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Add draft pattern for bone length along an axis #81
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a3821c6
Add yaml template file
rays22 f2284dc
Update the text definition
rays22 a5dc25c
adding annotations and examples
meghalithic 85a5382
adding restrictions
meghalithic 52dca42
improving syntax
meghalithic 3b321a2
Update boneLengthAlongAxis.yaml
meghalithic f872c13
Fix syntax errors
rays22 d83711c
Update boneLengthAlongAxis.yaml
meghalithic a23cb7c
Update boneLengthAlongAxis.yaml
matentzn 5efc5eb
Merge branch 'master' into issue80
rays22 e9f0f43
updating
meghalithic 237b99b
Merge branch 'issue80' of https://github.com/obophenotype/bio-attribu…
meghalithic 6adb96a
Implement data_lis_vars
rays22 f5494a2
Delete redundant vars and axioms
rays22 66303d5
renaming snake_case
meghalithic db5cc05
Update dosdp patterns file
9bde9ee
fixing pattern
meghalithic fd834e1
Merge branch 'issue80' of https://github.com/obophenotype/bio-attribu…
meghalithic 16864e6
Update length_along_axis.yaml
meghalithic 8b554fa
Update length_along_axis.yaml
meghalithic cf122c0
getting rid of unneeded syn
meghalithic 6804987
Merge branch 'master' into issue80
meghalithic 3fe6836
Update dosdp patterns file
16e3d11
Create length_along_axis.tsv
meghalithic 4033522
Merge branch 'issue80' of https://github.com/obophenotype/bio-attribu…
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Merge branch 'master' into issue80
matentzn ee14cb0
Update length_along_axis.yaml
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| 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 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,103 @@ | ||
| --- | ||
| pattern_name: length_along_axis | ||
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| pattern_iri: http://purl.obolibrary.org/obo/oba/patterns/length_along_axis.yaml | ||
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| description: "A length trait that is the line along an axis of an anatomical entity." | ||
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| # 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) | ||
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| 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 | ||
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| classes: | ||
| anatomical_entity: UBERON:0001062 | ||
| length: PATO:0000122 | ||
| anatomical_axis: BSPO:0000010 | ||
| taxon: OBI:0100026 | ||
| trait_term: PATO:0000051 | ||
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| relations: | ||
| characteristic_of: RO:0000052 | ||
| part_of: BFO:0000050 | ||
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| annotationProperties: | ||
| related_synonym: oio:hasRelatedSynonym | ||
| xref: oio:hasDbXref | ||
| measured_in_taxon: xsd:string | ||
| not_measured_in_taxon: xsd:string | ||
| comment: rdfs:comment | ||
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| data_list_vars: | ||
| def_ref: "'xref'" # reference(s) to the source(s) of definition | ||
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| 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" | ||
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| name: | ||
| text: "%s %s length" #e.g., humerus length | ||
| vars: | ||
| - element | ||
| - position | ||
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| 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 | ||
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| - annotationProperty: comment | ||
| text: "%s" | ||
| vars: | ||
| - your_comments | ||
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| def: | ||
| text: "The length of a %s along the %s." | ||
| vars: | ||
| - element | ||
| - axis | ||
| annotations: | ||
| - annotationProperty: xref | ||
| value: def_ref | ||
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| 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 | ||
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| logical_axioms: | ||
| - axiom_type: subClassOf | ||
| text: "%s" | ||
| vars: | ||
| - size_trait | ||
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