obophenotype / obophenotype/uberon

hair follicle/dermal papilla, mammary gland/breast, aorta/artery, etc

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Description

Similarly to the lung/bronchus issue that I commented on earlier. I noticed the following UBERON terms are not connected in the way I thought they might be since the FANTOM5 ontology seems to contradict with the labeled FANTOM sample tissue types (in the human samples file: http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_latest/basic/HumanSamples2.0.sdrf.xlsx). It's unclear to me which of the disagreements between the labeling is due to imprecision in the FANTOM tissue labeling and when it's due to a missing annotation, so here I'll first just list some things that I think are more likely to be due to missing links in the ontology.

I'm not trained in anatomy, and it depends on how the entities are defined, but I would imagine:
aorta is_a artery
dermal papilla part_of hair follical
mammary gland part_of some breast
If they are not related by any current relations, perhaps there should be another type of relation for closely related terms such as these in the ontology? ("connected_to"?)

Secondarily, I am wondering if there is a term that encompasses spinal cord and spine combined, since terms like "annulus fibrosus disci intervertebralis", "vertebra", "nucleus pulposus", and (spinal) "perineurium" seem to be related in some way to the spinal cord. (Again, FANTOM samples mapping to these UBERON terms via the FANTOM ontology are labeled "spinal cord" in the human sample file, which is how I stumbled upon them).

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Research direction

Start by comparing the listed UBERON terms with the FANTOM5 HumanSamples2.0.sdrf.xlsx labels and reviewing their current ontology relations. Determine which discrepancies reflect missing annotations versus imprecise tissue labels, and assess whether a suitable relation or combined spinal cord/spine term is needed. Done means the proposed ontology changes and their evidence are clearly documented.

Written by the indexing model from the issue text.

Assessment

Domain
content
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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