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[Prostate] Unmapped CL terms #53

Closed anitacaron closed 1 year ago

anitacaron commented 2 years ago

From the report listing CT terms without IDS: _2022-10-10 Release_

Some of the CL names in the report already exist in Cell Ontology as a general type. There's a work in progress to create compound CL types, combining location and cell type, as listed in the table:

N Terminal AS/ID Terminal AS/label Terminal AS/user_label CL Name CL term OLS link
1 UBERON:0004184 prostate gland stroma prostate stroma vascular smooth muscle CL:0000359 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000359
2 UBERON:0004184 prostate gland stroma prostate stroma prostate perictye CL:0000669 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000669
3 UBERON:0001335 prostatic urethra prostatic urethra basal cell of prostatic urethra CL:0000646 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000646
4 UBERON:0001335 prostatic urethra prostatic urethra club cell of prostatic urethra CL:4032000 New term added in 2022-09-15 CL release. CL version in OLS is from the previous release. https://ontobee.org/ontology/CL?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_4032000
5 UBERON:0001335 prostatic urethra prostatic urethra hillock cell of prostatic urethra CL:0017011 New term added in 2022-10-28 CL release. https://ontobee.org/ontology/CL?iri=http://purl.obolibrary.org/obo/CL_0017011
emquardokus commented 2 years ago

@anitacaron CL:0000669 is just pericyte, not prostate pericyte, is this the desired to map to generic term? There are tickets that were merged a while ago for CL for these: club cell of prostatic urethra July 15, 2022 added: https://github.com/obophenotype/cell-ontology/issues/1133 hillock cell of prostatic urethra PR and merge done August 25, 2022 https://github.com/obophenotype/cell-ontology/issues/1134

anitacaron commented 2 years ago

prostate pericyte: we identified many cases where we need to create a cell type related to location (https://github.com/hubmapconsortium/ccf-ontology/issues/16), and we can bulk add them using a ROBOT template. That's why I suggested changing to a generic pericyte.

club cell of prostatic urethra: Sorry, I didn't find the CL term in OLS because it's not showing the last CL release. I'll update the table here.

hillock cell of prostatic urethra: The PR linked to the NTR issue for hillock cell of prostatic urethra is not creating this term, but another 2, one generic hillock cell and one related to respiratory.

anitacaron commented 2 years ago

@emquardokus, hillock cell of prostatic urethra was finally added in the last CL release. I've updated the table here with its CURIE.

anitacaron commented 1 year ago

UPDATE:

Checking the latest report, all terms are not there, except basal cell of prostatic urethra, which was mapped to a general term basal cell, but it's important to be specific in this case.