diff --git a/src/patterns/data/default/length_along_axis.tsv b/src/patterns/data/default/length_along_axis.tsv new file mode 100644 index 00000000..5257fcca --- /dev/null +++ b/src/patterns/data/default/length_along_axis.tsv @@ -0,0 +1,2 @@ +defined_class defined_class_name element element_name axis axis_name taxa taxa_name exact_synonyms xrefs def_ref +OBA:2030003 pelvis length UBERON:0007830 pelvic girdle bone/zone BSPO:0000015 proximal-distal axis ISBN:9780873659505 diff --git a/src/patterns/dosdp-patterns/length_along_axis.yaml b/src/patterns/dosdp-patterns/length_along_axis.yaml new file mode 100644 index 00000000..c1236efb --- /dev/null +++ b/src/patterns/dosdp-patterns/length_along_axis.yaml @@ -0,0 +1,103 @@ +--- +pattern_name: length_along_axis + +pattern_iri: http://purl.obolibrary.org/obo/oba/patterns/length_along_axis.yaml + +description: "A length trait that is the line along an axis of an anatomical entity." + +# examples: +# - http://purl.obolibrary.org/obo/FOVT_0001308 # canine tooth medial-lateral diameter +# - http://purl.obolibrary.org/obo/FOVT_0001080 # calcaneous proximal breadth (synonym: calcaneous proximal length medial-lateral) + +contributors: + - https://orcid.org/0000-0002-7073-9172 # David Osumi-Sutherland + - https://orcid.org/0000-0001-8314-2140 # Ray Stefancsik + - https://orcid.org/0000-0002-7356-1779 # Nicolas Matentzoglu + - https://orcid.org/0000-0003-2699-3066 # Meghan A. Balk + +classes: + anatomical_entity: UBERON:0001062 + length: PATO:0000122 + anatomical_axis: BSPO:0000010 + taxon: OBI:0100026 + trait_term: PATO:0000051 + +relations: + characteristic_of: RO:0000052 + part_of: BFO:0000050 + +annotationProperties: + related_synonym: oio:hasRelatedSynonym + xref: oio:hasDbXref + measured_in_taxon: xsd:string + not_measured_in_taxon: xsd:string + comment: rdfs:comment + +data_list_vars: + def_ref: "'xref'" # reference(s) to the source(s) of definition + +vars: + element: 'anatomical_entity' + axis: 'anatomical_axis' + size_trait: 'trait_term' + fovt: "xsd:string" # FOVT id + def_ref: "xsd:string" + taxa: "taxon" + your_comments: "xsd:string" # comments, clarifications for users + your_synonym: "xsd:string" #synonym for other terms researchers use for measurement + position: "xsd:string" #lateral, medial, etc. + syn_ref: "xsd:string" + +name: + text: "%s %s length" #e.g., humerus length + vars: + - element + - position + +annotations: + - annotationProperty: related_synonym + text: "%s" + vars: + - your_synonym + annotations: + -annotationProperty: xref + value: syn_ref + - annotationProperty: xref + text: "FOVT:%s" # give FOVT id here + vars: + - fovt + - annotationProperty: measured_in_taxon + text: "%s" + vars: + - taxa + - annotationProperty: not_measured_in_taxon + text: "%s" + vars: + - taxa + + - annotationProperty: comment + text: "%s" + vars: + - your_comments + +def: + text: "The length of a %s along the %s." + vars: + - element + - axis + annotations: + - annotationProperty: xref + value: def_ref + +equivalentTo: + text: "'length' and ('characteristic_of' some ('part_of' some %s))" + # if part of a bone [e.g., 'distalmost' ('part of' some humerus)] + # NOTE: Everything is part of itself. + vars: + - element + +logical_axioms: + - axiom_type: subClassOf + text: "%s" + vars: + - size_trait