diff --git a/src/patterns/data/default/length_from_to.tsv b/src/patterns/data/default/length_from_to.tsv new file mode 100644 index 00000000..a2729ca0 --- /dev/null +++ b/src/patterns/data/default/length_from_to.tsv @@ -0,0 +1,2 @@ +defined_class defined_class_name element element_name from from_name to to_name fovt fovt_name taxa taxa_name position your_comments your_synonym def_ref +OBA:2069999 UBERON:0000981 femur UBERON:0006767 head of femur UBERON:0009985 lateral condyle of femur FOVT:0001070 femur length from caput to lateral condyle diff --git a/src/patterns/dosdp-patterns/length_from_to.yaml b/src/patterns/dosdp-patterns/length_from_to.yaml new file mode 100644 index 00000000..fa9361c5 --- /dev/null +++ b/src/patterns/dosdp-patterns/length_from_to.yaml @@ -0,0 +1,113 @@ +--- +pattern_name: length_from_to + +pattern_iri: http://purl.obolibrary.org/obo/oba/patterns/length_from_to.yaml + +description: 'A length trait that is the distance between two anatomical + reference points measured in a straight line.' + +# examples: +# - http://purl.obolibrary.org/obo/FOVT_0001070 +# # femur length from caput to lateral condyle +# - http://purl.obolibrary.org/obo/FOVT_0001077 +# # length of talus along the midline +# - http://purl.obolibrary.org/obo/FOVT_0000007 +# # femur length from caput to medial condyle + +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 + distance: PATO:0000040 + taxon: OBI:0100026 + +relations: + characteristic_of: RO:0000052 + part_of: BFO:0000050 + characteristic_of_part_of: RO:0002314 + towards: RO:0002503 + +annotationProperties: + related_synonym: oio:hasRelatedSynonym + xref: oio:hasDbXref + measured_in_taxon: xsd:string + not_measured_in_taxon: xsd:string + comment: rdfs:comment + +vars: + element: 'anatomical_entity' + from: 'anatomical_entity' + to: 'anatomical_entity' + fovt: "xsd:string" # FOVT id + taxa: "taxon" + position: "xsd:string" # e.g., lateral, medial + your_comments: "xsd:string" # comments, clarifications for users + your_synonym: "xsd:string" # related synonym + # for what other references may call the measurement + +data_list_vars: + def_ref: "'xref'" # reference(s) to the source(s) of definition + +name: + text: "%s length from %s to %s" + vars: + - element + - from + - to + +annotations: + + - annotationProperty: related_synonym + text: "%s" + vars: + - your_synonym + + - annotationProperty: xref + text: "%s" # give FOVT IRI 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 from %s to %s." # The length of a humerus from + # ventral tubercule of humerus to caput of humerus + vars: + - element # humerus + - from # ventral tubercule of humerus + - to # caput of humerus + annotations: + - annotationProperty: xref + value: def_ref + +subClassOf: + multi_clause: + sep: ' and ' + clauses: + - text: "'length' and ('characteristic_of_part_of' some %s)" + vars: + - element + - text: "'distance' and + ('characteristic_of' some %s) and + ('towards' some %s)" + vars: + - from + - to