From 5457dfcc0a46108b1cd2c495096bae8bf4293b7e Mon Sep 17 00:00:00 2001 From: AvolaAmg Date: Thu, 7 Mar 2024 12:39:13 +0000 Subject: [PATCH 1/3] NTR-border-associated-macrophage-and-subclasses Fixes #2285 --- src/ontology/cl-edit.owl | 77 ++++++++++++++++++++++++++++++++++------ 1 file changed, 66 insertions(+), 11 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 4d4d69bac..6825f7854 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3023,6 +3023,10 @@ Declaration(Class(obo:CL_4040002)) Declaration(Class(obo:CL_4040003)) Declaration(Class(obo:CL_4040004)) Declaration(Class(obo:CL_4040005)) +Declaration(Class(obo:CL_4042001)) +Declaration(Class(obo:CL_4042002)) +Declaration(Class(obo:CL_4042003)) +Declaration(Class(obo:CL_4042004)) Declaration(Class(obo:CP_0000000)) Declaration(Class(obo:CP_0000025)) Declaration(Class(obo:CP_0000027)) @@ -11260,26 +11264,32 @@ SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000878 obo:CL_0000864 # Class: obo:CL_0000879 (meningeal macrophage) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:ana") Annotation(oboInOwl:hasDbXref "GO_REF:0000031") Annotation(oboInOwl:hasDbXref "PMID:11591794") obo:IAO_0000115 obo:CL_0000879 "A central nervous system macrophage found in the meninges (the three membranes that surround the brain). This macrophage types is highly phagocytic and expresses scavenger receptors.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:ana") Annotation(oboInOwl:hasDbXref "GO_REF:0000031") Annotation(oboInOwl:hasDbXref "PMID:11591794") Annotation(oboInOwl:hasDbXref "PMID:24078900") Annotation(oboInOwl:hasDbXref "PMID:37232741") obo:IAO_0000115 obo:CL_0000879 "A central nervous system macrophage that is part of the meninges. This macrophage types is highly phagocytic, expresses scavenger receptors, has dynamic protrusions and extends its processes during inflammation. The cell body of this macrophage is elongated and amoeboid spindle-shaped with limited mobility.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33556248") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasExactSynonym obo:CL_0000879 "MM") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38347231") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasExactSynonym obo:CL_0000879 "MnMΦ") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33556248") oboInOwl:hasExactSynonym obo:CL_0000879 "subdural leptomeningeal macrophage") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:28323268") oboInOwl:hasExactSynonym obo:CL_0000879 "subdural meningeal macrophage") AnnotationAssertion(rdfs:label obo:CL_0000879 "meningeal macrophage") -EquivalentClasses(obo:CL_0000879 ObjectIntersectionOf(obo:CL_0000878 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002360) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0005044))) -SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000879 obo:CL_0000878) +EquivalentClasses(obo:CL_0000879 ObjectIntersectionOf(obo:CL_4042001 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002360) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0005044))) +SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000879 obo:CL_4042001) -# Class: obo:CL_0000880 (choroid-plexus macrophage) +# Class: obo:CL_0000880 (choroid plexus macrophage) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:ana") Annotation(oboInOwl:hasDbXref "GO_REF:0000031") Annotation(oboInOwl:hasDbXref "PMID:9550136") obo:IAO_0000115 obo:CL_0000880 "A central nervous system macrophage found at the interface between the blood and the cerebrospinal fluid in the brain. This cell expresses scavenger receptors.") -AnnotationAssertion(rdfs:label obo:CL_0000880 "choroid-plexus macrophage") -EquivalentClasses(obo:CL_0000880 ObjectIntersectionOf(obo:CL_0000878 ObjectSomeValuesFrom(obo:RO_0001025 obo:UBERON_0001886) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0005044))) -SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000880 obo:CL_0000878) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:ana") Annotation(oboInOwl:hasDbXref "GO_REF:0000031") Annotation(oboInOwl:hasDbXref "PMID:9550136") Annotation(oboInOwl:hasDbXref "PMID:37232741") obo:IAO_0000115 obo:CL_0000880 "A central nervous system macrophage found at the interface between the blood and the cerebrospinal fluid in the brain. This central nervous system macrophage expresses scavenger receptors, and has a star-like shaped body.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37232741") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasExactSynonym obo:CL_0000880 "cpMΦ") +AnnotationAssertion(rdfs:label obo:CL_0000880 "choroid plexus macrophage") +EquivalentClasses(obo:CL_0000880 ObjectIntersectionOf(obo:CL_4042001 ObjectSomeValuesFrom(obo:RO_0001025 obo:UBERON_0001886) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0005044))) +SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000880 obo:CL_4042001) # Class: obo:CL_0000881 (perivascular macrophage) -AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "GO_REF:0000031") Annotation(oboInOwl:hasDbXref "PMID:16507898") obo:IAO_0000115 obo:CL_0000881 "A central nervous system macrophage found in small blood vessels in the brain. Markers include CD14+CD16+CD163+.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "GOC:tfm") Annotation(oboInOwl:hasDbXref "GO_REF:0000031") Annotation(oboInOwl:hasDbXref "PMID:16507898") Annotation(oboInOwl:hasDbXref "PMID:37232741") obo:IAO_0000115 obo:CL_0000881 "
