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

  • 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

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. 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

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