diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md index d6fe17691..07f97e9a4 100644 --- a/docs/odk-workflows/RepositoryFileStructure.md +++ b/docs/odk-workflows/RepositoryFileStructure.md @@ -18,7 +18,6 @@ These are the current imports in CL | ------ | --- | ---- | | pr | https://raw.githubusercontent.com/obophenotype/pro_obo_slim/master/pr_slim.owl | None | | go | http://purl.obolibrary.org/obo/go.owl | None | -| caro | http://purl.obolibrary.org/obo/caro.owl | None | | uberon | http://purl.obolibrary.org/obo/uberon.owl | None | | ro | http://purl.obolibrary.org/obo/ro.owl | None | | pato | http://purl.obolibrary.org/obo/pato.owl | None | diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 22f0c9750..17bad87f4 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -1,7 +1,7 @@ # ---------------------------------------- # Makefile for cl # Generated using ontology-development-kit -# ODK Version: v1.4.1 +# ODK Version: v1.4.3 # ---------------------------------------- # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use cl.Makefile instead @@ -43,7 +43,7 @@ REPORT_PROFILE_OPTS = OBO_FORMAT_OPTIONS = SPARQL_VALIDATION_CHECKS = equivalent-classes owldef-self-reference nolabels pmid-not-dbxref obsolete-replaced_by obsolete-alt-id orcid-contributor illegal-annotation-property label-synonym-polysemy SPARQL_EXPORTS = basic-report -ODK_VERSION_MAKEFILE = v1.4.1 +ODK_VERSION_MAKEFILE = v1.4.3 TODAY ?= $(shell date +%Y-%m-%d) OBODATE ?= $(shell date +'%d:%m:%Y %H:%M') @@ -113,7 +113,7 @@ all_main: $(MAIN_FILES) # ---------------------------------------- -IMPORTS = pr go caro uberon ro pato ncbitaxon omo +IMPORTS = pr go uberon ro pato ncbitaxon omo IMPORT_ROOTS = $(IMPORTDIR)/merged_import IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl) @@ -456,14 +456,6 @@ mirror-go: | $(TMPDIR) $(ROBOT) convert -i $(MIRRORDIR)/go.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi -## ONTOLOGY: caro -.PHONY: mirror-caro -.PRECIOUS: $(MIRRORDIR)/caro.owl -mirror-caro: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/caro/caro-base.owl --create-dirs -o $(MIRRORDIR)/caro.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/caro.owl -o $@.tmp.owl && mv $@.tmp.owl $(TMPDIR)/$@.owl; fi - - ## ONTOLOGY: uberon .PHONY: mirror-uberon .PRECIOUS: $(MIRRORDIR)/uberon.owl diff --git a/src/ontology/cl-odk.yaml b/src/ontology/cl-odk.yaml index 31f687529..ab418c016 100644 --- a/src/ontology/cl-odk.yaml +++ b/src/ontology/cl-odk.yaml @@ -58,8 +58,6 @@ import_group: - http://purl.obolibrary.org/obo/GO_ - http://purl.obolibrary.org/obo/GOREL_ - http://purl.obolibrary.org/obo/GOCHE_ - - id: caro - use_base: TRUE - id: uberon use_base: TRUE - id: ro diff --git a/src/ontology/imports/caro_terms.txt b/src/ontology/imports/caro_terms.txt deleted file mode 100644 index 8b1378917..000000000 --- a/src/ontology/imports/caro_terms.txt +++ /dev/null @@ -1 +0,0 @@ - diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index b14ffd580..fba7f695f 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -14,7 +14,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -26,25 +25,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8102,7 +8082,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8158,8 +8137,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8228,7 +8205,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -8239,7 +8215,6 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) @@ -14045,8 +14020,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -14089,13 +14062,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -14127,7 +14093,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -14175,7 +14140,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -14183,7 +14147,6 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -14342,7 +14305,6 @@ Annotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http AnnotationAssertion( "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones"@en) AnnotationAssertion( "Chris Mungall"@en) AnnotationAssertion(rdfs:label "expand expression to"@en) -AnnotationAssertion(rdfs:label "expand expression to") # Annotation Property: (has ontology root term) @@ -14414,7 +14376,7 @@ AnnotationAssertion( "2023-03-03"^^xsd:date) AnnotationAssertion(rdfs:label "plural form") -# 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.") @@ -14535,34 +14497,6 @@ SubAnnotationPropertyOf( < SubAnnotationPropertyOf( ) -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - # Annotation Property: () SubAnnotationPropertyOf( ) @@ -14683,10 +14617,6 @@ SubAnnotationPropertyOf( < SubAnnotationPropertyOf( ) -# Annotation Property: () - -SubAnnotationPropertyOf( ) - # Annotation Property: () SubAnnotationPropertyOf( ) @@ -15120,7 +15050,6 @@ AnnotationAssertion( "unfolds_in"@en) AnnotationAssertion( "BFO:0000066") AnnotationAssertion( "external") -AnnotationAssertion( "gene_ontology") AnnotationAssertion( "occurs_in") AnnotationAssertion( ) AnnotationAssertion( ) @@ -15588,7 +15517,7 @@ ObjectPropertyDomain( ObjectIntersect ObjectPropertyRange(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.") ) ObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf())) -# Object Property: (boundary_of) +# Object Property: (2D boundary of) AnnotationAssertion( "the surface of my skin is a 2D boundary of my body"@en) AnnotationAssertion( "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity"@en) @@ -15601,11 +15530,10 @@ AnnotationAssertion( "surface of"@en) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "2D boundary of"@en) -AnnotationAssertion(rdfs:label "boundary_of") SubObjectPropertyOf( ) InverseObjectProperties( ) -# Object Property: (has_boundary) +# Object Property: (has 2D boundary) AnnotationAssertion( "my body has 2D boundary the surface of my skin"@en) AnnotationAssertion( "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity"@en) @@ -15620,13 +15548,10 @@ AnnotationAssertion( "has_boundary") AnnotationAssertion( "has_boundary") AnnotationAssertion(rdfs:label "has 2D boundary"@en) -AnnotationAssertion(rdfs:label "has_boundary"@en) AnnotationAssertion(rdfs:label "has 2D boundary") SubObjectPropertyOf( ) ObjectPropertyDomain( ) -ObjectPropertyDomain( ) ObjectPropertyRange( ) -ObjectPropertyRange( ) # Object Property: (innervated_by) @@ -15846,15 +15771,10 @@ SubObjectPropertyOf( ) AnnotationAssertion( "Relation between a neuron and a material anatomical entity that its soma is part of."@en) -AnnotationAssertion(Annotation( ) "Relation between a neuron and an anatomical structure that its soma is part of.") AnnotationAssertion( ) AnnotationAssertion( " some ( and some ?Y)") -AnnotationAssertion( "BFO_0000051 some (GO_0043025 and BFO_0000050 some ?Y)") AnnotationAssertion( ) -AnnotationAssertion( "RO:0002100") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "has_soma_location") AnnotationAssertion(rdfs:label "has soma location"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -15865,7 +15785,6 @@ ObjectPropertyRange( ) AnnotationAssertion( "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. "@en) -AnnotationAssertion(Annotation( ) "Relation between a neuron and the neuron projection bundle it fasciculates with. FOL: x fasciculates_with y iff: exists some 'neuron ; CL_0000540'(x), some 'neuron projection bundle ; CARO_0001001'(y), some 'neuron projection ; GO_0043005'(np), np part_of x AND np overlaps y AND np aligned_with y") AnnotationAssertion( ) AnnotationAssertion( "fasciculates with") AnnotationAssertion( "(forall (?x ?y) @@ -15890,9 +15809,6 @@ AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002101") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "fasciculates_with") AnnotationAssertion(rdfs:label "fasciculates with"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15919,15 +15835,12 @@ ObjectPropertyDomain( ) AnnotationAssertion( "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. "@en) -AnnotationAssertion(Annotation( ) "Relation between an anatomical structure and a neuron that chemically synapses to it.") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( " some ( that part_of some ( that has_part some ( that some Y?)))") -AnnotationAssertion( "BFO_0000051 some (GO_0045211 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0042734 that BFO_0000050 some ?Y)))") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "RO:0002103") -AnnotationAssertion( "fly_anatomy.ontology") AnnotationAssertion( "uberon") AnnotationAssertion( "synapsed_by") AnnotationAssertion( "synapsed_by") @@ -15960,16 +15873,11 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "synapsed in"@en) -AnnotationAssertion( "BFO_0000051 some (GO_0045211 and BFO_0000050 some (GO_0045202 and BFO_0000050 some ?Y))") AnnotationAssertion( "http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002110") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "has_postsynaptic_terminals_in") -AnnotationAssertion(rdfs:comment "Relation between a neuron and the structure in which its dendrite receives synapses.") AnnotationAssertion(rdfs:label "has postsynaptic terminal in"@en) SubObjectPropertyOf( ) InverseObjectProperties( ) @@ -15981,12 +15889,8 @@ AnnotationAssertion( "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input."@en) AnnotationAssertion( "synapses in"@en) AnnotationAssertion( " some ( that some ( that some Y?)"