diff --git a/src/ontology/cob-edit.owl b/src/ontology/cob-edit.owl index 1956d34..2d0e2a9 100644 --- a/src/ontology/cob-edit.owl +++ b/src/ontology/cob-edit.owl @@ -9,7 +9,8 @@ xmlns:xsd="http://www.w3.org/2001/XMLSchema#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:skos="http://www.w3.org/2004/02/skos/core#" - xmlns:terms="http://purl.org/dc/terms/"> + xmlns:terms="http://purl.org/dc/terms/" + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> COB brings together key terms from a wide range of OBO projects to improve interoperability. @@ -50,6 +51,12 @@ + + + + + + @@ -68,6 +75,14 @@ + + + + has exact synonym + + + + @@ -278,6 +293,25 @@ + + + + + cjm + has gene template + + + + + + + + cjm + gene template of + + + + @@ -527,7 +561,7 @@ - + protein @@ -596,6 +630,10 @@ + + + + A material entity that is a maximal functionally integrated unit that develops from a program encoded in a genome. "Maximal functionally integrated unit" is intended to express unity, which Barry considers synonymous with BFO 'object'. Includes virus - we will later have a class for cellular organisms. @@ -915,6 +953,12 @@ + + + + + + gene product @@ -1299,6 +1343,31 @@ + + + + + + + + + + + + + + + + + A sequence of nucleic acids that is part of a genome and is the template for one or more RNA molecules, where those molecules are either gene products or can be translated into gene products. + Add a GCI axiom: (gene and 'part of' some 'cellular organism') SubClassOf 'part of' some DNA + cjm + Genes are part of DNA in all organisms except RNA viruses. The definition needs tuning for positive-sense RNA viruses such as SARS-CoV-2. The viruses have an RNA genome that is directly translated and then cleaved into distinct functional polyproteins. + gene + + + + @@ -1340,6 +1409,111 @@ + + + + + + + + + + + + + + + + + + + + + + A molecular entity that is composed of nucleic acid bases connected in a continuous sequence in the 5' to 3' direction. + cjm + sequence of nucleic acids + nucleotide region + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A nucleotide region or a polypeptide region. + cjm + sequence of nucleotides or amino acids + region of nucleic acid polymer or protein + + + + + + In MSO this is not part of a molecular entity + + + + + + + + + + + + + + + + + + + + cjm + amino acid sequence + polypeptide region + + + + + + + + + + cjm + virus + + + + diff --git a/src/ontology/cob-idranges.owl b/src/ontology/cob-idranges.owl index 800b3d9..0fb7084 100644 --- a/src/ontology/cob-idranges.owl +++ b/src/ontology/cob-idranges.owl @@ -30,14 +30,21 @@ AnnotationProperty: idsfor: AnnotationProperty: allocatedto: -Datatype: idrange:1 +Datatype: idrange:0 Annotations: - allocatedto: "COB Core Team" + allocatedto: "Rebecca Jackson" EquivalentTo: - xsd:integer[>= 0 , <= 999] + xsd:integer[>= 0 , < 500] + +Datatype: idrange:1 + Annotations: + allocatedto: "Chris Mungall" + + EquivalentTo: + xsd:integer[>= 500 , < 1000] Datatype: idrange:2 diff --git a/src/ontology/components/cob-to-external.tsv b/src/ontology/components/cob-to-external.tsv index fc70787..295098e 100644 --- a/src/ontology/components/cob-to-external.tsv +++ b/src/ontology/components/cob-to-external.tsv @@ -34,7 +34,6 @@ COB:0000003 mass owl:equivalentClass PATO:0000125 mass . HumanCurated COB:0000004 charge owl:equivalentClass PATO:0002193 electric . HumanCurated COB:0000005 elementary charge rdfs:subClassOf owl:Thing owl:Thing Making ticket in PATO tracker HumanCurated COB:0000006 material entity owl:equivalentClass BFO:0000040 material entity . HumanCurated -COB:0000006 material entity sssom:superClassOf SO:0000110 sequence_feature . HumanCurated COB:0000006 material entity sssom:superClassOf SO:0001060 sequence_variant . HumanCurated COB:0000006 material entity sssom:superClassOf SO:0001260 sequence_collection . HumanCurated COB:0000007 subatomic particle owl:equivalentClass CHEBI:36342 subatomic particle . HumanCurated @@ -136,3 +135,12 @@ COB:0000029 realized in owl:equivalentProperty BFO:0000054 realized in . HumanCu COB:0000513 is about owl:equivalentProperty IAO:0000136 is about There is no inverse for 'is about' in IAO. HumanCurated COB:0000123 agent role owl:equivalentClass SEPIO:0000048 agent role HumanCurated COB:0000123 agent role sssom:superClassOf OBI:0000202 investigation agent role HumanCurated +COB:0000501 gene owl:equivalentClass SO:0000704 gene . +COB:0000501 gene owl:equivalentClass MSO:0000704 gene . +COB:0000503 nucleotide region owl:equivalentClass MSO:3100210 nucleotide region In MSO can be part of dsDNA molecule +COB:0000503 nucleotide region owl:subClassOf SO:0000001 region . +COB:0000504 region of nucleic acid polymer or protein owl:equivalentClass SO:0000001 region . +COB:0000504 region of nucleic acid polymer or protein owl:equivalentClass MSO:0000001 sequence molecular entity region MSO defines as two or more sequence units +COB:0000506 polypeptide region owl:equivalentClass SO:0000839 polypeptide region . +COB:0000506 polypeptide region owl:equivalentClass MSO:0000839 peptide region MSO defines as two or more sequence units +COB:0000507 virus owl:equivalentClass NCBITaxon:10239 Viruses .