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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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User instructions for alias editing #181

Closed khybiske closed 5 years ago

khybiske commented 5 years ago

@djow2019 thinking more about this... What might be helpful (and easy) is if you wrote a brief set of instructions inside the annotation wizard, so that users know what we'd like them to type in the alias box (or what's allowable). Or maybe provide examples? I am on board with following NCBI's naming... but that also seems very inconsistent. There are L2 genes that contain abbreviated names (ie CTL0006), and those that don't (CTL0245, which we discussed yesterday).

khybiske commented 5 years ago

I do find it off-putting that the abbreviated gene names (in the CTL0245 example) are practically buried as small-type aliases, when that's really the most important descriptor after the locus tag. To even find this gene (L2 ortholog), I search for 'glgb', click the Cpn ortholog search result (it's the only one that comes up), then click CTL0245 in the ortholog table. Not ideal, ya?

djow2019 commented 5 years ago

I think that the best way to address this might be to make a new wikidata property called "abbreviated name" and we manually add all the abbreviated names as a property of each gene

khybiske commented 5 years ago

I'd love that.

djow2019 commented 5 years ago

@khybiske do you have a table mapping locus tags to abbreviated names? Sadly, NCBI does not contain any structured form for abbreviated names, so we will have to create a spreadsheet ourselves.

khybiske commented 5 years ago

Shared a google sheet with you.

djow2019 commented 5 years ago

Perfect!

djow2019 commented 5 years ago

image.png

Just about done here. Will also display the gene symbol in the overview panel. All thats left is to get the remaining symbols in WD

djow2019 commented 5 years ago

Since we have a form for editing gene symbols, and that aliases, as a separate form, do not require any special naming conventions, I am marking this as resolved.

Also: briefly changed the placeholder text image.png