@en) -AnnotationAssertion( "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some ?Y))") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002113") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "has_presynaptic_terminals_in") AnnotationAssertion(rdfs:label "has presynaptic terminal in"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -15996,16 +15900,11 @@ ObjectPropertyDomain( ) AnnotationAssertion( " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. "@en) -AnnotationAssertion(Annotation( ) "Relation between a neuron and an anatomical structure that it chemically synapses to.") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( " some ( that part_of some ( that some ( that some Y?)))") -AnnotationAssertion( "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some ?Y)))") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002120") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "synapsed_to") AnnotationAssertion(rdfs:comment "N1 synapsed_to some N2 Expands to: N1 SubclassOf ( @@ -16021,17 +15920,11 @@ ObjectPropertyDomain( ObjectUnionOf(< AnnotationAssertion( ) AnnotationAssertion( "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input.") -AnnotationAssertion(Annotation( ) "A relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input.") AnnotationAssertion( ) AnnotationAssertion( "has synapse in") AnnotationAssertion( " some ( that some Y?)") -AnnotationAssertion( "RO_0002131 some (GO_0045202 and BFO_0000050 some ?Y)") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion( "RO:0002130") -AnnotationAssertion( "fly_anatomy.ontology") -AnnotationAssertion( "has_synaptic_terminals_in") -AnnotationAssertion(rdfs:comment "expands to - X overlaps some ('synapse ; GO_0045202' that part_of some ?Y)") AnnotationAssertion(rdfs:label "has synaptic terminal in"@en) SubObjectPropertyOf( ) ObjectPropertyDomain( ) @@ -16097,14 +15990,11 @@ AnnotationAssertion( "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R."@en) -AnnotationAssertion(Annotation( ) "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.") AnnotationAssertion( ) AnnotationAssertion( " some ( that ( some ( that some Y?)))") -AnnotationAssertion( "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some ?Y)))") AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( "RO:0002134") -AnnotationAssertion( "fly_anatomy.ontology") AnnotationAssertion( "uberon") AnnotationAssertion( "innervates") AnnotationAssertion( "innervates") @@ -16387,7 +16277,6 @@ AnnotationAssertion( "false"^^xsd:boolean) AnnotationAssertion( "RO:0002211") AnnotationAssertion( "external") -AnnotationAssertion( "gene_ontology") AnnotationAssertion( "regulates") AnnotationAssertion( ) AnnotationAssertion( ) @@ -16410,7 +16299,6 @@ AnnotationAssertion( ) AnnotationAssertion( "RO:0002212") AnnotationAssertion( "external") -AnnotationAssertion( "gene_ontology") AnnotationAssertion( "negatively_regulates") AnnotationAssertion( ) AnnotationAssertion( ) @@ -16431,7 +16319,6 @@ AnnotationAssertion( ) AnnotationAssertion( "RO:0002213") AnnotationAssertion( "external") -AnnotationAssertion( "gene_ontology") AnnotationAssertion( "positively_regulates") AnnotationAssertion( ) AnnotationAssertion( ) @@ -18935,406 +18822,14 @@ AnnotationAssertion(rdfs:label "imm SubClassOf( ) DisjointClasses( ObjectSomeValuesFrom( )) -# Class: (anatomical entity) - -AnnotationAssertion(Annotation( "CAROC:Brownsville2014") "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex. Or, a substance produced by a cellular organism with granularity above the level of a protein complex.") -AnnotationAssertion( "CARO:0000000") -AnnotationAssertion(rdfs:comment "Following BFO, material anatomical entities may have immaterial parts (the lumen of your stomach is part of your stomach). The granularity limit follows the limits set by the Gene Ontology on the granularity limit for GO:cellular_component. Note that substances produced by an organism (sweat, feaces, urine) do not need to be part of an organism to qualify as an anatomical structure.") -AnnotationAssertion(rdfs:label "anatomical entity") -SubClassOf( ) -DisjointUnion( ) - -# Class: (connected anatomical structure) - -AnnotationAssertion( "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.") -AnnotationAssertion( "CARO:0000003") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that the definition does not say 'generated exclusively by the co-ordinated expression of the organism's own genome', so this is still valid for cases where normal morphogenesis requires the actions of a facultative symbiont, or some looser dependency such as the a requirement for the presence of gut flora for normal gut development.") -AnnotationAssertion(rdfs:label "connected