bio-attribute-ontology/src/patterns/dosdp-patterns/boneLengthAlongAxis.yaml at f5494a25312cd1f298d2ffdf00486fb8b40f3cab · obophenotype/bio-attribute-ontology · GitHub

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---
pattern_name: boneLengthAlongAxis

pattern_iri: http://purl.obolibrary.org/obo/oba/patterns/boneLengthAlongAxis.yaml

description: "A bone length trait that is the line along an axis of a bone."

#  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:
  skeletal_element: UBERON:0004765
  length: PATO:0000122
  anatomical_axis: BSPO:0000010
  NCBITaxon: OBI:0100026

relations:
  characteristic_of: RO:0000052
  part_of: BFO:0000050

annotationProperties:
  exact_synonym: oio:hasExactSynonym
  related_synonym: oio:hasRelatedSynonym
  broad_synonym: oio:hasBroadSynonym
  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:
  bone: 'skeletal_element'
  axis: 'anatomical_axis'
  fovt: "xsd:string"  # FOVT id
  def_ref: "xsd:string"
  taxa: "NCBITaxon"
  your_comments: "xsd:string"  # comments, clarifications for users

name:
  text: "%s %s length"
  vars:
    - bone
    - axis

annotations:
  - annotationProperty: related_synonym
    text: "%s length %s"
    vars:
      - bone
      - axis
  - annotationProperty: broad_synonym
    text: "%s length %s"
    vars:
      - bone
      - axis
  - annotationProperty: exact_synonym
    text: "%s length %s"
    vars:
      - bone
      - axis
  - 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:
    - bone
    - axis
  annotations:
    - annotationProperty: xref
      value: def_ref

logical_axioms:
  - axiom_type: subClassOf
    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:
      - bone