obophenotype / obophenotype/uberon
"thigh" may not be an appropriate exact synonym of `hindlimb stylopod`
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Description
Uberon term
hindlimb stylopod, UBERON:0000376
(but may be a broader issue, affecting additional classes)
Bug description
Summary
Uberon seems to conflate two systems of axially dividing limbs into sections/segments:
- Developmental (anchored by corresponding bones)
- Clinical/regional - in terms of soft-tissue landmarks.
The titular issue appears to be a consequence of that conflation.
Details
Today I noticed that Uberon has "thigh" as an exact synonym of hindlimb stylopod (UBERON:0000376) - but that in practice, as far as I can tell, those two terms have different meanings:
-
hindlimb stylopod is the segment of the hindlimb from a developmental perspective, is anchored by the corresponding skeletal component - femur for humans. Consequence: femur is part-of hindlimb stylopod
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Meantime, "thigh" (in clinical & colloquial usage, possibly what UMLS:C0039866 means, though it's unclear) is defined in terms of soft-tissue landmarks - basically the region between the inguinal crease and the proximal edge of the patella. femur would NOT be part-of that "thigh".
The same issue seems to occur for other limb segments; thigh was where I first encountered it.
Has the question of those two systems (developmental vs clinical) of dividing up limb-segments come up during Uberon curation? Is there a policy or best-practice that was decided?
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the Uberon term hindlimb stylopod (UBERON:0000376) and the reported thigh exact synonym. Compare the developmental and clinical/regional meanings described in the issue, then determine whether a curation policy already distinguishes them. Done means resolving the synonym question and addressing any additional limb-segment classes affected by the same conflation.
Written by the indexing model from the issue text.
Assessment
- Domain
- content
- Issue type
- Bug
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Active
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100