cmungall
commented
5 years ago - Re: aorta is_a artery. We treat artery, arteriole and aorta as siblings under "arterial blood vessel". We can always revisit this if unintuitive. @tfhayamizu we got this from how you model it for mouse, do you want to comment?
- mammary glands can be part of non-breast regions in non-human mammals (we have various subtypes of MG in uberon for the different regions). But I appreciate this is an annoying detail if you are working just with human. What if we made a human export where there is only one MG and it's part of breast
will comment on others later...
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).