Add new bone length from to DOSDP pattern template #75
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If applied, this commit will fix #73.
If applied, this commit will fix #73.
Add multiple subClassOf axioms under the logical_axioms property instead of using one multi_clause axiom. If applied, this commit will fix #73.
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is there a way to change the label if needed? If so, what column would that be? |
Yes, you can override the automatic label. It think it is the |
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great, can we add that to the template? |
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@rays22 why is this failing? |
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@rays22 what is left to do on this? |
clarifying subclasses modifying definition
adding part of
to help annotate definitions with external references. Addresses #73.
rays22
requested review from
matentzn and
meghalithic
and removed request for
meghalithic
| 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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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).
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this is why we have the property chain for copo
…On Wed, Sep 7, 2022 at 4:02 AM Nico Matentzoglu ***@***.***> wrote:
***@***.**** commented on this pull request.
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In src/patterns/dosdp-patterns/length_from_to.yaml
<#75 (comment)>
:
> + - your_comments
+
+def:
+ text: "The length of a %s from %s to %s."
+ vars:
+ - 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.
The only relevant consequence is that the length of the *whole* would not
be classified under this term! It would be a sibling.
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Of course the issue here is that the whole exactly should not classify under this, only the parts! |
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@rays22 I updated the pattern. Can we meet to test the pattern? |
This commit intends to 1. add DOS-DP data filler 2. update DOS-DP yaml template
If applied, this commit will fix #73.