Need to be able to differentiate between different species in genes, proteins, etc.

TranslatorSRI / NameResolution

A service for finding CURIEs from lexical strings.

MIT License

3 stars 2 forks source link

Need to be able to differentiate between different species in genes, proteins, etc. #38

Open gaurav opened 1 year ago

gaurav commented 1 year ago

e.g. if you search NameRes for "fgf8", we get back several different UniProt IDs for human, zebrafish, etc. UI wants to make sure that users can clearly differentiate between the identifiers by means of the label (note that they use the canonical label from NodeNorm, NOT the label(s) from NameRes).

The ultimate fix for this is going to be the metadata service that will eventually fit into NodeNorm, but it would be good to have a short-term fix. This could be entirely on the UI's end (e.g. calling mygene.info for each UniProtKB identifier), but eventually the Node Metadata Service is the solution here.

Alternative: prioritize names with brackets to the canonical name in NodeNorm.

cbizon commented 1 year ago

Now that we have a more flexible document structure, would we like to include properties fields?

gaurav commented 1 year ago

[x] Produce a list of all cases where different clique share the same preferred name (https://github.com/TranslatorSRI/NameResolution/issues/40)

gaurav commented 1 month ago

We now include taxon information for all NCBIGene identifiers. I've just started work on a PR (https://github.com/TranslatorSRI/Babel/pull/349) that should include taxon information for all UniProtKB identifiers as well. NameRes now supports filtering by taxa (using NCBITaxon identifiers).

So I think the remaining tasks on this ticket are:

[ ] Get that PR tested, reviewed and merged.
[ ] See what proportion of genes and proteins are not covered (i.e. don't have either a NCBIGene or UniProtKB identifier).
[ ] Figure out some way to include taxonomic information in conflation (this will require changes to NodeNorm), but I don't think this is a priority right now.