A central nervous system macrophage that is part of small blood vessels in the brain. Markers include CD14, CD16, CD163. In homeostatic conditions, this central nervous system macrophage has a Non-motile cell body with extending and retracting projections through the blood vessel wall.") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37232741") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasExactSynonym obo:CL_0000881 "pvMΦ") AnnotationAssertion(rdfs:comment obo:CL_0000881 "Markers: Human/monkey, mice: CD163. Human: CD14+CD16+CD163+.") AnnotationAssertion(rdfs:label obo:CL_0000881 "perivascular macrophage") -EquivalentClasses(obo:CL_0000881 ObjectIntersectionOf(obo:CL_0000878 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001981) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001483) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001889) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001925))) -SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000881 obo:CL_0000878) +EquivalentClasses(obo:CL_0000881 ObjectIntersectionOf(obo:CL_4042001 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001981) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001483) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001889) ObjectSomeValuesFrom(obo:RO_0002104 obo:PR_000001925))) SubClassOf(obo:CL_0000881 obo:CL_4033054) +SubClassOf(Annotation(oboInOwl:is_inferred "true") obo:CL_0000881 obo:CL_4042001) # Class: obo:CL_0000882 (thymic medullary macrophage) @@ -31920,6 +31930,51 @@ AnnotationAssertion(rdfs:label obo:CL_4040005 "mesenchymal stem cell of apical p SubClassOf(obo:CL_4040005 obo:CL_0000134) SubClassOf(obo:CL_4040005 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0003677)) +# Class: obo:CL_4042001 (border associated macrophage) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37232741") Annotation(oboInOwl:hasDbXref "PMID:37626977") obo:IAO_0000115 obo:CL_4042001 "A central nervous system macrophage that is part of the choroid plexus, meningeal and perivascular spaces. A border associated macrophage interacts with various components of the CNS vasculature and meninges, it participates in immune surveillance and in the regulation of the blood brain barrier.") +AnnotationAssertion( obo:CL_4042001 ) +AnnotationAssertion( obo:CL_4042001 "2024-03-06T16:27:35Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:36945367") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasExactSynonym obo:CL_4042001 "BAM") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33556248") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasExactSynonym obo:CL_4042001 "CAM") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37232741") oboInOwl:hasExactSynonym obo:CL_4042001 "CNS-associated macrophage") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29426702") Annotation(oboInOwl:hasDbXref "PMID:37232741") rdfs:comment obo:CL_4042001 "A border associate macrophage expresses CD45 and CD11B. This cell is also known to have the following molecular signature: CD206, CD38, LYVE1, CD163, CD169") +AnnotationAssertion(rdfs:label obo:CL_4042001 "border associated macrophage"@en) +EquivalentClasses(obo:CL_4042001 ObjectIntersectionOf(obo:CL_0000878 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001886) ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001981) ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002360) ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002363) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0006955))) +SubClassOf(obo:CL_4042001 obo:CL_0000878) + +# Class: obo:CL_4042002 (stromal choroid plexus macrophage) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38347231") obo:IAO_0000115 obo:CL_4042002 "A choroid plexus macrophage that is part of the choroid plexus stroma.") +AnnotationAssertion( obo:CL_4042002 ) +AnnotationAssertion( obo:CL_4042002 "2024-03-06T18:53:05Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38347231") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasExactSynonym obo:CL_4042002 "stromal cpMΦ") +AnnotationAssertion(rdfs:label obo:CL_4042002 "stromal choroid plexus macrophage"@en) +EquivalentClasses(obo:CL_4042002 ObjectIntersectionOf(obo:CL_0000880 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0005206))) +SubClassOf(obo:CL_4042002 obo:CL_0000880) + +# Class: obo:CL_4042003 (choroid epiplexus macrophage) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31061494") Annotation(oboInOwl:hasDbXref "PMID:37232741") obo:IAO_0000115 obo:CL_4042003 "A choroid plexus macrophage that is part of the apical surface of the choroid plexus epithelium. This macrophage has a star-like shaped body.") +AnnotationAssertion( obo:CL_4042003 ) +AnnotationAssertion( obo:CL_4042003 "2024-03-06T18:53:24Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31433571") oboInOwl:hasExactSynonym obo:CL_4042003 "Kolmer’s cell") +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:38347231") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasExactSynonym obo:CL_4042003 "cpepiMΦ") +AnnotationAssertion(Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasExactSynonym obo:CL_4042003 "epiplexus cpMΦ") +AnnotationAssertion(rdfs:label obo:CL_4042003 "choroid epiplexus macrophage"@en) +EquivalentClasses(obo:CL_4042003 ObjectIntersectionOf(obo:CL_0000880 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0003911))) +SubClassOf(obo:CL_4042003 obo:CL_0000880) + +# Class: obo:CL_4042004 (dural macrophage) + +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:31061494") obo:IAO_0000115 obo:CL_4042004 "A central nervous system macrophage that is part of the dura matter. This macrophage phagocytoses intruding pathogens and foreign molecules detected in the bloodstream or in the cerebrospinal fluid. This cell has an amoeboid body with dynamic protrusions in homeostasis.") +AnnotationAssertion( obo:CL_4042004 ) +AnnotationAssertion( obo:CL_4042004 "2024-03-07T11:09:00Z"^^xsd:dateTime) +AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37232741") Annotation(oboInOwl:hasSynonymType obo:OMO_0003000) oboInOwl:hasExactSynonym obo:CL_4042004 "dmMΦ") +AnnotationAssertion(rdfs:label obo:CL_4042004 "dural macrophage"@en) +EquivalentClasses(obo:CL_4042004 ObjectIntersectionOf(obo:CL_4042001 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002363) ObjectSomeValuesFrom(obo:RO_0000053 obo:CL_0000732))) +SubClassOf(obo:CL_4042004 obo:CL_4042001) + # Class: obo:CP_0000000 (obsolete CP:0000000) AnnotationAssertion(obo:IAO_0100001 obo:CP_0000000 obo:CL_0017500) From 32f3cd4769ee8fa72b69e0c91610e04f4e4846ab Mon Sep 17 00:00:00 2001 From: AvolaAmg Date: Thu, 7 Mar 2024 12:47:13 +0000 Subject: [PATCH 2/3] Update cl-edit.owl --- src/ontology/cl-edit.owl | 1 - 1 file changed, 1 deletion(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 6825f7854..4fd3f96e2 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -31940,7 +31940,6 @@ AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:33556248") Annotation(ob AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:37232741") oboInOwl:hasExactSynonym obo:CL_4042001 "CNS-associated macrophage") AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:29426702") Annotation(oboInOwl:hasDbXref "PMID:37232741") rdfs:comment obo:CL_4042001 "A border associate macrophage expresses CD45 and CD11B. This