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[Blood] Unmapped CL terms #52

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:

N Terminal AS/ID Terminal AS/label Terminal AS/user_label CL Name CL term OLS link
1 UBERON:0000178 Blood Blood CD4 T cell memory CL:0000897 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000897
2 UBERON:0000178 Blood Blood CD4 T cell effector memory CD45RA CL:0000905 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000905
3 UBERON:0000178 Blood Blood CD8 T cell memory CL:0000909 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0000909
4 UBERON:0000178 Blood Blood mature CD8 T cell CL:0002437 https://www.ebi.ac.uk/ols/ontologies/cl/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCL_0002437
emquardokus commented 2 years ago

@anitacaron I just looked up CL:0000312 in OLS and it gives a very different identity than you list in this report, how is this possible?
keratinocyteCL:0000312

Image

When I look for "CD4 T cell memory" in OLS Cell Ontology, there is not exact match, but several possibilities that require immune cell expertise to disambiguate.

== "CD4 T cell effector memory CD45RA" is in ASCT+B table; the protein biomarker set has CD45RA positive as opposed to negative, this is what you've mapped it to here: effector memory CD4-positive, alpha-beta T cell CL:0000905, which in the definition states "CD4-positive, alpha-beta memory T cell with the phenotype CCR7-negative, CD127-positive, CD45RA-negative, CD45RO-positive, and CD25-negative. [ http://purl.obolibrary.org/obo/go/references/0000031 http://www.ncbi.nlm.nih.gov/pubmed/22343568 GOC : add GOC : tfm GOC : pam ] "

What is the evidence used to map this?

=== CD8 T cell memory in ASCT+B table--> CD8-positive, alpha-beta memory T cell CL:0000909

=== mature CD8 T cell in ASCT+B table--> mature CD8 single-positive thymocyte

===

Will double check with authors.

anitacaron commented 2 years ago

Sorry, I pasted the wrong CL id, but if you check the OLS link, it's pointing to the CD4-positive, alpha-beta memory T cell. It should be CL:0000897. I'll edit the table.

== Please, consider all these unmapped-terms reports as a suggestion. You or the specialist should always certify this.

emquardokus commented 2 years ago

Blood v1.3 DRAFT Added mapping to 2 instances of CD4 T cell memory (note that biomarkers are different; likely subtypes; need to ask author for clarity on this).

CD4 T cell memory CD4-positive, alpha-beta memory T cell CL:0000897
CD4 T cell memory CD4-positive, alpha-beta memory T cell CL:0000897
anitacaron commented 1 year ago

UPDATE:

The last report listing CT terms without IDS: 2023-10-31 Release is empty, so all terms were mapped.