anatomical structure") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) - -# Class: (organism substance) - -AnnotationAssertion( "Examples include feces, urine, blood, blood plasma, lymph, hemolymph, cerbro-spinal fluid. This class does not encompass anatomical entities with inherent 3D structure such as dentine and arthropod cuticle.") -AnnotationAssertion( "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body and that does not have inherent 3D shape generated by coordinated expression of the organism's own genome.") -AnnotationAssertion( "portion of organism substance") -AnnotationAssertion( "CARO:0000004") -AnnotationAssertion(rdfs:comment "Note - CARO explicitly declares organisms substances to be part of (some) organism.") -AnnotationAssertion(rdfs:label "organism substance") -SubClassOf( ) - -# Class: (material anatomical entity) - -AnnotationAssertion( "An anatomical entity that has mass.") -AnnotationAssertion( "CARO:0000006") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "material anatomical entity") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -DisjointClasses( ) -DisjointClasses( ObjectSomeValuesFrom( )) - -# Class: (immaterial anatomical entity) - -AnnotationAssertion( "Anatomical entity that has no mass.") -AnnotationAssertion( "CARO:0000007") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "immaterial anatomical entity") -EquivalentClasses( ObjectIntersectionOf( ObjectComplementOf(ObjectSomeValuesFrom( )))) -SubClassOf( ) -SubClassOf( ) -DisjointClasses( ObjectSomeValuesFrom( )) - -# Class: (anatomical boundary) - -AnnotationAssertion( "A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures.") -AnnotationAssertion(rdfs:comment "Except in the case of abstracted fiat boundaries such as the midline plane of an organism, all 2D anatomical entities have a 3 dimensional projection. For example, the surface of the shell of a muscle has a distinct shape that projects into the third dimension. Note that boundaries are 2D structures. They have no thickness - and so can not be sites of gene expression or gene product localisation. For this, use boundary region terms.") -AnnotationAssertion(rdfs:label "anatomical boundary") -SubClassOf( ) -SubClassOf( ) - -# Class: (multicellular organism) - -AnnotationAssertion( "Anatomical structure that is an individual member of a clade and, at some point in its life-cycle, consists of more than one cell.") -AnnotationAssertion( "CARO:0000012") -AnnotationAssertion(rdfs:comment "MH: Can't define this class based on 2 or more cells because most multi cellular organisms (if not all) have only a single cell at some point in life history. - -MH: sexual subtypes should probably be logically defined based on sexual processes or sex qualities.") -AnnotationAssertion(rdfs:label "multicellular organism") -SubClassOf( ) - -# Class: (cell) - -AnnotationAssertion( "An anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.") -AnnotationAssertion( "CL:0000000") -AnnotationAssertion( "GO:0005623") -AnnotationAssertion( "CARO:0000013") -AnnotationAssertion(rdfs:comment "deprecate and replace with CL or GO term?") -AnnotationAssertion(rdfs:label "cell") -SubClassOf( ) -DisjointClasses( ) -DisjointClasses( ) -DisjointClasses( ) -DisjointClasses( ) -DisjointClasses( ) - -# Class: (cell part) - -AnnotationAssertion( "Anatomical structure that is part of a cell and that has a granularity level equal to that of a protein complex or higher.") -AnnotationAssertion( "cell component") -AnnotationAssertion( "CARO:0000014") -AnnotationAssertion(rdfs:comment "This is declared equivalent with GO:0044464. The definition should be co-ordinated with GO. We could obsolete the CARO class and just use the GO class.") -AnnotationAssertion(rdfs:label "cell part"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -DisjointClasses( ) -DisjointClasses( ) -DisjointClasses( ) -DisjointClasses( ) - -# Class: (organism subdivision) - -AnnotationAssertion( "Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument."