that has its soma in the posterior section of the substantia nigra pars reticulata. This GABAergic interneuron is characterised by the expression of the transcription factors Pax5, Ctip2 and Pou6f2 and it develops from the ventrolateral r1 neuroepithelium expresing NKX61.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:36148148") oboInOwl:hasRelatedSynonym obo:CL_4042027 "pSNpr") +AnnotationAssertion(rdfs:label obo:CL_4042027 "GABAergic interneuron of the posterior substantia nigra pars reticulata"@en) +SubClassOf(obo:CL_4042027 obo:CL_0002614) +SubClassOf(obo:CL_4042027 ObjectSomeValuesFrom(obo:RO_0002292 obo:PR_000001903)) + # Class: obo:CL_4047006 (fetal artery endothelial cell) AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:34497389") obo:IAO_0000115 obo:CL_4047006 "An endothelial cell that lines an artery in the fetal circulatory system.") diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 1c98886ad..4278d16e8 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 "2024-09-23") + +Annotation(owl:versionInfo "2024-09-24") Declaration(Class()) Declaration(Class()) @@ -44,7 +44,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8573,6 +8572,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8591,6 +8591,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8623,9 +8624,9 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8634,6 +8635,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8675,7 +8677,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8720,7 +8721,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8742,6 +8743,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8839,7 +8841,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8910,7 +8911,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -9002,6 +9002,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -9011,6 +9012,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -9071,6 +9073,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -9085,6 +9088,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -9100,13 +9104,16 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -10117,6 +10124,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -116922,7 +116930,7 @@ AnnotationAssertion( "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") SubClassOf( ) -SubClassOf( ) +SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) SubClassOf( ObjectSomeValuesFrom( )) @@ -118505,6 +118513,7 @@ 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") @@ -120107,6 +120116,23 @@ AnnotationAssertion(rdfs:comment " AnnotationAssertion(rdfs:label "tyrosine-protein kinase receptor UFO") SubClassOf( ) +# Class: (B-cell lymphoma/leukemia 11B) + +AnnotationAssertion(Annotation( "PRO:DNx") "A protein that is a translation product of the human BCL11B gene or a 1:1 ortholog thereof.") +AnnotationAssertion( "B-cell CLL/lymphoma 11B") +AnnotationAssertion( "BCL-11B") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "BCL11B") +AnnotationAssertion( "COUP-TF-interacting protein 2") +AnnotationAssertion( "Rit1") +AnnotationAssertion( "radiation-induced tumor suppressor gene 1 protein") +AnnotationAssertion( "protein") +AnnotationAssertion(Annotation( ) "CTIP2") +AnnotationAssertion(Annotation( ) "RIT1") +AnnotationAssertion( "PR:000004691") +AnnotationAssertion(rdfs:comment "Category=gene.") +AnnotationAssertion(rdfs:label "B-cell lymphoma/leukemia 11B") +SubClassOf( ) + # Class: (bestrophin-4) AnnotationAssertion(Annotation( "PRO:DNx") "A protein that is a translation product of the human BEST4 gene or a 1:1 ortholog thereof.") @@ -120374,6 +120400,18 @@ AnnotationAssertion(rdfs:comment " AnnotationAssertion(rdfs:label "forkhead box protein N1") SubClassOf( ) +# Class: (forkhead box protein P1) + +AnnotationAssertion(Annotation( "PRO:DNx") "A protein that is a translation product of the human FOXP1 gene or a 1:1 ortholog thereof.") