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SuLab / WikiGenomesBase

A configurable codebase for launching organism specific WikiGenomes spinoff applications (e.g. ChlamBase.org) This is a web application framework for creating a model organism database leveraging the taxonomic, genetic and functional data that has been loaded to Wikidata.org by the Gene Wiki Project.
https://chlambase.org/
MIT License
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Missing WD Item for CT_222 #56

Open djow2019 opened 6 years ago

djow2019 commented 6 years ago

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

andrewsu commented 6 years ago

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 commented 6 years ago

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 commented 6 years ago

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 commented 6 years ago

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 commented 6 years ago

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

andrewsu commented 6 years ago

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

khybiske commented 6 years ago

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 commented 6 years ago

Has the request been sent?

khybiske commented 6 years ago

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