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AIRR Community Data Standards
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MiAIRR Cell Subset field - request additional option #152

Closed bukharilab closed 5 years ago

bukharilab commented 6 years ago

I am helping a person from the NCBI to submit AIRR compliant data and he reported the following issue to me through email.

Hi Ahmed,

I’m trying to use the web-based MiAIRR metadata tool to get my data prepped for repository submission. It was going ok but I ran into an issue with the Cell Subset field under Processing. There’s an option called B cell, which I could use, but it doesn’t really differentiate my samples as they are all B cells, just different types (Naïve, memory, GC, etc). The field won’t accept anything typed in (eg. Naïve B cell) that is not part of the drop down list. I type it in, hit OK, but whatever I just typed disappears. It seems from the help I could type in whatever I wanted, but wanted to check with you.

Thanks for your help,

I reported this issue to the CEDAR team https://github.com/metadatacenter/cedar-project/issues/870. They suggested I should I also discuss this issue to AIRR standards team as well. Following is the CEDAR team reply

Per John:

We'll have to check what help suggests this, as the suggestion is incorrect. For controlled terms, users may only choose from among the options defined by the template.

You may want to refer this ticket to the metadata working group, since they can recommend a change to the selected terms.

Any thoughts?

lgcowell commented 6 years ago

Does CEDAR not allow selection from Cell ontology subtypes of lymphocyte?

bussec commented 6 years ago

Along @lgcowell's comment: Which CV/ontology is CEDAR currently using?

bukharilab commented 6 years ago

Its using the cell ontology. I found naive T cell but not Naive B cell in the drop down. Here is the ticket on CEDAR GitHub repo https://github.com/metadatacenter/cedar-project/issues/870

schristley commented 6 years ago

The purl is slow to load or gets an error, but B cell is in the CL, as well as a few subsets.

bussec commented 5 years ago

I just had a look again at CL and as @schristley already pointed out, B cell exists in CL as node for several common subpopulations. Therefore this issue is not MiAIRR related. Further note that the respective issue 870 at CEDAR has been closed, too.