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "FOXP1") +AnnotationAssertion( "protein") +AnnotationAssertion(Annotation( ) "HSPC215") +AnnotationAssertion( "forkhead-related transcription factor 1") +AnnotationAssertion( "PR:000007643") +AnnotationAssertion(rdfs:comment "Category=gene.") +AnnotationAssertion(rdfs:label "forkhead box protein P1") +SubClassOf( ) + # Class: (glutamate decarboxylase 1) AnnotationAssertion(Annotation( "PRO:DNx") "A protein that is a translation product of the human GAD1 gene or a 1:1 ortholog thereof.") @@ -120852,6 +120890,19 @@ AnnotationAssertion(rdfs:comment " AnnotationAssertion(rdfs:label "proenkephalin-B") SubClassOf( ) +# Class: (POU domain, class 6, transcription factor 2) + +AnnotationAssertion(Annotation( "PRO:DNx") "A protein that is a translation product of the human POU6F2 gene or a 1:1 ortholog thereof.") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "POU6F2") +AnnotationAssertion( "RPF-1") +AnnotationAssertion( "retina-derived POU domain factor 1") +AnnotationAssertion( "protein") +AnnotationAssertion(Annotation( ) "RPF1") +AnnotationAssertion( "PR:000013047") +AnnotationAssertion(rdfs:comment "Category=gene.") +AnnotationAssertion(rdfs:label "POU domain, class 6, transcription factor 2") +SubClassOf( ) + # Class: (bone marrow proteoglycan) AnnotationAssertion(Annotation( "PRO:DNx") "A protein that is a translation product of the human PRG2 gene or a 1:1 ortholog thereof.") @@ -120876,21 +120927,6 @@ AnnotationAssertion(rdfs:comment " AnnotationAssertion(rdfs:label "prolactin") SubClassOf( ) -# Class: (parathyroid hormone-related protein) - -AnnotationAssertion(Annotation( "PRO:DNx") "A protein that is a translation product of the human PTHLH gene or a 1:1 ortholog thereof.") -AnnotationAssertion( "PTH-rP") -AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "PTHLH") -AnnotationAssertion( "PTHrP") -AnnotationAssertion( "parathyroid hormone-like protein") -AnnotationAssertion( "protein") -AnnotationAssertion( "PLP") -AnnotationAssertion(Annotation( ) "PTHRP") -AnnotationAssertion( "PR:000013433") -AnnotationAssertion(rdfs:comment "Category=gene.") -AnnotationAssertion(rdfs:label "parathyroid hormone-related protein") -SubClassOf( ) - # Class: (parvalbumin alpha) AnnotationAssertion(Annotation( "PRO:DNx") "A protein that is a translation product of the human PVALB gene or a 1:1 ortholog thereof.") @@ -121022,6 +121058,17 @@ AnnotationAssertion(rdfs:comment " AnnotationAssertion(rdfs:label "sonic hedgehog protein") SubClassOf( ) +# Class: (homeobox protein SIX3) + +AnnotationAssertion(Annotation( "PRO:DNx") "A protein that is a translation product of the human SIX3 gene or a 1:1 ortholog thereof.") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "SIX3") +AnnotationAssertion( "sine oculis homeobox homolog 3") +AnnotationAssertion( "protein") +AnnotationAssertion( "PR:000014898") +AnnotationAssertion(rdfs:comment "Category=gene.") +AnnotationAssertion(rdfs:label "homeobox protein SIX3") +SubClassOf( ) + # Class: (gamma-synuclein) AnnotationAssertion(Annotation( "PRO:DNx") "A protein that is a translation product of the human SNCG gene or a 1:1 ortholog thereof.") @@ -121555,19 +121602,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (parathyroid hormone-related protein proteolytic cleavage product) - -AnnotationAssertion(Annotation( "PRO:DNx") "A parathyroid hormone-related protein that has been processed by proteolytic cleavage.") -AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "PTHLH/ClvPrd") -AnnotationAssertion( "protein") -AnnotationAssertion( "PR:000021172") -AnnotationAssertion(rdfs:comment "Category=modification.") -AnnotationAssertion(rdfs:label "parathyroid hormone-related protein proteolytic cleavage product") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (sonic hedgehog protein proteolytic cleavage product) AnnotationAssertion(Annotation( "PRO:DNx") "A sonic hedgehog protein that has been processed by proteolytic cleavage.") @@ -122104,20 +122138,20 @@ 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: (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: (SCO-spondin (human)) @@ -122358,7 +122392,7 @@ SubClassOf( ObjectSomeValuesFrom( (natural killer cells antigen CD94 (mouse)) -AnnotationAssertion(Annotation( "OMA:O54707") Annotation( "PRO:DNx") "A killer cell lectin-like receptor subfamily D member 1 that is encoded in the genome of mouse.") +AnnotationAssertion(Annotation( "OMA:O54707") Annotation( "PANTHER:PTHR22800:SF15") Annotation( "PRO:DNx") "A killer cell lectin-like receptor subfamily D member 1 that is encoded in the genome of mouse.") AnnotationAssertion( "UniProtKB:O54707") AnnotationAssertion(Annotation( "UniProtKB:O54707") "CD94 (mouse)") AnnotationAssertion(Annotation( "UniProtKB:O54707") "killer cell lectin-like receptor subfamily D member 1 (mouse)") @@ -122459,7 +122493,7 @@ SubClassOf( ObjectSomeValuesFrom( (CD83 antigen (mouse)) -AnnotationAssertion(Annotation( "OMA:O88324") Annotation( "PRO:DNx") "A CD83 molecule that is encoded in the genome of mouse.") +AnnotationAssertion(Annotation( "OMA:O88324") Annotation( "PANTHER:PTHR15193:SF0") Annotation( "PRO:DNx") "A CD83 molecule that is encoded in the genome of mouse.") AnnotationAssertion( "UniProtKB:O88324") AnnotationAssertion(Annotation( "UniProtKB:O88324") "CD83 (mouse)") AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "mCD83") @@ -122538,10 +122572,25 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (homeobox protein SIX3 (human)) + +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( "UniProtKB:O95343") "A homeobox protein SIX3 that is encoded in the genome of human.") +AnnotationAssertion( "UniProtKB:O95343") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "hSIX3") +AnnotationAssertion(Annotation( "UniProtKB:O95343") "sine oculis homeobox homolog 3 (human)") +AnnotationAssertion( "protein") +AnnotationAssertion(Annotation( "UniProtKB:O95343") Annotation( ) "SIX3") +AnnotationAssertion( "PR:O95343") +AnnotationAssertion(rdfs:comment "Category=organism-gene.") +AnnotationAssertion(rdfs:label "homeobox protein SIX3 (human)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (eomesodermin homolog (human)) AnnotationAssertion(Annotation( "PRO:CNA") Annotation( "UniProtKB:O95936") "An eomesodermin that is encoded in the genome of human.") -AnnotationAssertion(Annotation(rdfs:label "PR:O95936 located_in GO:0005654") "Reactome:R-HSA-452232") AnnotationAssertion( "UniProtKB:O95936") AnnotationAssertion(Annotation( "UniProtKB:O95936") "T-box brain protein 2 (human)") AnnotationAssertion(Annotation( "UniProtKB:O95936") "T-brain-2 (human)") @@ -124433,25 +124482,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (parathyroid hormone-related protein (human)) - -AnnotationAssertion(Annotation( "PRO:DNx") Annotation( "UniProtKB:P12272") "A parathyroid hormone-related protein that is encoded in the genome of human.") -AnnotationAssertion(Annotation( "UniProtKB:P12272") "PLP (human)") -AnnotationAssertion( "UniProtKB:P12272") -AnnotationAssertion(Annotation( "UniProtKB:P12272") "PTH-rP (human)") -AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "hPTHLH") -AnnotationAssertion(Annotation( "UniProtKB:P12272") "parathyroid hormone-like protein (human)") -AnnotationAssertion( "protein") -AnnotationAssertion(Annotation( "UniProtKB:P12272") Annotation( ) "PTHLH") -AnnotationAssertion(Annotation( "UniProtKB:P12272") Annotation( ) "PTHRP") -AnnotationAssertion( "PR:P12272") -AnnotationAssertion(rdfs:comment "Category=organism-gene.") -AnnotationAssertion(rdfs:label "parathyroid hormone-related protein (human)") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (high affinity immunoglobulin gamma Fc receptor I (human)) AnnotationAssertion(Annotation( "PRO:CNA") Annotation( "UniProtKB:P12314") "A high affinity immunoglobulin gamma Fc receptor I that is encoded in the genome of human.") @@ -125894,26 +125924,6 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) -# Class: (parathyroid hormone-related protein (mouse)) - -AnnotationAssertion(Annotation( "OMA:P22858") Annotation( "PRO:DNx") "A parathyroid hormone-related protein that is encoded in the genome of mouse.") -AnnotationAssertion( "UniProtKB:P22858") -AnnotationAssertion(Annotation( "UniProtKB:P22858") "PTH-rP (mouse)") -AnnotationAssertion(Annotation( "UniProtKB:P22858") "PTHrP (mouse)") -AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "mPTHLH") -AnnotationAssertion(Annotation( "UniProtKB:P22858") "parathyroid hormone-like protein (mouse)") -AnnotationAssertion( "protein") -AnnotationAssertion(Annotation( "UniProtKB:P22858") "PLP (mouse)") -AnnotationAssertion(Annotation( "UniProtKB:P22858") Annotation( ) "Pthlh") -AnnotationAssertion(Annotation( "UniProtKB:P22858") Annotation( ) "Pthrp") -AnnotationAssertion( "PR:P22858") -AnnotationAssertion(rdfs:comment "Category=organism-gene.") -AnnotationAssertion(rdfs:label "parathyroid hormone-related protein (mouse)") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - # Class: (macrophage mannose receptor 1 (human)) AnnotationAssertion(Annotation( "PRO:CNA") Annotation( "UniProtKB:P22897") "A macrophage mannose receptor 1 that is encoded in the genome of human.") @@ -126353,7 +126363,7 @@ 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") @@ -127774,7 +127784,7 @@ 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") @@ -127787,6 +127797,22 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (forkhead box protein P1 (mouse)) + +AnnotationAssertion(Annotation( "OMA:P58462") Annotation( "PRO:DNx") "A forkhead box protein P1 that is encoded in the genome of mouse.") +AnnotationAssertion( "UniProtKB:P58462") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "mFOXP1") +AnnotationAssertion( "protein") +AnnotationAssertion(Annotation( "UniProtKB:P58462") Annotation( ) "Foxp1") +AnnotationAssertion(Annotation( "UniProtKB:P58462") "forkhead-related transcription factor 1 (mouse)") +AnnotationAssertion( "PR:P58462") +AnnotationAssertion(rdfs:comment "Category=organism-gene.") +AnnotationAssertion(rdfs:label "forkhead box protein P1 (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (leukocyte immunoglobulin-like receptor subfamily A member 4 (human)) AnnotationAssertion(Annotation( "PRO:WCB") Annotation( "UniProtKB:P59901") "A