@en) -AnnotationAssertion( "Old definition: Anatomical structure which is a primary subdivision of whole organism. The mereological sum of these is the whole organism.") -AnnotationAssertion( "CARO:0000032") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "organism subdivision") -SubClassOf( ) - -# Class: (acellular anatomical structure) - -AnnotationAssertion( "An anatomical structure that has no cells or cell parts as a part.") -AnnotationAssertion( "CARO:0000040") -AnnotationAssertion(rdfs:comment "Example. Insect cuticle, eggshell, hair.") -AnnotationAssertion(rdfs:label "acellular anatomical structure") -EquivalentClasses( ObjectIntersectionOf( ObjectExactCardinality(0 ) ObjectExactCardinality(0 ))) -DisjointClasses( ) -DisjointClasses( ) -DisjointClasses( ) - -# Class: (extraembryonic structure) - -AnnotationAssertion( "A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis.") -AnnotationAssertion( "CARO:0000042") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "MH: define as not part of embryo, or will not develop into embryo? MH: changed def to exclude cells so this class could be included in gross anatomical part. DOS: Changed to something that I think works for both vertebrates and invertebrates and that keeps the restriction to multicellular structures. Old def: \"Anatomical structure that is contiguous with the embryo and is comprised of portions of tissue that will not contribute to the embryo.\". One remaining question - perhaps zygote is too restrictive given that some organisms have parthenogenesis e.g. aphids? -") -AnnotationAssertion(rdfs:label "extraembryonic structure") -SubClassOf( ) -DisjointClasses( ) -DisjointClasses( ) - -# Class: (multi-cell-part structure) - -AnnotationAssertion( "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.") -AnnotationAssertion( "multi-cell-component structure") -AnnotationAssertion( "CARO:0001000") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Examples: a bundle of neuron projections in the brain; a region neuropil in an arthropod central nervous system; a region of cortex (preikaryal rind) in an arthropod brain.") -AnnotationAssertion(rdfs:label "multi-cell-part structure") -SubClassOf( ObjectIntersectionOf( ObjectAllValuesFrom( ObjectComplementOf()) ObjectMinCardinality(2 ))) -DisjointClasses( ) - -# Class: (gross anatomical part) - -AnnotationAssertion( "Anatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells. ") -AnnotationAssertion( ) -AnnotationAssertion( "10.7.2011") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "gross anatomical part"@en) -EquivalentClasses( ObjectUnionOf( )) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (organism) - -AnnotationAssertion( "Material anatomical entity that is a member of an individual species or is a viral or viroid particle.") -AnnotationAssertion( "Melissa Haendel") -AnnotationAssertion( "9/18/11") -AnnotationAssertion( "organism or virus or viroid") -AnnotationAssertion(rdfs:label "organism") -SubClassOf( ) - -# Class: (multicellular anatomical structure) - -AnnotationAssertion( "An anatomical structure that has more than one cell as a part.") -AnnotationAssertion( "djs93") -AnnotationAssertion( "Sun Feb 27 10:53:00 GMT 2011") -AnnotationAssertion( "CARO:0010000") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "multicellular anatomical structure") -EquivalentClasses(Annotation(rdfs:comment "There is a cost to burying this in PATO. We lose that we could relax the cardinality assertion to subClassOf has_part some cell. I'm sure having this axiom inherited would come in handy. DOS") ObjectIntersectionOf( ObjectSomeValuesFrom( ))) - -# Class: (cellular organism) - -AnnotationAssertion( "An individual member of a clade of cellular organisms.") -AnnotationAssertion( ) -AnnotationAssertion( "7.16.2011") -AnnotationAssertion( "CARO:0010004") -AnnotationAssertion(rdfs:comment "A general term for organism that is agnostic about single cell vs multi-cellular. Note that this is a subclass of 'anatomical structure', meaning that an organism must be a connected structure. For example, if I take one plant and make a rooted cutting from a it, I now have two (clonally related) organisms. ") -AnnotationAssertion(rdfs:label "cellular organism") -SubClassOf( ) -SubClassOf( ) - -# Class: (disconnected anatomical group) - -AnnotationAssertion( "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other.") -AnnotationAssertion( "CARO:0000054") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "disconnected anatomical group") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectMinCardinality(2 ))) - -# Class: (cellular anatomical structure) - -AnnotationAssertion( "An anatomical structure consisting of one or more cells.") -AnnotationAssertion( ) -AnnotationAssertion( "2018-09-28T14:20:19Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "cellular anatomical structure"@en) -EquivalentClasses(Annotation( "With a reflexive part_of relation this might safely be defined as 'anatomical structure' that has_part some cell") ObjectUnionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - -# Class: (biological entity) - -AnnotationAssertion( "Entity that is, is part of, or derived from an organism, virus, or viroid or a collection of them.") -AnnotationAssertion(rdfs:comment "Important for alignment with Darwin Core class \"Organism\".") -AnnotationAssertion(rdfs:label "biological entity") -SubClassOf( ) - -# Class: () - -AnnotationAssertion(Annotation( "ANON:ANON") "Actylcholine is an ester of acetic acid and choline, which acts as a neurotransmitter.") -AnnotationAssertion(Annotation( "IUPAC:") Annotation( ) "2-acetyloxy-N,N,N-trimethylethanaminium") -AnnotationAssertion(Annotation( "PDBeChem:") "ACETYLCHOLINE") -AnnotationAssertion(Annotation( "KEGG COMPOUND:") "Acetylcholine") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChemIDplus:") "ACh") -AnnotationAssertion(Annotation( "ChEBI:") "Azetylcholin") -AnnotationAssertion(Annotation( "KEGG COMPOUND:") Annotation( ) "C7H16NO2") -AnnotationAssertion(Annotation( "ChEBI:") Annotation( ) "CC(=O)OCC[N+](C)(C)C") -AnnotationAssertion(Annotation( "ChEBI:") Annotation( ) "InChI=1S/C7H16NO2/c1-7(9)10-6-5-8(2,3)4/h5-6H2,1-4H3/q+1") -AnnotationAssertion(Annotation( "ChEBI:") Annotation( ) "InChIKey=OIPILFWXSMYKGL-UHFFFAOYSA-N") -AnnotationAssertion(Annotation( "KEGG COMPOUND:") "O-Acetylcholine") -AnnotationAssertion(Annotation( "ChemIDplus:") "choline acetate") -AnnotationAssertion( "CHEBI:15355") - -# Class: () - -AnnotationAssertion(Annotation( "ANON:ANON") "Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid.") -AnnotationAssertion(Annotation( "KEGG COMPOUND:") "Peptide") -AnnotationAssertion(Annotation( "IUPAC:") Annotation( ) "peptides") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "KEGG COMPOUND:") Annotation( ) "C2H4NO2R(C2H2NOR)n") -AnnotationAssertion(Annotation( "ChEBI:") "Peptid") -AnnotationAssertion(Annotation( "ChEBI:") "peptido") -AnnotationAssertion(Annotation( "ChEBI:") "peptidos") -AnnotationAssertion( "CHEBI:16670") - -# Class: () - -AnnotationAssertion(Annotation( "ANON:ANON") "'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids.") -AnnotationAssertion(Annotation( "KEGG COMPOUND:") "Lipid") -AnnotationAssertion(Annotation( "UniProt:") "lipid") -AnnotationAssertion(Annotation( "IUPAC:") Annotation( ) "lipids") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion( "CHEBI:18059") - # Class: () -AnnotationAssertion(Annotation( "ANON:ANON") "A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion( "CHEBI:24431") SubClassOf( ) -# Class: () - -AnnotationAssertion(Annotation( "ANON:ANON") "A five-membered organic heterocycle containing two nitrogen atoms at positions 1 and 3, or any of its derivatives; compounds containing an imidazole skeleton.") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion( "CHEBI:24780") - -# Class: () - -AnnotationAssertion(Annotation( "ANON:ANON") "Any compound containing an indole skeleton.") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion( "CHEBI:24828") - -# Class: () - -AnnotationAssertion(Annotation( "ChEBI:") "oxygen molecular entity") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI:") "oxygen molecular entities") -AnnotationAssertion( "CHEBI:25806") - -# Class: () - -AnnotationAssertion(Annotation( "ANON:ANON") "A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups.") -AnnotationAssertion(Annotation( "KEGG COMPOUND:") "Amine") -AnnotationAssertion(Annotation( "IUPAC:") Annotation( ) "amines") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI:") "Amin") -AnnotationAssertion(Annotation( "UniProt:") "an amine") -AnnotationAssertion( "CHEBI:32952") - -# Class: () - -AnnotationAssertion(Annotation( "ANON:ANON") "An amide is a derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.") -AnnotationAssertion(Annotation( "KEGG COMPOUND:") "Amide") -AnnotationAssertion(Annotation( "IUPAC:") Annotation( ) "amides") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion( "CHEBI:32988") - -# Class: () - -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion( "CHEBI:33566") - -# Class: () - -AnnotationAssertion(Annotation( "ANON:ANON") "4-(2-Aminoethyl)pyrocatechol [4-(2-aminoethyl)benzene-1,2-diol] and derivatives formed by substitution.") -AnnotationAssertion(Annotation( "KEGG COMPOUND:") "Catecholamine") -AnnotationAssertion(Annotation( "IUPAC:") Annotation( ) "catecholamines") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "KEGG COMPOUND:") Annotation( ) "C8H9NO2R2") -AnnotationAssertion(Annotation( "ChEBI:") "catecholamines") -AnnotationAssertion( "CHEBI:33567") - -# Class: () - -AnnotationAssertion(Annotation( "ANON:ANON") "A cyclically conjugated molecular entity with a stability (due to delocalization) significantly greater than that of a hypothetical localized structure (e.g. Kekule structure) is said to possess aromatic character.") -AnnotationAssertion(Annotation( "IUPAC:") Annotation( ) "aromatic compounds") -AnnotationAssertion(Annotation( "IUPAC:") Annotation( ) "aromatic molecular entity") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI:") "aromatics") -AnnotationAssertion(Annotation( "ChEBI:") "aromatische Verbindungen") -AnnotationAssertion( "CHEBI:33655") - -# Class: () - -AnnotationAssertion(Annotation( "ANON:ANON") "A carboxylic acid containing one or more amino groups.") