Skip to content
Open
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
25 commits
Select commit Hold shift + click to select a range
3acbac9
Add new bone length from to DOSDP pattern template
rays22 Mar 17, 2022
66185aa
Fix multi_clause syntax in pattern template
rays22 Mar 21, 2022
8d97a2a
Add multiple subClassOf axioms
rays22 Mar 22, 2022
7e6c4cf
Add missing fovt var
rays22 Mar 24, 2022
113703e
Fix text definition
rays22 Mar 25, 2022
5877961
Add an xref on the definition
rays22 Apr 1, 2022
b8211e9
adding my edits
meghalithic Apr 1, 2022
82eb444
Update bone_length_from_to.yaml
meghalithic Jul 28, 2022
956219c
Update bone_length_from_to.yaml
meghalithic Jul 28, 2022
d7b3b93
Merge branch 'master' into issue73
rays22 Aug 19, 2022
ad9d851
Implement data_lis_vars
rays22 Aug 19, 2022
06e82cf
Update bone_length_from_to.yaml
meghalithic Aug 19, 2022
1560a76
Add comment field to template
rays22 Aug 19, 2022
fbfbc71
Merge branch 'issue73' of github.com:obophenotype/bio-attribute-ontol…
rays22 Aug 19, 2022
2e912b9
Fix xref annotation
rays22 Aug 19, 2022
2d61e2c
Delete redundant vars and axioms
rays22 Aug 19, 2022
8e9ab15
fixing pattern
meghalithic Aug 26, 2022
ea7f682
Update dosdp patterns file
Aug 26, 2022
599e0a1
getting rid of unneeded syn
meghalithic Aug 26, 2022
57fadc6
Merge branch 'master' into issue73
matentzn Nov 26, 2022
55481cb
Update length_from_to.yaml
meghalithic Feb 9, 2023
4869992
Update length_from_to.yaml
meghalithic Feb 9, 2023
fc03cf1
Merge branch 'master' into issue73
rays22 Feb 16, 2023
fef5f75
Merge branch 'master' into issue73
rays22 Feb 22, 2023
e3dc2fe
Update pattern templates
rays22 Mar 2, 2023
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions src/patterns/data/default/length_from_to.tsv
Original file line number Diff line number Diff line change
@@ -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
113 changes: 113 additions & 0 deletions src/patterns/dosdp-patterns/length_from_to.yaml
Original file line number Diff line number Diff line change
@@ -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