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[Urinary bladder] Unmapped CL terms #59

Open anitacaron opened 2 years ago

anitacaron commented 2 years ago

From the report listing CT terms without IDS: _2022-10-17 Release_

Some of the CL names in the report already exist in Cell Ontology:

Terminal AS/ID Terminal AS/label Terminal AS/user_label CL Name CL term OLS link
UBERON:0004645 urinary bladder urothelium urinary bladder urothelium basal cell of bladder urothelium CL:1000486 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_1000486
UBERON:0001261 lamina propria of urinary bladder lamina propria of urinary bladder myofibroblast cell of bladder CL:0000186 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000186
UBERON:0012239 urinary bladder vasculature urinary bladder vasculature endothelial cell of bladder CL:0000115 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000115
UBERON:0012239 urinary bladder vasculature urinary bladder vasculature vascular smooth muscle cell of bladder CL:0000359 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000359
UBERON:0012239 urinary bladder vasculature urinary bladder vasculature pericyte cell of bladder CL:0000669 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000669
emquardokus commented 2 years ago

@anitacaron this whole table is in the process of a major rework by author; will revisit for April 2023 CCF release They have determined differences in the different regions of the urinary tract, so not sure we should use generic cell ontology terms for basal cell of urothelium for the entire urinary tract. Likewise myofibroblast cell, generic endothelial cell CL:0000115 where we know there are differences and heterogeity. Basically, these were purposefully not mapped to generic cell types by author.

anitacaron commented 2 years ago

@emquardokus I suggested changing to a generic cell type to ensure that we can bulk create using this approach explained in https://github.com/hubmapconsortium/ccf-ontology/issues/16