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Add new bone length from to DOSDP pattern template #75

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Add new bone length from to DOSDP pattern template #75

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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
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fixing pattern
  • Loading branch information
@meghalithic
meghalithic committed Aug 26, 2022
commit 8e9ab15596fe93384b1d17bd70f1614c97b643d8
47 changes: 24 additions & 23 deletions ...s/dosdp-patterns/bone_length_from_to.yaml → ...tterns/dosdp-patterns/length_from_to.yaml
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
---
pattern_name: bone_length_from_to
pattern_name: length_from_to

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

description: 'A bone length trait that is the distance between two anatomical
description: 'A length trait that is the distance between two anatomical
reference points measured in a straight line.'

# examples:
Expand All @@ -18,10 +18,10 @@ contributors:
- https://orcid.org/0000-0003-2699-3066 # Meghan A. Balk

classes:
skeletal_element: UBERON:0004765
anatomical_entity: UBERON:0001062
length: PATO:0000122
NCBITaxon: OBI:0100026
taxon: OBI:0100026
trait_term: PATO:0000051

relations:
characteristic_of: RO:0000052
Expand All @@ -37,32 +37,28 @@ annotationProperties:
comment: rdfs:comment

vars:
bone: "'skeletal_element'"
from: "'anatomical_entity'"
to: "'anatomical_entity'"
element: 'anatomical_entity'
from: 'anatomical_entity'
to: 'anatomical_entity'
size_trait: 'trait_term'
fovt: "xsd:string" # FOVT id
taxa: "NCBITaxon"
taxa: "taxon"
your_comments: "xsd:string" # comments, clarifications for users

data_list_vars:
def_ref: "'xref'" # reference(s) to the source(s) of definition

name:
text: "%s length"
vars:
- element

annotations:
- annotationProperty: related_synonym
text: "%s length"
vars:
- bone

- annotationProperty: exact_synonym
text: "%s length"
vars:
- bone

- annotationProperty: broad_synonym
text: "%s length"
vars:
- bone
- element

- annotationProperty: xref
text: "%s" # give FOVT IRI here
Expand All @@ -87,18 +83,23 @@ annotations:
def:
text: "The length of a %s from %s to %s."
vars:
- bone
- element
- from
- to
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.
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It turns out that BFO:0000050 part of is actually not reflexive. You can check it by opening ro.owl in Protege and checking the Characteristics' pane in the 'Object Properties' tab.

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should we use "characteristic of part of"?

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"characteristic of part of" would cover the whole and all parts

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ah, so what should I use for just part of it if that part of the bone (e.g., distal side of a talus) isn't in the ontology?

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For that case the solution here is ok! But you may have to create a pattern for "side" of "anatomy" if non exists. But for the case you just want to express: some part of the thalamus (distal side or otherwise), the solution we already have is sufficient.

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No, it would have to be:

length and characteristic of some (calcaneus and (part of some distal side))

Or some such. i don't know whether part of is the correct relationship. To determine this you will have to ask in Uberon slack. Basically just "can i use part of to connect an anatomical entity to a region like 'distal side'?"

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based on how distal epiphyses are defined, it'd be: length and characteristic of some (in distal side some calcaneus)

do I ask UBERON or OBA?

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definitely OBA!

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I will add to the agenda to discuss. I am struggling to explain over chat.

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Sorry I misunderstood your question. Uberon. You need to make an issue on Uberon tracker asking for the term:

  • (in distal side some calcaneus)

Linking to this issue here, and asking for advice on how to logically define it. You can say that the issue has emerged because @cmungall does not like the complex composition in OBA (not sure I share his views here, but lets roll with it).

What should happen: someone saying: you can define in distal side some calcaneus using XYZ logical definition, then creating a dosdp pattern for it. You can then just add a row in the table for each such term you need. Ping me if you get grieve from @dosumis or @shawntanzk about the request (term proliferation argument).

vars:
- element

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.
text: "%s"
vars:
- bone
- size_trait
...