leukocyte immunoglobulin-like receptor subfamily A member 4 that is encoded in the genome of human.") @@ -127992,6 +128018,24 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (POU domain, class 6, transcription factor 2 (human)) + +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( "UniProtKB:P78424") "A POU domain, class 6, transcription factor 2 that is encoded in the genome of human.") +AnnotationAssertion( "UniProtKB:P78424") +AnnotationAssertion(Annotation( "UniProtKB:P78424") "RPF-1 (human)") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "hPOU6F2") +AnnotationAssertion(Annotation( "UniProtKB:P78424") "retina-derived POU domain factor 1 (human)") +AnnotationAssertion( "protein") +AnnotationAssertion(Annotation( "UniProtKB:P78424") Annotation( ) "POU6F2") +AnnotationAssertion(Annotation( "UniProtKB:P78424") Annotation( ) "RPF1") +AnnotationAssertion( "PR:P78424") +AnnotationAssertion(rdfs:comment "Category=organism-gene.") +AnnotationAssertion(rdfs:label "POU domain, class 6, transcription factor 2 (human)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (reelin (human)) AnnotationAssertion(Annotation( "PRO:DNx") Annotation( "UniProtKB:P78509") "A reelin that is encoded in the genome of human.") @@ -129201,6 +129245,22 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (homeobox protein SIX3 (mouse)) + +AnnotationAssertion(Annotation( "OMA:Q62233") Annotation( "PRO:DNx") "A homeobox protein SIX3 that is encoded in the genome of mouse.") +AnnotationAssertion( "UniProtKB:Q62233") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "mSIX3") +AnnotationAssertion(Annotation( "UniProtKB:Q62233") "sine oculis homeobox homolog 3 (mouse)") +AnnotationAssertion( "protein") +AnnotationAssertion(Annotation( "UniProtKB:Q62233") Annotation( ) "Six3") +AnnotationAssertion( "PR:Q62233") +AnnotationAssertion(rdfs:comment "Category=organism-gene.") +AnnotationAssertion(rdfs:label "homeobox protein SIX3 (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (transferrin receptor protein 1 (mouse)) AnnotationAssertion(Annotation( "OMA:Q62351") Annotation( "PRO:DNx") "A transferrin receptor protein 1 that is encoded in the genome of mouse.") @@ -129472,6 +129532,21 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (POU domain, class 6, transcription factor 2 (mouse)) + +AnnotationAssertion(Annotation( "PRO:DNx") "A POU domain, class 6, transcription factor 2 that is encoded in the genome of mouse.") +AnnotationAssertion( "UniProtKB:Q8BJI4") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "mPOU6F2") +AnnotationAssertion( "protein") +AnnotationAssertion(Annotation( "UniProtKB:Q8BJI4") Annotation( ) "Pou6f2") +AnnotationAssertion( "PR:Q8BJI4") +AnnotationAssertion(rdfs:comment "Category=organism-gene.") +AnnotationAssertion(rdfs:label "POU domain, class 6, transcription factor 2 (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (natural cytotoxicity triggering receptor 1 (mouse)) AnnotationAssertion(Annotation( "OMA:Q8C567") Annotation( "PRO:WCB") "A natural cytotoxicity triggering receptor 1 that is encoded in the genome of mouse.") @@ -129763,6 +129838,28 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (B-cell lymphoma/leukemia 11B (mouse)) + +AnnotationAssertion(Annotation( "OMA:Q99PV8") Annotation( "PRO:DNx") "A B-cell lymphoma/leukemia 11B that is encoded in the genome of mouse.") +AnnotationAssertion( "UniProtKB:Q99PV8") +AnnotationAssertion(Annotation( "UniProtKB:Q99PV8") "B-cell CLL/lymphoma 11B (mouse)") +AnnotationAssertion(Annotation( "UniProtKB:Q99PV8") "BCL-11B (mouse)") +AnnotationAssertion(Annotation( "UniProtKB:Q99PV8") "COUP-TF-interacting protein 2 (mouse)") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "mBCL11B") +AnnotationAssertion(Annotation( "UniProtKB:Q99PV8") "mRit1") +AnnotationAssertion(Annotation( "UniProtKB:Q99PV8") "radiation-induced tumor suppressor gene 1 protein (mouse)") +AnnotationAssertion( "protein") +AnnotationAssertion(Annotation( "UniProtKB:Q99PV8") Annotation( ) "Bcl11b") +AnnotationAssertion(Annotation( "UniProtKB:Q99PV8") Annotation( ) "Ctip2") +AnnotationAssertion(Annotation( "UniProtKB:Q99PV8") Annotation( ) "Rit1") +AnnotationAssertion( "PR:Q99PV8") +AnnotationAssertion(rdfs:comment "Category=organism-gene.") +AnnotationAssertion(rdfs:label "B-cell lymphoma/leukemia 11B (mouse)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (C-type lectin domain family 7 member A (human)) AnnotationAssertion(Annotation( "PRO:WCB") Annotation( "UniProtKB:Q9BXN2") "A C-type lectin domain family 7 member A that is encoded in the genome of human.") @@ -129851,6 +129948,28 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (B-cell lymphoma/leukemia 11B (human)) + +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( "UniProtKB:Q9C0K0") "A B-cell lymphoma/leukemia 11B that is encoded in the genome of human.") +AnnotationAssertion( "UniProtKB:Q9C0K0") +AnnotationAssertion(Annotation( "UniProtKB:Q9C0K0") "B-cell CLL/lymphoma 11B (human)") +AnnotationAssertion(Annotation( "UniProtKB:Q9C0K0") "BCL-11B (human)") +AnnotationAssertion(Annotation( "UniProtKB:Q9C0K0") "COUP-TF-interacting protein 2 (human)") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "hBCL11B") +AnnotationAssertion(Annotation( "UniProtKB:Q9C0K0") "hRit1") +AnnotationAssertion(Annotation( "UniProtKB:Q9C0K0") "radiation-induced tumor suppressor gene 1 protein (human)") +AnnotationAssertion( "protein") +AnnotationAssertion(Annotation( "UniProtKB:Q9C0K0") Annotation( ) "BCL11B") +AnnotationAssertion(Annotation( "UniProtKB:Q9C0K0") Annotation( ) "CTIP2") +AnnotationAssertion(Annotation( "UniProtKB:Q9C0K0") Annotation( ) "RIT1") +AnnotationAssertion( "PR:Q9C0K0") +AnnotationAssertion(rdfs:comment "Category=organism-gene.") +AnnotationAssertion(rdfs:label "B-cell lymphoma/leukemia 11B (human)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (chondrolectin (mouse)) AnnotationAssertion(Annotation( "OMA:Q9CXM0") Annotation( "PRO:DNx") "A chondrolectin that is encoded in the genome of mouse.") @@ -129905,6 +130024,24 @@ SubClassOf( ) SubClassOf( ObjectSomeValuesFrom( )) +# Class: (forkhead box protein P1 (human)) + +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( "UniProtKB:Q9H334") "A forkhead box protein P1 that is encoded in the genome of human.") +AnnotationAssertion( "UniProtKB:Q9H334") +AnnotationAssertion(Annotation( "UniProtKB:Q9H334") "MFH (human)") +AnnotationAssertion(Annotation( "UniProtKB:Q9H334") "Mac-1-regulated forkhead (human)") +AnnotationAssertion(Annotation( "PRO:DNx") Annotation( ) "hFOXP1") +AnnotationAssertion( "protein") +AnnotationAssertion(Annotation( "UniProtKB:Q9H334") Annotation( ) "FOXP1") +AnnotationAssertion(Annotation( "UniProtKB:Q9H334") Annotation( ) "HSPC215") +AnnotationAssertion( "PR:Q9H334") +AnnotationAssertion(rdfs:comment "Category=organism-gene.") +AnnotationAssertion(rdfs:label "forkhead box protein P1 (human)") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + # Class: (chondrolectin (human)) AnnotationAssertion(Annotation( "PRO:DNx") Annotation( "UniProtKB:Q9H9P2") "A