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obophenotype / xenopus-phenotype-ontology

XPO represents anatomical, cellular, and gene function phenotypes occurring throughout the development of the African frogs Xenopus laevis and X. tropicalis.
http://www.xenbase.org/
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Proposal for new pattern/terms related to membrane potentials. #160

Open malcolmfisher103 opened 1 year ago

malcolmfisher103 commented 1 year ago

Xenbase curators are interested in creating some terms related to membrane potentials.

We would suggest a parent term 'abnormal membrane potential' using the PATO term 'membrane potential' (PATO:0001462) and children based on GO terms 'membrane hyperpolarization' (GO:0060081) and 'membrane depolarization' (GO:0051899). These might also be expanded to have child abnormalBiologicalProcessInLocation.yaml based terms for selected tissues or cell types.

This is a preliminary exploration of the idea in case it needs to be discuss with the larger phenotype design pattern community. I believe some of the other MOD phenotpye ontologies have similar terms such as melanocyte membrane potential, abnormal from the ZP.

If this is doable then we can provide a list of cell and tissue types for the more granular terms.

seger commented 1 year ago

@malcolmfisher103 It seems feasible to create a new pattern for membrane potential, but I am unsure whether the two GO-based terms would automatically become children of the 'abnormal membrane potential' term. @matentzn could you comment on that? If it's just a matter of needing a parent grouping term for the GO-based terms, we could also add 'abnormal regulation of membrane potential' (GO:0042391).

matentzn commented 1 year ago

This seems like a new pattern and should be raised with the uPheno curator team: https://github.com/obophenotype/upheno/issues

Mention also the various membrane potential classes in OBA: http://purl.obolibrary.org/obo/OBA_0000046

In OBA there seems to be a bit of a mix, including using "electric potential" in PATO with GO.. Something in this direction will be the way to go I think but best ask there and tag @rays22 and @sbello in that issue to discuss it during the next phenotype editors call.