cell is also known to have the following molecular signature: CD206, CD38, LYVE1, CD163, CD169") AnnotationAssertion(rdfs:label obo:CL_4042001 "border associated macrophage"@en) -EquivalentClasses(obo:CL_4042001 ObjectIntersectionOf(obo:CL_0000878 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001886) ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0001981) ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002360) ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002363) ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0006955))) SubClassOf(obo:CL_4042001 obo:CL_0000878) # Class: obo:CL_4042002 (stromal choroid plexus macrophage) From 71559a89cb1036a9c96e52651b5f0bf77d2f4fde Mon Sep 17 00:00:00 2001 From: AvolaAmg Date: Thu, 7 Mar 2024 13:14:55 +0000 Subject: [PATCH 3/3] removing conflicting axioms in dural macrophages --- src/ontology/cl-edit.owl | 15 -- src/ontology/imports/merged_import.owl | 237 ++++++++++++------------- 2 files changed, 117 insertions(+), 135 deletions(-) diff --git a/src/ontology/cl-edit.owl b/src/ontology/cl-edit.owl index 4fd3f96e2..bd0a54803 100644 --- a/src/ontology/cl-edit.owl +++ b/src/ontology/cl-edit.owl @@ -3405,7 +3405,6 @@ AnnotationAssertion(oboInOwl:inSubset obo:CL_0000000 "PERSON:Daniel Schober"@en) AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion(rdfs:label "definition"@en) AnnotationAssertion(rdfs:label "definition") +AnnotationAssertion(rdfs:label "definition"@en) # Annotation Property: (editor note) @@ -14258,8 +14258,8 @@ AnnotationAssertion( "editor_note") AnnotationAssertion( "true"^^xsd:boolean) AnnotationAssertion( "editor_note") -AnnotationAssertion(rdfs:label "editor note"@en) AnnotationAssertion(rdfs:label "editor note") +AnnotationAssertion(rdfs:label "editor note"@en) # Annotation Property: (has obsolescence reason) @@ -14285,8 +14285,8 @@ AnnotationAssertion( "true"^^xsd:boolean) AnnotationAssertion( "term_tracker_item") AnnotationAssertion(rdfs:comment "The 'tracker item' can associate a tracker with a specific ontology term."@en) -AnnotationAssertion(rdfs:label "term tracker item"@en) AnnotationAssertion(rdfs:label "term tracker item") +AnnotationAssertion(rdfs:label "term tracker item"@en) # Annotation Property: (expand expression to) @@ -14311,8 +14311,8 @@ AnnotationAssertion( "true"^^xsd:boolean) AnnotationAssertion( "true"^^xsd:boolean) AnnotationAssertion( "has_ontology_root_term") -AnnotationAssertion(rdfs:label "has ontology root term"@en) AnnotationAssertion(rdfs:label "has ontology root term") +AnnotationAssertion(rdfs:label "has ontology root term"@en) # Annotation Property: (term replaced by) @@ -14322,8 +14322,8 @@ AnnotationAssertion( "Person:Alan Ruttenberg"@en) AnnotationAssertion( "Person:Alan Ruttenberg"@en) AnnotationAssertion(rdfs:comment "Add as annotation triples in the granting ontology"@en) -AnnotationAssertion(rdfs:label "term replaced by"@en) AnnotationAssertion(rdfs:label "term replaced by") +AnnotationAssertion(rdfs:label "term replaced by"@en) # Annotation Property: (defined by construct) @@ -14383,7 +14383,7 @@ SubAnnotationPropertyOf( ) -# Annotation Property: (never in taxon) +# Annotation Property: (never_in_taxon) AnnotationAssertion( "tooth SubClassOf 'never in taxon' value 'Aves'") AnnotationAssertion(Annotation( "PMID:20973947") "S never_in_taxon T iff: S SubClassOf in_taxon only not T.") @@ -14970,13 +14970,13 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "part_of") -AnnotationAssertion(rdfs:label "part of"@en) AnnotationAssertion(rdfs:label "part of") +AnnotationAssertion(rdfs:label "part of"@en) AnnotationAssertion(rdfs:label "part_of") AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Part_of"^^xsd:anyURI) AnnotationAssertion(rdfs:seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Part_of"^^xsd:anyURI) SubObjectPropertyOf( ) InverseObjectProperties( ) TransitiveObjectProperty() @@ -15004,8 +15004,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_part") -AnnotationAssertion(rdfs:label "has part"@en) AnnotationAssertion(rdfs:label "has part") +AnnotationAssertion(rdfs:label "has part"@en) AnnotationAssertion(rdfs:label "has_part") SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -15024,8 +15024,8 @@ AnnotationAssertion( "preceded_by") AnnotationAssertion( ) AnnotationAssertion( "preceded_by") -AnnotationAssertion(rdfs:label "preceded by"@en) AnnotationAssertion(rdfs:label "preceded by") +AnnotationAssertion(rdfs:label "preceded by"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) TransitiveObjectProperty() @@ -15042,8 +15042,8 @@ AnnotationAssertion( "precedes") AnnotationAssertion( ) AnnotationAssertion( "precedes") -AnnotationAssertion(rdfs:label "precedes"@en) AnnotationAssertion(rdfs:label "precedes") +AnnotationAssertion(rdfs:label "precedes"@en) SubObjectPropertyOf( ) TransitiveObjectProperty() ObjectPropertyDomain( ) @@ -15065,8 +15065,8 @@ AnnotationAssertion( "occurs_in") AnnotationAssertion(rdfs:comment "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant") AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "occurs in"@en) AnnotationAssertion(rdfs:label "occurs in") +AnnotationAssertion(rdfs:label "occurs in"@en) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Occurs_in"^^xsd:anyURI) InverseObjectProperties( ) ObjectPropertyDomain( ) @@ -15082,8 +15082,8 @@ AnnotationAssertion( "contains_process") AnnotationAssertion(rdfs:comment "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant") AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "contains process"@en) AnnotationAssertion(rdfs:label "contains process") +AnnotationAssertion(rdfs:label "contains process"@en) # Object Property: (anterior to) @@ -15324,8 +15324,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "bearer_of") AnnotationAssertion( "bearer_of") -AnnotationAssertion(rdfs:label "has characteristic"@en) AnnotationAssertion(rdfs:label "bearer of") +AnnotationAssertion(rdfs:label "has characteristic"@en) InverseFunctionalObjectProperty() ObjectPropertyRange( ) @@ -15342,8 +15342,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "participates_in") AnnotationAssertion( "participates_in") -AnnotationAssertion(rdfs:label "participates in"@en) AnnotationAssertion(rdfs:label "participates in") +AnnotationAssertion(rdfs:label "participates in"@en) InverseObjectProperties( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15362,8 +15362,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "has_participant") AnnotationAssertion( "has_participant") -AnnotationAssertion(rdfs:label "has participant"@en) AnnotationAssertion(rdfs:label "has participant") +AnnotationAssertion(rdfs:label "has participant"@en) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15425,8 +15425,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "has_quality") AnnotationAssertion( "has_quality") -AnnotationAssertion(rdfs:label "has quality"@en) AnnotationAssertion(rdfs:label "has quality") +AnnotationAssertion(rdfs:label "has quality"@en) SubObjectPropertyOf( ) ObjectPropertyRange( ) @@ -15495,8 +15495,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "location_of") AnnotationAssertion( "location_of") -AnnotationAssertion(rdfs:label "location of"@en) AnnotationAssertion(rdfs:label "location of") +AnnotationAssertion(rdfs:label "location of"@en) InverseObjectProperties( ) TransitiveObjectProperty() @@ -15516,8 +15516,8 @@ AnnotationAssertion( "located_in") AnnotationAssertion( ) AnnotationAssertion( "located_in") -AnnotationAssertion(rdfs:label "located in"@en) AnnotationAssertion(rdfs:label "located in") +AnnotationAssertion(rdfs:label "located in"@en) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Located_in"^^xsd:anyURI) TransitiveObjectProperty() ObjectPropertyDomain(Annotation( "This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.") ) @@ -15555,8 +15555,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "has_boundary") AnnotationAssertion( "has_boundary") -AnnotationAssertion(rdfs:label "has 2D boundary"@en) AnnotationAssertion(rdfs:label "has 2D boundary") +AnnotationAssertion(rdfs:label "has 2D boundary"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15569,8 +15569,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "innervated_by") AnnotationAssertion( "innervated_by") -AnnotationAssertion(rdfs:label "innervated_by"@en) AnnotationAssertion(rdfs:label "innervated_by") +AnnotationAssertion(rdfs:label "innervated_by"@en) InverseObjectProperties( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -15602,8 +15602,8 @@ AnnotationAssertion( ) AnnotationAssertion( "bounding_layer_of") AnnotationAssertion(rdfs:comment "A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane.") -AnnotationAssertion(rdfs:label "bounding layer of"@en) AnnotationAssertion(rdfs:label "bounding layer of") +AnnotationAssertion(rdfs:label "bounding layer of"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectPropertyRange( ) @@ -15728,8 +15728,8 @@ AnnotationAssertion( ) AnnotationAssertion( "simultaneous_with") AnnotationAssertion(rdfs:comment "t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2)"@en) -AnnotationAssertion(rdfs:label "simultaneous with"@en) AnnotationAssertion(rdfs:label "simultaneous with") +AnnotationAssertion(rdfs:label "simultaneous with"@en) SubObjectPropertyOf( ) SymmetricObjectProperty() TransitiveObjectProperty() @@ -15753,8 +15753,8 @@ AnnotationAssertion( "immediately_preceded_by") AnnotationAssertion( "immediately_preceded_by") AnnotationAssertion(rdfs:comment "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)"@en) -AnnotationAssertion(rdfs:label "immediately preceded by"@en) AnnotationAssertion(rdfs:label "immediately preceded by") +AnnotationAssertion(rdfs:label "immediately preceded by"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15771,8 +15771,8 @@ AnnotationAssertion( ) AnnotationAssertion( "immediately_precedes") AnnotationAssertion(rdfs:comment "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)"@en) -AnnotationAssertion(rdfs:label "immediately precedes"@en) AnnotationAssertion(rdfs:label "immediately precedes") +AnnotationAssertion(rdfs:label "immediately precedes"@en) SubObjectPropertyOf( ) # Object Property: (has soma location) @@ -15852,8 +15852,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "synapsed_by") AnnotationAssertion( "synapsed_by") -AnnotationAssertion(rdfs:label "synapsed by"@en) AnnotationAssertion(rdfs:label "synapsed by") +AnnotationAssertion(rdfs:label "synapsed by"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) ObjectPropertyRange( ObjectUnionOf( ObjectSomeValuesFrom( ))) @@ -15951,8 +15951,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "overlaps") -AnnotationAssertion(rdfs:label "overlaps"@en) AnnotationAssertion(rdfs:label "overlaps") +AnnotationAssertion(rdfs:label "overlaps"@en) SubObjectPropertyOf( ) SymmetricObjectProperty() @@ -16006,8 +16006,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "innervates") AnnotationAssertion( "innervates") -AnnotationAssertion(rdfs:label "innervates"@en) AnnotationAssertion(rdfs:label "innervates") +AnnotationAssertion(rdfs:label "innervates"@en) ObjectPropertyDomain( ) # Object Property: (continuous with) @@ -16022,8 +16022,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "continuous_with") AnnotationAssertion( "continuous_with") -AnnotationAssertion(rdfs:label "continuous with"@en) AnnotationAssertion(rdfs:label "continuous with") +AnnotationAssertion(rdfs:label "continuous with"@en) AnnotationAssertion(rdfs:seeAlso "FMA:85972") SubObjectPropertyOf( ) SymmetricObjectProperty() @@ -16106,8 +16106,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "connected_to") AnnotationAssertion( "connected_to") -AnnotationAssertion(rdfs:label "connected to"@en) AnnotationAssertion(rdfs:label "connected to") +AnnotationAssertion(rdfs:label "connected to"@en) AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern"^^xsd:anyURI) AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern"^^xsd:anyURI) SubObjectPropertyOf( ) @@ -16124,8 +16124,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "connects") AnnotationAssertion( "connects") -AnnotationAssertion(rdfs:label "connects"@en) AnnotationAssertion(rdfs:label "connects") +AnnotationAssertion(rdfs:label "connects"@en) AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern"^^xsd:anyURI) AnnotationAssertion(rdfs:seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern"^^xsd:anyURI) SubObjectPropertyOf( ) @@ -16140,8 +16140,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "attaches_to_part_of") AnnotationAssertion( "attaches_to_part_of") -AnnotationAssertion(rdfs:label "attached to part of"@en) AnnotationAssertion(rdfs:label "attached to part of") +AnnotationAssertion(rdfs:label "attached to part of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -16156,8 +16156,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "supplies") AnnotationAssertion( "supplies") -AnnotationAssertion(rdfs:label "supplies"@en) AnnotationAssertion(rdfs:label "supplies") +AnnotationAssertion(rdfs:label "supplies"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -16170,8 +16170,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "drains") AnnotationAssertion( "drains") -AnnotationAssertion(rdfs:label "drains"@en) AnnotationAssertion(rdfs:label "drains") +AnnotationAssertion(rdfs:label "drains"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -16188,8 +16188,8 @@ AnnotationAssertion( "has_component") AnnotationAssertion( ) AnnotationAssertion( "has_component") -AnnotationAssertion(rdfs:label "has component"@en) AnnotationAssertion(rdfs:label "has component") +AnnotationAssertion(rdfs:label "has component"@en) AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) @@ -16206,8 +16206,8 @@ AnnotationAssertion( "develops_from") AnnotationAssertion( "develops_from") AnnotationAssertion(rdfs:comment "This is the transitive form of the develops from relation") -AnnotationAssertion(rdfs:label "develops from"@en) AnnotationAssertion(rdfs:label "develops from") +AnnotationAssertion(rdfs:label "develops from"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -16227,8 +16227,8 @@ AnnotationAssertion( "develops_into") AnnotationAssertion( ) AnnotationAssertion( "develops_into") -AnnotationAssertion(rdfs:label "develops into"@en) AnnotationAssertion(rdfs:label "develops into") +AnnotationAssertion(rdfs:label "develops into"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -16261,8 +16261,8 @@ AnnotationAssertion( "directly_develops_from") AnnotationAssertion( "directly_develops_from") AnnotationAssertion(rdfs:comment "TODO - add child relations from DOS") -AnnotationAssertion(rdfs:label "directly develops from"@en) AnnotationAssertion(rdfs:label "directly develops from") +AnnotationAssertion(rdfs:label "directly develops from"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) ObjectPropertyDomain( ObjectUnionOf( )) @@ -16295,8 +16295,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "regulates") -AnnotationAssertion(rdfs:label "regulates"@en) AnnotationAssertion(rdfs:label "regulates") +AnnotationAssertion(rdfs:label "regulates"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) TransitiveObjectProperty() @@ -16317,8 +16317,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "negatively_regulates") -AnnotationAssertion(rdfs:label "negatively regulates"@en) AnnotationAssertion(rdfs:label "negatively regulates") +AnnotationAssertion(rdfs:label "negatively regulates"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -16337,8 +16337,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "positively_regulates") -AnnotationAssertion(rdfs:label "positively regulates"@en) AnnotationAssertion(rdfs:label "positively regulates") +AnnotationAssertion(rdfs:label "positively regulates"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -16360,8 +16360,8 @@ AnnotationAssertion( "capable_of") AnnotationAssertion( ) AnnotationAssertion( "capable_of") -AnnotationAssertion(rdfs:label "capable of"@en) AnnotationAssertion(rdfs:label "capable of") +AnnotationAssertion(rdfs:label "capable of"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -16376,8 +16376,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "capable_of_part_of") AnnotationAssertion( "capable_of_part_of") -AnnotationAssertion(rdfs:label "capable of part of"@en) AnnotationAssertion(rdfs:label "capable of part of") +AnnotationAssertion(rdfs:label "capable of part of"@en) AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -16392,8 +16392,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "surrounded_by") AnnotationAssertion( "surrounded_by") -AnnotationAssertion(rdfs:label "surrounded by"@en) AnnotationAssertion(rdfs:label "surrounded by") +AnnotationAssertion(rdfs:label "surrounded by"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -16416,8 +16416,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "adjacent_to") -AnnotationAssertion(rdfs:label "adjacent to"@en) AnnotationAssertion(rdfs:label "adjacent to") +AnnotationAssertion(rdfs:label "adjacent to"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -16433,8 +16433,8 @@ AnnotationAssertion( "surrounds") AnnotationAssertion( ) AnnotationAssertion( "surrounds") -AnnotationAssertion(rdfs:label "surrounds"@en) AnnotationAssertion(rdfs:label "surrounds") +AnnotationAssertion(rdfs:label "surrounds"@en) SubObjectPropertyOf( ) # Object Property: (temporally related to) @@ -16462,8 +16462,8 @@ AnnotationAssertion( "starts") AnnotationAssertion( ) AnnotationAssertion( "starts") -AnnotationAssertion(rdfs:label "starts"@en) AnnotationAssertion(rdfs:label "starts") +AnnotationAssertion(rdfs:label "starts"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -16482,8 +16482,8 @@ AnnotationAssertion( "starts_with") AnnotationAssertion( ) AnnotationAssertion( "starts_with") -AnnotationAssertion(rdfs:label "starts with"@en) AnnotationAssertion(rdfs:label "starts with") +AnnotationAssertion(rdfs:label "starts with"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -16497,8 +16497,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "develops_from_part_of") AnnotationAssertion( "develops_from_part_of") -AnnotationAssertion(rdfs:label "develops from part of"@en) AnnotationAssertion(rdfs:label "develops from part of") +AnnotationAssertion(rdfs:label "develops from part of"@en) SubObjectPropertyOf( ) # Object Property: (develops in) @@ -16512,8 +16512,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "develops_in") AnnotationAssertion( "develops_in") -AnnotationAssertion(rdfs:label "develops in"@en) AnnotationAssertion(rdfs:label "develops in") +AnnotationAssertion(rdfs:label "develops in"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -16528,8 +16528,8 @@ AnnotationAssertion( "ends") AnnotationAssertion( ) AnnotationAssertion( "ends") -AnnotationAssertion(rdfs:label "ends"@en) AnnotationAssertion(rdfs:label "ends") +AnnotationAssertion(rdfs:label "ends"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -16547,8 +16547,8 @@ AnnotationAssertion( "ends_with") AnnotationAssertion( ) AnnotationAssertion( "ends_with") -AnnotationAssertion(rdfs:label "ends with"@en) AnnotationAssertion(rdfs:label "ends