Abnormal/Increased/Decreased proportion of CD4+ central memory cells cell type confirmation

[LCCarmody]

HPO term

HP_0025620|HP_0025621|HP_0025622 | Abnormal proportion of CD4+ central memory cells|Elevated proportion of CD4+ central memory cells |Reduced proportion of CD4+ central memory cells
-- | --
HP text def: An abnormal proportion of central memory CD4+ T cells. These are memory cells that are located in the secondary lymphoid organs. These cells may have a CD3/CD4/CD62L+/CD45RA- phenotype.

Bug description

1. IN A DIFFERENT part of HP, there also exists

HP_0410393|HP_0410388	Decreased, Increased proportion of central memory CD4-positive, alpha-beta T cells

Are these the same as the other HP terms?

2. Are all these the same as this CL term? If so, some terms need to be obsoleted.

CL_0000904	central memory CD4-positive, alpha-beta T cell
CL text def: CD4-positive, alpha-beta memory T cell with the phenotype CCR7-positive, CD127-positive, CD45RA-negative, CD45RO-positive, and CD25-negative.

#4289

[nicolevasilevsky]

The latter terms (HP_0410393 Decreased proportion of central memory CD4-positive, alpha-beta T cells and HP_0410388 Increased proportion of central memory CD4-positive, alpha-beta T cells) have a different set of markers in the def:

These cells have the phenotype of CCR7-positive, CD127-positive, CD45RA-negative, CD45RO-positive, and CD25-negative.

These HPO terms should use the CL term CL_0000904.

I think the former terms are correct too and are duplicates and the terms should be merged.

• obsolete HP_0025621 and replace with HP_0410393. Add HP_0025620 'Abnormal proportion of CD4+ central memory cells' as a parent
• obsolete HP_0025622 and replace with HP_0410388. Add HP_0025620 'Abnormal proportion of CD4+ central memory cells' as a parent

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4810120/

[LCCarmody]

I can add these to the spreadsheet, BUT I don't know how to obsolete in HP. @drseb

[nicolevasilevsky]

I regularly obsolete terms in Mondo, and I think it's the same process in HPO. I could give it a try, if that's okay?

[nicolevasilevsky]

I can do it on PR

[LCCarmody]

Let me merge my current PR. Could you make sure to add the labels as new synonyms? Thanks.

[nicolevasilevsky]

Sounds good - yes, will add the old labels as synonyms.

I'm in meetings until this afternoon, so I'll work on this when your workday is over :)

[drseb]

All annotations should be moved to the new term. Definition needs to be manually handled. Does that work? Sent from mobile

…

Am 18.05.2020 um 20:01 schrieb Nicole Vasilevsky ***@***.***>:  Sounds good - yes, will add the old labels as synonyms. I'm in meetings until this afternoon, so I'll work on this when your workday is over :) — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

[nicolevasilevsky]

Yes - @LCCarmody and I created a PR