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI:") "Aminocarbonsaeure") -AnnotationAssertion(Annotation( "ChEBI:") "Aminokarbonsaeure") -AnnotationAssertion(Annotation( "ChEBI:") "Aminosaeure") -AnnotationAssertion(Annotation( "ChEBI:") "amino acids") -AnnotationAssertion( "CHEBI:33709") - -# Class: () - -AnnotationAssertion(Annotation( "ANON:ANON") "An organic compound having at least one hydroxy group attached to a carbon atom.") -AnnotationAssertion(Annotation( "IUPAC:") Annotation( ) "hydroxy compounds") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI:") "organic hydroxy compounds") -AnnotationAssertion( "CHEBI:33822") - -# Class: () - -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI:") "organic cyclic compounds") -AnnotationAssertion( "CHEBI:33832") - -# Class: () - -AnnotationAssertion(Annotation( "ANON:ANON") "Compounds having one or more hydroxy groups attached to a benzene or other arene ring.") -AnnotationAssertion(Annotation( "IUPAC:") Annotation( ) "phenols") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "KEGG COMPOUND:") "Aryl alcohol") -AnnotationAssertion(Annotation( "IUPAC:") "arenols") -AnnotationAssertion(Annotation( "UniProt:") "aryl alcohol") -AnnotationAssertion( "CHEBI:33853") - -# Class: () - -AnnotationAssertion(Annotation( "ANON:ANON") "Any heteroorganic entity containing at least one carbon-nitrogen bond.") -AnnotationAssertion(Annotation( "IUPAC:") Annotation( ) "organonitrogen compounds") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI:") "organonitrogens") -AnnotationAssertion( "CHEBI:35352") - # Class: () EquivalentClasses( ) -# Class: () - -AnnotationAssertion(Annotation( "ANON:ANON") "A compound formally derived from ammonia by replacing one, two or three hydrogen atoms by organyl groups.") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI:") "organic amino compounds") -AnnotationAssertion( "CHEBI:50047") - -# Class: () - -AnnotationAssertion(Annotation( "ANON:ANON") "Any molecular entity that contains carbon.") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI:") "organic compounds") -AnnotationAssertion(Annotation( "ChEBI:") "organic entity") -AnnotationAssertion(Annotation( "ChEBI:") "organic molecular entities") -AnnotationAssertion( "CHEBI:50860") - -# Class: () - -AnnotationAssertion(Annotation( "ANON:ANON") "A compound formally derived from ammonia by replacing one hydrogen atom by an organyl group.") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "ChEBI:") "primary amino compounds") -AnnotationAssertion( "CHEBI:50994") - -# Class: () - -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "KEGG COMPOUND:") "Nitrogenous compounds") -AnnotationAssertion(Annotation( "ChEBI:") "nitrogen compounds") -AnnotationAssertion(Annotation( "ChEBI:") "nitrogen molecular entities") -AnnotationAssertion( "CHEBI:51143") - -# Class: () - -AnnotationAssertion(Annotation( "ANON:ANON") "A cyclic compound having as ring members atoms of at least two different elements.") -AnnotationAssertion(Annotation( "KEGG COMPOUND:") "Heterocyclic compound") -AnnotationAssertion( "chebi_ontology") -AnnotationAssertion(Annotation( "IUPAC:") "compuesto heterociclico") -AnnotationAssertion(Annotation( "IUPAC:") "compuestos heterociclicos") -AnnotationAssertion(Annotation( "ChEBI:") "heterocycle") -AnnotationAssertion(Annotation( "ChEBI:") "heterocyclic compounds") -AnnotationAssertion( "CHEBI:5686") - # Class: () DisjointClasses( ) @@ -114859,9 +114354,7 @@ SubClassOf( (quality) AnnotationAssertion(Annotation( "PATOC:GVG") "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities") -AnnotationAssertion(Annotation( "PATOC:GVG") "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities.") AnnotationAssertion( "PATO:0000072") -AnnotationAssertion( "trait") AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0000001") AnnotationAssertion(rdfs:label "quality") @@ -114940,18 +114433,6 @@ AnnotationAssertion( "size") SubClassOf( ) -# Class: (mass) - -AnnotationAssertion(Annotation( "PATOC:GVG") "A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.") -AnnotationAssertion( "quality") -AnnotationAssertion( "PATO:0000125") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "For any biological use of PATO, the concept that should be used is 'mass' and not 'weight'. For example, increased weight of an