From a19337543e7669026aaf6376784c16e5d7d95cce Mon Sep 17 00:00:00 2001 From: "alida.avola@icloud.com" Date: Tue, 21 May 2024 14:43:21 +0100 Subject: [PATCH 1/6] update HBA bridge mappings to nerves to point to nerve roots Fixes some #3264 --- src/ontology/imports/merged_import.owl | 45 +++++++++++++------------- src/ontology/uberon-edit.obo | 20 +++++++----- 2 files changed, 34 insertions(+), 31 deletions(-) diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 3483590de..10f34029a 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -12396,8 +12396,8 @@ Declaration(AnnotationProperty()) # Annotation Property: (example of usage) AnnotationAssertion( "A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold."@en) -AnnotationAssertion(rdfs:label "example of usage"@en) AnnotationAssertion(rdfs:label "example of usage") +AnnotationAssertion(rdfs:label "example of usage"@en) # Annotation Property: (definition) @@ -12422,14 +12422,14 @@ We don't have definitions of 'meaning' or 'expression' or 'property'. For 'refer Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with."@en) -AnnotationAssertion(rdfs:label "definition"@en) AnnotationAssertion(rdfs:label "definition") +AnnotationAssertion(rdfs:label "definition"@en) # Annotation Property: (editor note) AnnotationAssertion( "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology."@en) -AnnotationAssertion(rdfs:label "editor note"@en) AnnotationAssertion(rdfs:label "editor note") +AnnotationAssertion(rdfs:label "editor note"@en) # Annotation Property: (has obsolescence reason) @@ -12439,8 +12439,8 @@ AnnotationAssertion(rdfs:label "has # Annotation Property: (curator note) AnnotationAssertion( "An administrative note of use for a curator but of no use for a user"@en) -AnnotationAssertion(rdfs:label "curator note"@en) AnnotationAssertion(rdfs:label "curator note") +AnnotationAssertion(rdfs:label "curator note"@en) # Annotation Property: (term tracker item) @@ -12456,8 +12456,8 @@ Label: spatially disjoint from Annotations: expand_assertion_to \"DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\" "@en) AnnotationAssertion( "A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom."@en) -AnnotationAssertion(rdfs:label "expand assertion to"@en) AnnotationAssertion(rdfs:label "expand assertion to") +AnnotationAssertion(rdfs:label "expand assertion to"@en) # Annotation Property: (has ontology root term) @@ -12475,8 +12475,8 @@ AnnotationAssertion(rdfs:label "sch AnnotationAssertion( "Use on obsolete terms, relating the term to another term that can be used as a substitute"@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: (abbreviation) @@ -12786,7 +12786,7 @@ SubAnnotationPropertyOf( ) -# Annotation Property: () +# Annotation Property: (a mis-spelling that is in common use and thus recorded) SubAnnotationPropertyOf( ) @@ -12920,13 +12920,13 @@ 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() @@ -12950,8 +12950,8 @@ 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() @@ -13707,8 +13707,8 @@ AnnotationAssertion( ) AnnotationAssertion( "overlaps") AnnotationAssertion(rdfs:comment "\"(forall (x y) (iff (overlaps x y) (exists (z) (and (part of z x) (part of z y)))))\" CLIF []") -AnnotationAssertion(rdfs:label "overlaps"@en) AnnotationAssertion(rdfs:label "overlaps") +AnnotationAssertion(rdfs:label "overlaps"@en) SubObjectPropertyOf( ) SymmetricObjectProperty() @@ -13832,8 +13832,8 @@ AnnotationAssertion( "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.") AnnotationAssertion( "RO:0002176") 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( ) @@ -14015,8 +14015,8 @@ SubObjectPropertyOf( "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x") AnnotationAssertion( "RO:0002219") AnnotationAssertion( "surrounded_by") -AnnotationAssertion(rdfs:label "surrounded by"@en) AnnotationAssertion(rdfs:label "surrounded by") +AnnotationAssertion(rdfs:label "surrounded by"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -14035,8 +14035,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "adjacent_to") -AnnotationAssertion(rdfs:label "adjacent to"@en) AnnotationAssertion(rdfs:label "adjacent to") +AnnotationAssertion(rdfs:label "adjacent to"@en) SubObjectPropertyOf( ) SymmetricObjectProperty() ObjectPropertyDomain( ) @@ -14336,8 +14336,8 @@ SubObjectPropertyOf( (results in formation of anatomical entity) -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( "RO:0002297") AnnotationAssertion( ) AnnotationAssertion( ) @@ -14350,8 +14350,8 @@ InverseObjectProperties( (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( "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( "RO:0002298") AnnotationAssertion( ) @@ -14364,8 +14364,8 @@ SubObjectPropertyOf( (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( "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( "RO:0002299") AnnotationAssertion( ) @@ -32937,7 +32937,7 @@ SubClassOf(Annotation( # Class: (polyploid cell) -AnnotationAssertion(Annotation( "https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Biology_(Kimball)/07%3A_Cell_Division/7.04%3A_Polyploidy"^^xsd:anyURI) Annotation( "FB:ma") Annotation( "PMID:32646579") "A cell that contains more than two haploid sets of chromosomes.") +AnnotationAssertion(Annotation( "FB:ma") Annotation( "PMID:32646579") Annotation( "https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Biology_(Kimball)/07%3A_Cell_Division/7.04%3A_Polyploidy"^^xsd:anyURI) "A cell that contains more than two haploid sets of chromosomes.") AnnotationAssertion(rdfs:label "polyploid cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -70297,7 +70297,6 @@ AnnotationAssertion(Annotation( "GO:0021559") AnnotationAssertion(rdfs:label "trigeminal nerve development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) # Class: (abducens nerve development) @@ -142342,8 +142341,8 @@ SubClassOf( "\"Behavior related to the promotion of personal hygiene.\" [wikipedia:Social_grooming]") AnnotationAssertion( "George Gkoutos") AnnotationAssertion( "NBO:0000058") -AnnotationAssertion( "autohygiene"@en) AnnotationAssertion( "auto-grooming") +AnnotationAssertion( "autohygiene"@en) AnnotationAssertion( "preening") AnnotationAssertion( "self-grooming") AnnotationAssertion( "behavior_ontology") @@ -155731,7 +155730,7 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) ) SubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) ) -DLSafeRule(Annotation(rdfs:comment "This can't be added as a property chain because it causes a circularity violation for 'part of'.") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "This can't be added as a property chain because it causes a circularity violation for 'part of'.") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "This can't be added as a property chain because it causes a circularity violation for 'part of'.") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "This can't be added as a property chain because it causes a circularity violation for 'part of'.") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "This can't be added as a property chain because it causes a circularity violation for 'part of'.") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "This can't be added as a property chain because it causes a circularity violation for 'part of'.") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) ) \ No newline at end of file diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 08df42a41..98ad615cd 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -218,6 +218,10 @@ treat-xrefs-as-reverse-genus-differentia: XAO part_of NCBITaxon:8353 treat-xrefs-as-reverse-genus-differentia: ZFA part_of NCBITaxon:7954 treat-xrefs-as-reverse-genus-differentia: ZFS part_of NCBITaxon:7954 +[Term] +id: GO:0021545 ! cranial nerve development +equivalent_to: GO:0021559 ! trigeminal nerve development + [Term] id: UBERON:0000000 name: processual entity @@ -26920,7 +26924,6 @@ xref: EHDAA:3738 xref: EMAPA:17576 xref: FMA:50866 xref: GAID:726 -xref: HBA:9322 xref: MA:0001100 xref: MBA:901 xref: MESH:D014276 @@ -27153,7 +27156,6 @@ xref: EHDAA:3733 xref: EMAPA:17268 xref: FMA:50870 xref: GAID:827 -xref: HBA:9334 xref: MA:0001093 xref: MBA:808 xref: MESH:D005930 @@ -27208,7 +27210,6 @@ xref: EHDAA:2859 xref: EMAPA:17269 xref: FMA:50871 xref: GAID:828 -xref: HBA:9343 xref: MA:0001094 xref: MBA:813 xref: MESH:D007002 @@ -30347,7 +30348,6 @@ xref: EMAPA:37797 {source="MA:th"} xref: FMA:5731 xref: GAID:721 xref: galen:VagusNerve -xref: HBA:9337 xref: MA:0001106 xref: MBA:917 xref: MESH:D014630 @@ -31161,7 +31161,6 @@ xref: EHDAA2:0000323 xref: EMAPA:17264 xref: FMA:5865 xref: GAID:802 -xref: HBA:9299 xref: MA:0000215 xref: MBA:967 xref: MESH:D003391 @@ -38549,7 +38548,6 @@ xref: EMAPA:17265 xref: FMA:6720 xref: FMA:80284 xref: GAID:825 -xref: HBA:9340 xref: MA:0001088 xref: MBA:717 xref: MESH:D000055 @@ -72999,8 +72997,8 @@ id: UBERON:0003532 name: hindlimb skin def: "A zone of skin that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic] synonym: "hind limb skin" EXACT [OBOL:automatic] -synonym: "lower limb skin" EXACT [https://orcid.org/0000-0002-0819-0473] synonym: "lower limb skin" EXACT [FMA:23102] +synonym: "lower limb skin" EXACT [https://orcid.org/0000-0002-0819-0473] synonym: "skin of hind limb" EXACT [OBOL:automatic] synonym: "skin of hindlimb" EXACT [OBOL:automatic] synonym: "skin of lower extremity" EXACT [OBOL:automatic] @@ -90008,6 +90006,7 @@ xref: BIRNLEX:1346 xref: DHBA:12865 xref: DMBA:17739 xref: FMA:52610 +xref: HBA:9322 xref: SCTID:280185007 xref: TAO:0000192 xref: ZFA:0000192 @@ -90065,6 +90064,7 @@ xref: BIRNLEX:1588 xref: DHBA:12886 xref: DMBA:17750 xref: FMA:72632 +xref: HBA:9343 xref: neuronames:798 xref: UMLS:C0175555 is_a: UBERON:0006843 {source="FMA"} ! root of cranial nerve @@ -116679,6 +116679,7 @@ subset: vertebrate_core synonym: "cranial nerve root" EXACT [FMA:52609] synonym: "cranial neural root" EXACT [FMA:52609] xref: FMA:52609 +xref: HBA:9299 xref: SCTID:280161004 xref: TAO:0002190 xref: ZFA:0001663 @@ -137228,7 +137229,7 @@ def: "A tapetum lucidum that is part of the retina, within the cytoplasm of the xref: Wikipedia:Tapetum_lucidum#Classification intersection_of: UBERON:0004868 ! tapetum lucidum of camera-type eye intersection_of: part_of UBERON:0000966 ! retina -relationship: present_in_taxon NCBITaxon:30559 {editor="cjm", source="PMID:14738502"} ! Megachiroptera +relationship: present_in_taxon NCBITaxon:30559 {editor="cjm", source="PMID:14738502"} ! Yinpterochiroptera relationship: present_in_taxon NCBITaxon:32443 {editor="cjm", source="PMID:14738502"} ! Teleostei relationship: present_in_taxon NCBITaxon:8493 {editor="cjm", source="PMID:14738502"} ! Crocodylidae relationship: present_in_taxon NCBITaxon:9263 {editor="cjm", source="PMID:14738502"} ! Metatheria @@ -144540,6 +144541,7 @@ xref: BIRNLEX:1456 xref: DHBA:12888 xref: DMBA:17748 xref: FMA:6213 +xref: HBA:9337 xref: ZFA:0007011 intersection_of: UBERON:0002211 ! nerve root intersection_of: extends_fibers_into UBERON:0001759 ! vagus nerve @@ -161020,6 +161022,7 @@ xref: BAMS:c11n xref: BIRNLEX:1580 xref: DHBA:12883 xref: DMBA:17749 +xref: HBA:9340 xref: neuronames:703 {source="BIRNLEX:1580"} xref: SCTID:280187004 xref: Wikipedia:Cranial_root_of_accessory_nerves @@ -174095,6 +174098,7 @@ synonym: "glossopharyngeal nerve root" EXACT [BIRNLEX:1533] xref: BIRNLEX:1533 xref: DHBA:12887 xref: DMBA:17747 +xref: HBA:9334 intersection_of: UBERON:0002211 ! nerve root intersection_of: extends_fibers_into UBERON:0001649 ! glossopharyngeal nerve relationship: part_of UBERON:0001896 ! medulla oblongata From 4f186e3338a907aa5b20a058b70a55adc0a1e2bb Mon Sep 17 00:00:00 2001 From: "alida.avola@icloud.com" Date: Tue, 21 May 2024 15:24:21 +0100 Subject: [PATCH 2/6] Update uberon-edit.obo --- src/ontology/uberon-edit.obo | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 98ad615cd..02ba00002 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -220,7 +220,10 @@ treat-xrefs-as-reverse-genus-differentia: ZFS part_of NCBITaxon:7954 [Term] id: GO:0021545 ! cranial nerve development -equivalent_to: GO:0021559 ! trigeminal nerve development + +[Term] +id: GO:0021559 ! trigeminal nerve development +is_a: GO:0021545 ! cranial nerve development [Term] id: UBERON:0000000 From 85ce1c266051036b50f9edf77ee50846d94a5897 Mon Sep 17 00:00:00 2001 From: "alida.avola@icloud.com" Date: Thu, 23 May 2024 12:27:26 +0100 Subject: [PATCH 3/6] Update uberon-edit.obo --- src/ontology/uberon-edit.obo | 3 --- 1 file changed, 3 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 02ba00002..6c12de79e 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -218,9 +218,6 @@ treat-xrefs-as-reverse-genus-differentia: XAO part_of NCBITaxon:8353 treat-xrefs-as-reverse-genus-differentia: ZFA part_of NCBITaxon:7954 treat-xrefs-as-reverse-genus-differentia: ZFS part_of NCBITaxon:7954 -[Term] -id: GO:0021545 ! cranial nerve development - [Term] id: GO:0021559 ! trigeminal nerve development is_a: GO:0021545 ! cranial nerve development From adcb58e08a680b1a08113f068b10bd40101382b6 Mon Sep 17 00:00:00 2001 From: "alida.avola@icloud.com" Date: Thu, 23 May 2024 13:32:38 +0100 Subject: [PATCH 4/6] Update merged_import.owl --- src/ontology/imports/merged_import.owl | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 10f34029a..6611aeb2c 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -12614,7 +12614,7 @@ SubAnnotationPropertyOf( ) -# Annotation Property: () +# Annotation Property: (blood_and_immune_upper_slim) SubAnnotationPropertyOf( ) @@ -12622,15 +12622,15 @@ SubAnnotationPropertyOf( ) -# Annotation Property: () +# Annotation Property: (eye_upper_slim) SubAnnotationPropertyOf( ) -# Annotation Property: () +# Annotation Property: (general_cell_types_upper_slim) SubAnnotationPropertyOf( ) -# Annotation Property: () +# Annotation Property: (kidney_upper_slim) SubAnnotationPropertyOf( ) @@ -70292,9 +70292,7 @@ SubClassOf( "GOC:cls") Annotation( "GOC:dgh") Annotation( "GOC:dph") Annotation( "GOC:jid") Annotation( "GO_REF:0000021") Annotation( "ISBN:0838580343") "The process whose specific outcome is the progression of the trigeminal nerve over time, from its formation to the mature structure. The trigeminal nerve is composed of three large branches. They are the ophthalmic (V1, sensory), maxillary (V2, sensory) and mandibular (V3, motor and sensory) branches. The sensory ophthalmic branch travels through the superior orbital fissure and passes through the orbit to reach the skin of the forehead and top of the head. The maxillary nerve contains sensory branches that reach the pterygopalatine fossa via the inferior orbital fissure (face, cheek and upper teeth) and pterygopalatine canal (soft and hard palate, nasal cavity and pharynx). The motor part of the mandibular branch is distributed to the muscles of mastication, the mylohyoid muscle and the anterior belly of the digastric. The mandibular nerve also innervates the tensor veli palatini and tensor tympani muscles. The sensory part of the mandibular nerve is composed of branches that carry general sensory information from the mucous membranes of the mouth and cheek, anterior two-thirds of the tongue, lower teeth, skin of the lower jaw, side of the head and scalp and meninges of the anterior and middle cranial fossae.") AnnotationAssertion(Annotation( "GOC:cls") "cranial nerve 5 development") AnnotationAssertion(Annotation( "GOC:cls") "cranial nerve V development") -AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:cls") "CN V development") -AnnotationAssertion( "GO:0021559") AnnotationAssertion(rdfs:label "trigeminal nerve development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) @@ -155730,7 +155728,7 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) ) SubObjectPropertyOf(ObjectPropertyChain(ObjectInverseOf() ) ) -DLSafeRule(Annotation(rdfs:comment "This can't be added as a property chain because it causes a circularity violation for 'part of'.") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "This can't be added as a property chain because it causes a circularity violation for 'part of'.") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "This can't be added as a property chain because it causes a circularity violation for 'part of'.") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "This can't be added as a property chain because it causes a circularity violation for 'part of'.") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "This can't be added as a property chain because it causes a circularity violation for 'part of'.") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "This can't be added as a property chain because it causes a circularity violation for 'part of'.") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) ) \ No newline at end of file From 55d1c29c3b4dd6946523727e7c5fe02860c1d81c Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Thu, 23 May 2024 13:47:06 +0100 Subject: [PATCH 5/6] revert changes on `merged_import.owl` --- src/ontology/imports/merged_import.owl | 49 ++++++++++++++------------ 1 file changed, 26 insertions(+), 23 deletions(-) diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 6611aeb2c..3483590de 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -12396,8 +12396,8 @@ Declaration(AnnotationProperty()) # Annotation Property: (example of usage) AnnotationAssertion( "A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold."@en) -AnnotationAssertion(rdfs:label "example of usage") AnnotationAssertion(rdfs:label "example of usage"@en) +AnnotationAssertion(rdfs:label "example of usage") # Annotation Property: (definition) @@ -12422,14 +12422,14 @@ We don't have definitions of 'meaning' or 'expression' or 'property'. For 'refer Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with."@en) -AnnotationAssertion(rdfs:label "definition") AnnotationAssertion(rdfs:label "definition"@en) +AnnotationAssertion(rdfs:label "definition") # Annotation Property: (editor note) AnnotationAssertion( "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology."@en) -AnnotationAssertion(rdfs:label "editor note") AnnotationAssertion(rdfs:label "editor note"@en) +AnnotationAssertion(rdfs:label "editor note") # Annotation Property: (has obsolescence reason) @@ -12439,8 +12439,8 @@ AnnotationAssertion(rdfs:label "has # Annotation Property: (curator note) AnnotationAssertion( "An administrative note of use for a curator but of no use for a user"@en) -AnnotationAssertion(rdfs:label "curator note") AnnotationAssertion(rdfs:label "curator note"@en) +AnnotationAssertion(rdfs:label "curator note") # Annotation Property: (term tracker item) @@ -12456,8 +12456,8 @@ Label: spatially disjoint from Annotations: expand_assertion_to \"DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\" "@en) AnnotationAssertion( "A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom."@en) -AnnotationAssertion(rdfs:label "expand assertion to") AnnotationAssertion(rdfs:label "expand assertion to"@en) +AnnotationAssertion(rdfs:label "expand assertion to") # Annotation Property: (has ontology root term) @@ -12475,8 +12475,8 @@ AnnotationAssertion(rdfs:label "sch AnnotationAssertion( "Use on obsolete terms, relating the term to another term that can be used as a substitute"@en) AnnotationAssertion(rdfs:comment "Add as annotation triples in the granting ontology"@en) -AnnotationAssertion(rdfs:label "term replaced by") AnnotationAssertion(rdfs:label "term replaced by"@en) +AnnotationAssertion(rdfs:label "term replaced by") # Annotation Property: (abbreviation) @@ -12614,7 +12614,7 @@ SubAnnotationPropertyOf( ) -# Annotation Property: (blood_and_immune_upper_slim) +# Annotation Property: () SubAnnotationPropertyOf( ) @@ -12622,15 +12622,15 @@ SubAnnotationPropertyOf( ) -# Annotation Property: (eye_upper_slim) +# Annotation Property: () SubAnnotationPropertyOf( ) -# Annotation Property: (general_cell_types_upper_slim) +# Annotation Property: () SubAnnotationPropertyOf( ) -# Annotation Property: (kidney_upper_slim) +# Annotation Property: () SubAnnotationPropertyOf( ) @@ -12786,7 +12786,7 @@ SubAnnotationPropertyOf( ) -# Annotation Property: (a mis-spelling that is in common use and thus recorded) +# Annotation Property: () SubAnnotationPropertyOf( ) @@ -12920,13 +12920,13 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "part_of") -AnnotationAssertion(rdfs:label "part of") AnnotationAssertion(rdfs:label "part of"@en) +AnnotationAssertion(rdfs:label "part of") AnnotationAssertion(rdfs:label "part_of") AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion(rdfs:seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of") AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Part_of"^^xsd:anyURI) +AnnotationAssertion(rdfs:seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of") SubObjectPropertyOf( ) InverseObjectProperties( ) TransitiveObjectProperty() @@ -12950,8 +12950,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "has_part") -AnnotationAssertion(rdfs:label "has part") AnnotationAssertion(rdfs:label "has part"@en) +AnnotationAssertion(rdfs:label "has part") AnnotationAssertion(rdfs:label "has_part") SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -13707,8 +13707,8 @@ AnnotationAssertion( ) AnnotationAssertion( "overlaps") AnnotationAssertion(rdfs:comment "\"(forall (x y) (iff (overlaps x y) (exists (z) (and (part of z x) (part of z y)))))\" CLIF []") -AnnotationAssertion(rdfs:label "overlaps") AnnotationAssertion(rdfs:label "overlaps"@en) +AnnotationAssertion(rdfs:label "overlaps") SubObjectPropertyOf( ) SymmetricObjectProperty() @@ -13832,8 +13832,8 @@ AnnotationAssertion( "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.") AnnotationAssertion( "RO:0002176") AnnotationAssertion( "connects") -AnnotationAssertion(rdfs:label "connects") AnnotationAssertion(rdfs:label "connects"@en) +AnnotationAssertion(rdfs:label "connects") 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( ) @@ -14015,8 +14015,8 @@ SubObjectPropertyOf( "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x") AnnotationAssertion( "RO:0002219") AnnotationAssertion( "surrounded_by") -AnnotationAssertion(rdfs:label "surrounded by") AnnotationAssertion(rdfs:label "surrounded by"@en) +AnnotationAssertion(rdfs:label "surrounded by") SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -14035,8 +14035,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "adjacent_to") -AnnotationAssertion(rdfs:label "adjacent to") AnnotationAssertion(rdfs:label "adjacent to"@en) +AnnotationAssertion(rdfs:label "adjacent to") SubObjectPropertyOf( ) SymmetricObjectProperty() ObjectPropertyDomain( ) @@ -14336,8 +14336,8 @@ SubObjectPropertyOf( (results in formation of anatomical entity) -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( "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( "RO:0002297") AnnotationAssertion( ) AnnotationAssertion( ) @@ -14350,8 +14350,8 @@ InverseObjectProperties( (results in morphogenesis of) -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( "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( "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( "RO:0002298") AnnotationAssertion( ) @@ -14364,8 +14364,8 @@ SubObjectPropertyOf( (results in maturation of) -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( " 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( "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( "RO:0002299") AnnotationAssertion( ) @@ -32937,7 +32937,7 @@ SubClassOf(Annotation( # Class: (polyploid cell) -AnnotationAssertion(Annotation( "FB:ma") Annotation( "PMID:32646579") Annotation( "https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Biology_(Kimball)/07%3A_Cell_Division/7.04%3A_Polyploidy"^^xsd:anyURI) "A cell that contains more than two haploid sets of chromosomes.") +AnnotationAssertion(Annotation( "https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Biology_(Kimball)/07%3A_Cell_Division/7.04%3A_Polyploidy"^^xsd:anyURI) Annotation( "FB:ma") Annotation( "PMID:32646579") "A cell that contains more than two haploid sets of chromosomes.") AnnotationAssertion(rdfs:label "polyploid cell") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) @@ -70292,9 +70292,12 @@ SubClassOf( "GOC:cls") Annotation( "GOC:dgh") Annotation( "GOC:dph") Annotation( "GOC:jid") Annotation( "GO_REF:0000021") Annotation( "ISBN:0838580343") "The process whose specific outcome is the progression of the trigeminal nerve over time, from its formation to the mature structure. The trigeminal nerve is composed of three large branches. They are the ophthalmic (V1, sensory), maxillary (V2, sensory) and mandibular (V3, motor and sensory) branches. The sensory ophthalmic branch travels through the superior orbital fissure and passes through the orbit to reach the skin of the forehead and top of the head. The maxillary nerve contains sensory branches that reach the pterygopalatine fossa via the inferior orbital fissure (face, cheek and upper teeth) and pterygopalatine canal (soft and hard palate, nasal cavity and pharynx). The motor part of the mandibular branch is distributed to the muscles of mastication, the mylohyoid muscle and the anterior belly of the digastric. The mandibular nerve also innervates the tensor veli palatini and tensor tympani muscles. The sensory part of the mandibular nerve is composed of branches that carry general sensory information from the mucous membranes of the mouth and cheek, anterior two-thirds of the tongue, lower teeth, skin of the lower jaw, side of the head and scalp and meninges of the anterior and middle cranial fossae.") AnnotationAssertion(Annotation( "GOC:cls") "cranial nerve 5 development") AnnotationAssertion(Annotation( "GOC:cls") "cranial nerve V development") +AnnotationAssertion( "biological_process") AnnotationAssertion(Annotation( "GOC:cls") "CN V development") +AnnotationAssertion( "GO:0021559") AnnotationAssertion(rdfs:label "trigeminal nerve development") EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) # Class: (abducens nerve development) @@ -142339,8 +142342,8 @@ SubClassOf( "\"Behavior related to the promotion of personal hygiene.\" [wikipedia:Social_grooming]") AnnotationAssertion( "George Gkoutos") AnnotationAssertion( "NBO:0000058") -AnnotationAssertion( "auto-grooming") AnnotationAssertion( "autohygiene"@en) +AnnotationAssertion( "auto-grooming") AnnotationAssertion( "preening") AnnotationAssertion( "self-grooming") AnnotationAssertion( "behavior_ontology") From 2d6ed23c44d970bfb13f7b6575187acdeef610dc Mon Sep 17 00:00:00 2001 From: Anita Caron Date: Thu, 23 May 2024 13:55:26 +0100 Subject: [PATCH 6/6] remove GO classification from uberon-edit.obo --- src/ontology/uberon-edit.obo | 4 ---- 1 file changed, 4 deletions(-) diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 6c12de79e..5a8eccffa 100644 --- a/src/ontology/uberon-edit.obo +++ b/src/ontology/uberon-edit.obo @@ -218,10 +218,6 @@ treat-xrefs-as-reverse-genus-differentia: XAO part_of NCBITaxon:8353 treat-xrefs-as-reverse-genus-differentia: ZFA part_of NCBITaxon:7954 treat-xrefs-as-reverse-genus-differentia: ZFS part_of NCBITaxon:7954 -[Term] -id: GO:0021559 ! trigeminal nerve development -is_a: GO:0021545 ! cranial nerve development - [Term] id: UBERON:0000000 name: processual entity