with") +AnnotationAssertion(rdfs:label "ends with"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -16564,8 +16564,8 @@ AnnotationAssertion( "has_start_location") AnnotationAssertion( ) AnnotationAssertion( "has_start_location") -AnnotationAssertion(rdfs:label "has start location"@en) AnnotationAssertion(rdfs:label "has start location") +AnnotationAssertion(rdfs:label "has start location"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -16581,8 +16581,8 @@ AnnotationAssertion( "has_end_location") AnnotationAssertion( ) AnnotationAssertion( "has_end_location") -AnnotationAssertion(rdfs:label "has end location"@en) AnnotationAssertion(rdfs:label "has end location") +AnnotationAssertion(rdfs:label "has end location"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -16601,8 +16601,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_input") -AnnotationAssertion(rdfs:label "has input"@en) AnnotationAssertion(rdfs:label "has input") +AnnotationAssertion(rdfs:label "has input"@en) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Has_input"^^xsd:anyURI) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -16622,8 +16622,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_output") -AnnotationAssertion(rdfs:label "has output"@en) AnnotationAssertion(rdfs:label "has output") +AnnotationAssertion(rdfs:label "has output"@en) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Has_output"^^xsd:anyURI) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -16661,8 +16661,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "has_developmental_contribution_from") AnnotationAssertion( "has_developmental_contribution_from") -AnnotationAssertion(rdfs:label "has developmental contribution from"@en) AnnotationAssertion(rdfs:label "has developmental contribution from") +AnnotationAssertion(rdfs:label "has developmental contribution from"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) ObjectPropertyDomain( ) @@ -16694,8 +16694,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "developmentally_induced_by") AnnotationAssertion( "developmentally_induced_by") -AnnotationAssertion(rdfs:label "developmentally induced by"@en) AnnotationAssertion(rdfs:label "developmentally induced by") +AnnotationAssertion(rdfs:label "developmentally induced by"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) ObjectPropertyDomain( ) @@ -16754,8 +16754,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "developmentally_replaces") AnnotationAssertion( "developmentally_replaces") -AnnotationAssertion(rdfs:label "developmentally replaces"@en) AnnotationAssertion(rdfs:label "developmentally replaces") +AnnotationAssertion(rdfs:label "developmentally replaces"@en) SubObjectPropertyOf( ) # Object Property: (developmentally succeeded by) @@ -16792,8 +16792,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "results_in_developmental_progression_of") AnnotationAssertion( "results_in_developmental_progression_of") -AnnotationAssertion(rdfs:label "results in developmental progression of"@en) AnnotationAssertion(rdfs:label "results in developmental progression of") +AnnotationAssertion(rdfs:label "results in developmental progression of"@en) AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -16813,15 +16813,15 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_development_of") -AnnotationAssertion(rdfs:label "results in development of"@en) AnnotationAssertion(rdfs:label "results in development of") +AnnotationAssertion(rdfs:label "results in development of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) # Object Property: (results in formation of) -AnnotationAssertion( "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)"@en) AnnotationAssertion( "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.") +AnnotationAssertion( "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)"@en) AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "GOC:mtg_berkeley_2013") @@ -16832,16 +16832,16 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_formation_of") -AnnotationAssertion(rdfs:label "results in formation of"@en) AnnotationAssertion(rdfs:label "results in formation of") +AnnotationAssertion(rdfs:label "results in formation of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) # Object Property: (results in morphogenesis of) -AnnotationAssertion( "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)"@en) AnnotationAssertion( "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape.") +AnnotationAssertion( "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)"@en) AnnotationAssertion( ) AnnotationAssertion( "The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.") AnnotationAssertion( ) @@ -16853,15 +16853,15 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_morphogenesis_of") -AnnotationAssertion(rdfs:label "results in morphogenesis of"@en) AnnotationAssertion(rdfs:label "results in morphogenesis of") +AnnotationAssertion(rdfs:label "results in morphogenesis of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) # Object Property: (results in maturation of) -AnnotationAssertion( "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)"@en) AnnotationAssertion( " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process") +AnnotationAssertion( "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)"@en) AnnotationAssertion( ) AnnotationAssertion( "The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity.") AnnotationAssertion( ) @@ -16873,8 +16873,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_maturation_of") -AnnotationAssertion(rdfs:label "results in maturation of"@en) AnnotationAssertion(rdfs:label "results in maturation of") +AnnotationAssertion(rdfs:label "results in maturation of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -16936,8 +16936,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_acquisition_of_features_of") -AnnotationAssertion(rdfs:label "results in acquisition of features of"@en) AnnotationAssertion(rdfs:label "results in acquisition of features of") +AnnotationAssertion(rdfs:label "results in acquisition of features of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) ObjectPropertyRange( ) @@ -16990,8 +16990,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "functionally_related_to") AnnotationAssertion( "functionally_related_to") -AnnotationAssertion(rdfs:label "functionally related to"@en) AnnotationAssertion(rdfs:label "functionally