organism.") -AnnotationAssertion(rdfs:label "mass") -SubClassOf( ) - # Class: (closure) AnnotationAssertion(Annotation( "PATOC:CJM") Annotation( "PATOC:GVG") "A morphological quality pertaining to the degree to which an object contains an opening, aperture, orifice or vent.") @@ -115300,7 +114781,6 @@ AnnotationAssertion( "snap:Quality") AnnotationAssertion( "monadic quality of a continuant") AnnotationAssertion( "multiply inhering quality of a physical entity") -AnnotationAssertion( "multiply inhering quality of a physical entity ") AnnotationAssertion( "quality of a continuant") AnnotationAssertion( "quality of a single physical entity") AnnotationAssertion( "quality of an object") @@ -115578,36 +115058,6 @@ AnnotationAssertion( "quality of a liquid") SubClassOf( ) -# Class: (decreased mass) - -AnnotationAssertion(Annotation( "PATO:GVG") "A mass which is lower than normal or average.") -AnnotationAssertion( ) -AnnotationAssertion( "PATO:0000579") -AnnotationAssertion( "low mass") -AnnotationAssertion( "small mass") -AnnotationAssertion( "quality") -AnnotationAssertion( "PATO:0001562") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "decreased mass") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) - -# Class: (increased mass) - -AnnotationAssertion(Annotation( "PATO:GVG") "A mass which is higher than normal or average.") -AnnotationAssertion( ) -AnnotationAssertion( "PATO:0000578") -AnnotationAssertion( "high mass") -AnnotationAssertion( "large mass") -AnnotationAssertion( "quality") -AnnotationAssertion( "PATO:0001563") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "increased mass") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) - # Class: (contractility) AnnotationAssertion(Annotation( "WordNet:WordNet") "A physical quality that is the ability to contract or shrink.") @@ -115920,7 +115370,6 @@ SubClassOf( (saccular) AnnotationAssertion(Annotation( "PATOC:MAH") "A structural quality inhering in a bearer by virtue of the bearer's having a three dimensional cavity with a narrow or no opening, and often containing an anatomical substance.") -AnnotationAssertion(Annotation( "EXACT") "sacular") AnnotationAssertion( "sacular") AnnotationAssertion( "quality") AnnotationAssertion( "PATO:0001987") @@ -116409,17 +115858,6 @@ AnnotationAssertion( "keratinous") SubClassOf( ) -# Class: (maximally connected) - -AnnotationAssertion(Annotation( "GOC:dos") "A structural quality inhering in the bearer by virtue of the bearer consisting of a single, maximally connected structure.") -AnnotationAssertion( ) -AnnotationAssertion( "2014-12-12T08:41:11Z") -AnnotationAssertion( "quality") -AnnotationAssertion( "PATO:0010000") -AnnotationAssertion(rdfs:comment "What counts as maximally connected may be relative to some specification of granularity.") -AnnotationAssertion(rdfs:label "maximally connected") -SubClassOf( ) - # Class: (disconnected) AnnotationAssertion(Annotation( "GOC:dos") "A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other.") @@ -116538,19 +115976,6 @@ EquivalentClasses( ObjectIntersecti SubClassOf( ) SubClassOf( ) -# Class: (normal mass) - -AnnotationAssertion( "A mass which is relatively normal or average.") -AnnotationAssertion( ) -AnnotationAssertion( "2017-12-22T14:16:43Z") -AnnotationAssertion( "quality") -AnnotationAssertion( "PATO:0045030") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "normal mass") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) -SubClassOf( ) - # Class: (normal size) AnnotationAssertion( "A size quality which is relatively normal or average") @@ -225445,7 +224870,6 @@ EquivalentClasses(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectIntersectionOf( ObjectExactCardinality(2 ))) EquivalentClasses(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectIntersectionOf( ObjectExactCardinality(1 ))) EquivalentClasses(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectIntersectionOf( ObjectMinCardinality(2 ))) -EquivalentClasses(Annotation(rdfs:comment "Should belong in BFO, but lives in caro for now.") ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) SubClassOf(Annotation( "hagfish have median nostril") ObjectIntersectionOf( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) @@ -225608,12 +225032,10 @@ SubClassOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) SubClassOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) SubClassOf(ObjectSomeValuesFrom( ) ObjectUnionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))) -DisjointClasses( ) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) -DisjointClasses(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( )) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) )