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a3821c6
Add yaml template file
rays22 Mar 24, 2022
f2284dc
Update the text definition
rays22 Mar 25, 2022
a5dc25c
adding annotations and examples
meghalithic Apr 1, 2022
85a5382
adding restrictions
meghalithic Apr 1, 2022
52dca42
improving syntax
meghalithic Apr 1, 2022
3b321a2
Update boneLengthAlongAxis.yaml
meghalithic Apr 13, 2022
f872c13
Fix syntax errors
rays22 May 18, 2022
d83711c
Update boneLengthAlongAxis.yaml
meghalithic Jul 28, 2022
a23cb7c
Update boneLengthAlongAxis.yaml
matentzn Aug 19, 2022
5efc5eb
Merge branch 'master' into issue80
rays22 Aug 19, 2022
e9f0f43
updating
meghalithic Aug 19, 2022
237b99b
Merge branch 'issue80' of https://github.com/obophenotype/bio-attribu…
meghalithic Aug 19, 2022
6adb96a
Implement data_lis_vars
rays22 Aug 19, 2022
f5494a2
Delete redundant vars and axioms
rays22 Aug 19, 2022
66303d5
renaming snake_case
meghalithic Aug 26, 2022
db5cc05
Update dosdp patterns file
Aug 26, 2022
9bde9ee
fixing pattern
meghalithic Aug 26, 2022
fd834e1
Merge branch 'issue80' of https://github.com/obophenotype/bio-attribu…
meghalithic Aug 26, 2022
16864e6
Update length_along_axis.yaml
meghalithic Aug 26, 2022
8b554fa
Update length_along_axis.yaml
meghalithic Aug 26, 2022
cf122c0
getting rid of unneeded syn
meghalithic Aug 26, 2022
6804987
Merge branch 'master' into issue80
meghalithic Oct 13, 2022
3fe6836
Update dosdp patterns file
Oct 13, 2022
16e3d11
Create length_along_axis.tsv
meghalithic Oct 13, 2022
4033522
Merge branch 'issue80' of https://github.com/obophenotype/bio-attribu…
meghalithic Oct 13, 2022
e0ad993
Merge branch 'master' into issue80
matentzn Nov 26, 2022
ee14cb0
Update length_along_axis.yaml
meghalithic Feb 9, 2023
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2 changes: 2 additions & 0 deletions src/patterns/data/default/length_along_axis.tsv
Original file line number Diff line number Diff line change
@@ -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
103 changes: 103 additions & 0 deletions src/patterns/dosdp-patterns/length_along_axis.yaml
Original file line number Diff line number Diff line change
@@ -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