chondrolectin that is encoded in the genome of human.") @@ -161311,6 +161448,53 @@ SubClassOf(Annotation( "NCB SubClassOf( ObjectSomeValuesFrom( )) DisjointClasses(Annotation( "lexical") ) +# Class: (median eminence of neurohypophysis) + +AnnotationAssertion(Annotation( "BIRNLEX:925") "Elevation on the ventral surface of the brain located at the zone of attachment between the hypothalamic floor and the hypophysis (Butler and Hodos, Comparative Vertebrate Neuroanatomy, 2nd ed., 2005, pg. 446).") +AnnotationAssertion(Annotation( "BIRNLEX:925") Annotation( "NIFSTD:NeuroNames_abbrevSource") Annotation( ) "ME") +AnnotationAssertion( "AAO:0010539") +AnnotationAssertion( "BAMS:ME") +AnnotationAssertion( "BIRNLEX:925") +AnnotationAssertion( "BM:ME") +AnnotationAssertion( "BTO:0001954") +AnnotationAssertion( "DHBA:13338") +AnnotationAssertion( "DMBA:15689") +AnnotationAssertion( "EHDAA2:0001080") +AnnotationAssertion( "EHDAA:7540") +AnnotationAssertion( "EMAPA:17521") +AnnotationAssertion( "FMA:74634") +AnnotationAssertion( "GAID:463") +AnnotationAssertion( "HBA:12916") +AnnotationAssertion( "MA:0000859") +AnnotationAssertion( "MBA:10671") +AnnotationAssertion( "MESH:D008473") +AnnotationAssertion( "SCTID:369121004") +AnnotationAssertion(Annotation( "BIRNLEX:925") "UMLS:C0025056") +AnnotationAssertion( "VHOG:0001179") +AnnotationAssertion( "Wikipedia:Median_eminence") +AnnotationAssertion(Annotation( "BIRNLEX:925") "neuronames:402") +AnnotationAssertion(Annotation( "FMA:74634") Annotation( "FMA:TA") Annotation( ) "eminentia mediana hypothalami") +AnnotationAssertion( "median eminence") +AnnotationAssertion( "median eminence of hypothalamus") +AnnotationAssertion( "median eminence of posterior lobe of pituitary gland") +AnnotationAssertion( "median eminence of tuber cinereum") +AnnotationAssertion( "uberon") +AnnotationAssertion(Annotation( "NeuroNames:402") Annotation( ) "eminentia medialis (Shantha)") +AnnotationAssertion(Annotation( "NeuroNames:402") Annotation( ) "eminentia mediana") +AnnotationAssertion(Annotation( "Wikipedia:Median_eminence") Annotation( ) "eminentia mediana hypothalami") +AnnotationAssertion(Annotation( "NeuroNames:402") Annotation( ) "eminentia postinfundibularis") +AnnotationAssertion(Annotation( "NeuroNames:402") "medial eminence") +AnnotationAssertion( "UBERON:0002197") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "median eminence of neurohypophysis") +AnnotationAssertion( "http://upload.wikimedia.org/wikipedia/commons/8/8c/HypothalamicNuclei.PNG"^^xsd:anyURI) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf(Annotation( "ISBN:0471888893") ObjectSomeValuesFrom( )) + # Class: (neurohypophysis) AnnotationAssertion(Annotation( "MP:0004164") "The posterior part of the pituitary gland that secretes hormones involved in blood pressure regulation such as oxytocin and antidiuretic hormon.") diff --git a/src/ontology/imports/pr_terms.txt b/src/ontology/imports/pr_terms.txt index c61d0d3b1..7b765ffd9 100644 --- a/src/ontology/imports/pr_terms.txt +++ b/src/ontology/imports/pr_terms.txt @@ -42,5 +42,7 @@ PR:000004919 PR:000014419 PR:000007489 PR:000007479 -PR:000013433 -PR:000010529 \ No newline at end of file +PR:000014898 +PR:000007643 +PR:000004691 +PR:000013047 diff --git a/src/patterns/definitions.owl b/src/patterns/definitions.owl index 7e67a5623..5fc7c7cd2 100644 --- a/src/patterns/definitions.owl +++ b/src/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-09-23") + +Annotation(owl:versionInfo "2024-09-24") Declaration(Class()) Declaration(Class())