related to") +AnnotationAssertion(rdfs:label "functionally related to"@en) # Object Property: (part of structure that is capable of) @@ -17032,8 +17032,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "regulates_levels_of") AnnotationAssertion( "regulates_levels_of") -AnnotationAssertion(rdfs:label "regulates levels of"@en) AnnotationAssertion(rdfs:label "regulates levels of") +AnnotationAssertion(rdfs:label "regulates levels of"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -17058,8 +17058,8 @@ AnnotationAssertion( "regulated_by") AnnotationAssertion( ) AnnotationAssertion( "regulated_by") -AnnotationAssertion(rdfs:label "regulated by"@en) AnnotationAssertion(rdfs:label "regulated by") +AnnotationAssertion(rdfs:label "regulated by"@en) SubObjectPropertyOf( ) TransitiveObjectProperty() ObjectPropertyDomain( ) @@ -17074,8 +17074,8 @@ AnnotationAssertion( "negatively_regulated_by") AnnotationAssertion( ) AnnotationAssertion( "negatively_regulated_by") -AnnotationAssertion(rdfs:label "negatively regulated by"@en) AnnotationAssertion(rdfs:label "negatively regulated by") +AnnotationAssertion(rdfs:label "negatively regulated by"@en) SubObjectPropertyOf( ) # Object Property: (positively regulated by) @@ -17087,8 +17087,8 @@ AnnotationAssertion( "positively_regulated_by") AnnotationAssertion( ) AnnotationAssertion( "positively_regulated_by") -AnnotationAssertion(rdfs:label "positively regulated by"@en) AnnotationAssertion(rdfs:label "positively regulated by") +AnnotationAssertion(rdfs:label "positively regulated by"@en) SubObjectPropertyOf( ) # Object Property: (related via localization to) @@ -17111,8 +17111,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_target_start_location") -AnnotationAssertion(rdfs:label "has target start location"@en) AnnotationAssertion(rdfs:label "has target start location") +AnnotationAssertion(rdfs:label "has target start location"@en) SubObjectPropertyOf( ) # Object Property: (has target end location) @@ -17126,8 +17126,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_target_end_location") -AnnotationAssertion(rdfs:label "has target end location"@en) AnnotationAssertion(rdfs:label "has target end location") +AnnotationAssertion(rdfs:label "has target end location"@en) SubObjectPropertyOf( ) # Object Property: (results in transport along) @@ -17138,8 +17138,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "results_in_transport_along") AnnotationAssertion( "results_in_transport_along") -AnnotationAssertion(rdfs:label "results in transport along"@en) AnnotationAssertion(rdfs:label "results in transport along") +AnnotationAssertion(rdfs:label "results in transport along"@en) SubObjectPropertyOf( ) # Object Property: (results in transport across) @@ -17151,8 +17151,8 @@ AnnotationAssertion( "results_in_transport_across") AnnotationAssertion( ) AnnotationAssertion( "results_in_transport_across") -AnnotationAssertion(rdfs:label "results in transport across"@en) AnnotationAssertion(rdfs:label "results in transport across") +AnnotationAssertion(rdfs:label "results in transport across"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -17164,8 +17164,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "results_in_growth_of") AnnotationAssertion( "results_in_growth_of") -AnnotationAssertion(rdfs:label "results in growth of"@en) AnnotationAssertion(rdfs:label "results in growth of") +AnnotationAssertion(rdfs:label "results in growth of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -17177,8 +17177,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "results_in_transport_to_from_or_in") AnnotationAssertion( "results_in_transport_to_from_or_in") -AnnotationAssertion(rdfs:label "results in transport to from or in"@en) AnnotationAssertion(rdfs:label "results in transport to from or in") +AnnotationAssertion(rdfs:label "results in transport to from or in"@en) SubObjectPropertyOf( ) # Object Property: (member of) @@ -17202,8 +17202,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "has_member") AnnotationAssertion( "has_member") -AnnotationAssertion(rdfs:label "has member"@en) AnnotationAssertion(rdfs:label "has member") +AnnotationAssertion(rdfs:label "has member"@en) SubObjectPropertyOf( ) IrreflexiveObjectProperty() @@ -17217,8 +17217,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "input_of") -AnnotationAssertion(rdfs:label "input of"@en) AnnotationAssertion(rdfs:label "input of") +AnnotationAssertion(rdfs:label "input of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -17233,8 +17233,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "output_of") -AnnotationAssertion(rdfs:label "output of"@en) AnnotationAssertion(rdfs:label "output of") +AnnotationAssertion(rdfs:label "output of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -17261,8 +17261,8 @@ AnnotationAssertion( "attaches_to") AnnotationAssertion( ) AnnotationAssertion( "attaches_to") -AnnotationAssertion(rdfs:label "attached to"@en) AnnotationAssertion(rdfs:label "attached to") +AnnotationAssertion(rdfs:label "attached to"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) SymmetricObjectProperty() @@ -17276,8 +17276,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "has_muscle_origin") AnnotationAssertion( "has_muscle_origin") -AnnotationAssertion(rdfs:label "has muscle origin"@en) AnnotationAssertion(rdfs:label "has muscle origin") +AnnotationAssertion(rdfs:label "has muscle origin"@en) AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -17292,8 +17292,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "has_muscle_insertion") AnnotationAssertion( "has_muscle_insertion") -AnnotationAssertion(rdfs:label "has muscle insertion"@en) AnnotationAssertion(rdfs:label "has muscle insertion") +AnnotationAssertion(rdfs:label "has muscle insertion"@en) AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -17332,8 +17332,8 @@ AnnotationAssertion( "tributary_of") AnnotationAssertion( ) AnnotationAssertion( "tributary_of") -AnnotationAssertion(rdfs:label "tributary of"@en) AnnotationAssertion(rdfs:label "tributary of") +AnnotationAssertion(rdfs:label "tributary of"@en) AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso "http://en.wikipedia.org/wiki/Tributary"^^xsd:anyURI) SubObjectPropertyOf( ) @@ -17358,8 +17358,8 @@ AnnotationAssertion( "branching_part_of") AnnotationAssertion( ) AnnotationAssertion( "branching_part_of") -AnnotationAssertion(rdfs:label "branching part of"@en) AnnotationAssertion(rdfs:label "branching part of") +AnnotationAssertion(rdfs:label "branching part of"@en) AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso "FMA:85994") SubObjectPropertyOf( ) @@ -17386,8 +17386,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "has_potential_to_developmentally_contribute_to") AnnotationAssertion( "has_potential_to_developmentally_contribute_to") -AnnotationAssertion(rdfs:label "has potential to developmentally contribute to"@en) AnnotationAssertion(rdfs:label "has potential to developmentally contribute to") +AnnotationAssertion(rdfs:label "has potential to developmentally contribute to"@en) SubObjectPropertyOf( ) # Object Property: (has potential to developmentally induce) @@ -17407,8 +17407,8 @@ AnnotationAssertion( "uberon") AnnotationAssertion( "has_potential_to_develop_into") AnnotationAssertion( "has_potential_to_develop_into") -AnnotationAssertion(rdfs:label "has potential to develop into"@en) AnnotationAssertion(rdfs:label "has potential to develop into") +AnnotationAssertion(rdfs:label "has potential to develop into"@en) SubObjectPropertyOf( ) # Object Property: (has potential to directly develop into) @@ -17428,8 +17428,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "causally_downstream_of") AnnotationAssertion( "causally_downstream_of") -AnnotationAssertion(rdfs:label "causally downstream of"@en) AnnotationAssertion(rdfs:label "causally downstream of") +AnnotationAssertion(rdfs:label "causally downstream of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -17442,8 +17442,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "immediately_causally_downstream_of") AnnotationAssertion( "immediately_causally_downstream_of") -AnnotationAssertion(rdfs:label "immediately causally downstream of"@en) AnnotationAssertion(rdfs:label "immediately causally downstream of") +AnnotationAssertion(rdfs:label "immediately causally downstream of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -17504,8 +17504,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "causally_upstream_of") -AnnotationAssertion(rdfs:label "causally upstream of"@en) AnnotationAssertion(rdfs:label "causally upstream of") +AnnotationAssertion(rdfs:label "causally upstream of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -17519,8 +17519,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "immediately_causally_upstream_of") AnnotationAssertion( "immediately_causally_upstream_of") -AnnotationAssertion(rdfs:label "immediately causally upstream of"@en) AnnotationAssertion(rdfs:label "immediately causally upstream of") +AnnotationAssertion(rdfs:label "immediately causally upstream of"@en) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -17616,8 +17616,8 @@ SubObjectPropertyOf( (interacts with) AnnotationAssertion( "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.") -AnnotationAssertion( "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) AnnotationAssertion( "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.") +AnnotationAssertion( "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) AnnotationAssertion( ) AnnotationAssertion( "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.") AnnotationAssertion( "in pairwise interaction with") @@ -18232,8 +18232,8 @@ AnnotationAssertion( ) AnnotationAssertion( "produces") AnnotationAssertion(rdfs:comment "Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.") -AnnotationAssertion(rdfs:label "produces"@en) AnnotationAssertion(rdfs:label "produces") +AnnotationAssertion(rdfs:label "produces"@en) InverseObjectProperties( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -18249,8 +18249,8 @@ AnnotationAssertion( "produced_by") AnnotationAssertion( ) AnnotationAssertion( "produced_by") -AnnotationAssertion(rdfs:label "produced by"@en) AnnotationAssertion(rdfs:label "produced by") +AnnotationAssertion(rdfs:label "produced by"@en) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -18392,8 +18392,8 @@ AnnotationAssertion( "external") AnnotationAssertion( "has_small_molecule_activator") AnnotationAssertion( "has_small_molecule_activator") -AnnotationAssertion(rdfs:label "has small molecule activator"@en) AnnotationAssertion(rdfs:label "has small molecule activator") +AnnotationAssertion(rdfs:label "has small molecule activator"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -18409,8 +18409,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "acts_on_population_of") -AnnotationAssertion(rdfs:label "acts on population of"@en) AnnotationAssertion(rdfs:label "acts on population of") +AnnotationAssertion(rdfs:label "acts on population of"@en) SubObjectPropertyOf( ) # Object Property: (is small molecule regulator of) @@ -18442,8 +18442,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "results_in_fusion_of") -AnnotationAssertion(rdfs:label "results in fusion of"@en) AnnotationAssertion(rdfs:label "results in fusion of") +AnnotationAssertion(rdfs:label "results in fusion of"@en) SubObjectPropertyOf( ) # Object Property: (indirectly causally upstream of) @@ -18763,7 +18763,6 @@ SubObjectPropertyOf( < AnnotationAssertion( "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts."@en) AnnotationAssertion(rdfs:label "continuant"@en) -SubClassOf( ObjectAllValuesFrom( )) DisjointClasses( ) DisjointClasses( ObjectSomeValuesFrom( )) @@ -18780,7 +18779,6 @@ AnnotationAssertion( "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything."@en) AnnotationAssertion(rdfs:label "independent continuant"@en) SubClassOf( ) -SubClassOf( ObjectAllValuesFrom( )) DisjointClasses( ) DisjointClasses( ) @@ -18866,7 +18864,7 @@ SubClassOf( ) -# Class: () +# Class: (cell) DisjointClasses( ) DisjointClasses( ) @@ -131182,7 +131180,6 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "anatomical structure") SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) # Class: (organ) @@ -225322,10 +225319,10 @@ SubObjectPropertyOf(ObjectPropertyChain() ) ) SubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) ) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z") Annotation(rdfs:label "infer input from direct reg") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:comment "GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) @@ -225334,17 +225331,17 @@ DLSafeRule(Body(ObjectPropertyAtom( V DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) ) \ No newline at end of file