Missing WD Item for CT_222

[djow2019]

CT_222 is not found in WD even though its referenced here Q36281361
also update ortholog CTL_0475 to include CT_222

[andrewsu]

Looks like CT_222 was discontinued: https://www.ncbi.nlm.nih.gov/gene/884897 which is why there is no WD item. On the scale of things, I think this is the correct behavior. @khybiske can you have a look and if you agree, close the issue?

[khybiske]

This is a head-scratcher. On the surface of things, I am inclined to disagree with NCBI. This gene has been tested in at least 3 studies, PMIDs: 26416906, 18391011, and 20331642. For Chlamydia, that is pretty rigorous. Its ortholog in 434/L2 is CTL0475, also validated experimentally but discontinued by NCBI. I'll let you guys make the executive decision. If it's easier to align with NCBI, and leave open for users to request an add later on, that's fine with me. ?
cc @andrewsu @djow2019

[andrewsu]

Yes, I think we should stay aligned with NCBI, but rather than waiting for users to complain I think we should proactively ask NCBI to review this case. They have a form to request corrections here:
https://www.ncbi.nlm.nih.gov/projects/RefSeq/update.cgi. @khybiske, want to fill this out or shall I? either way, we should point them back to this github issues so they have the ability to comment here (though it's also possible that it would only get an email response of course)...

Also, it doesn't look like CTL0475 is discontinued https://www.ncbi.nlm.nih.gov/gene/5858542 or am I missing something?

[khybiske]

Before we ping NCBI, I want to hear back from a colleague (Dan Rockey) to get his two cents. Make sure I am not imagining something.

[khybiske]

@andrewsu What would we specify in the request form? Clarification on why the gene was discontinued? or request that it be reissued?

[andrewsu]

Both/either? I think we want to propose a reexamination of that discontinuation, and hopefully they'd share with us the rationale.

[khybiske]

Sorry, I have not yet sent in the request. I'm dealing with a stack of grant and paper deadlines. As soon as the dust settles, I can do this.

[djow2019]

Has the request been sent?

[khybiske]

Ack, no.. I'll try to deal with it