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mwang87 / ReDU-MS2-GNPS

User interface to reanalyze and explore all public data in Metabolomics Public Data
https://redu.ucsd.edu/
MIT License
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Improve taxonomical coverage through the bioregistry prefixes #241

Open Adafede opened 2 years ago

Adafede commented 2 years ago

Hi!

As many species will likely appear soon on ReDU and the coverage of NCBI taxonomy even if very good will not be enough, I would suggest adding the possibility to add taxa through the Bioregistry.

This way, there won't be n issues for n taxonomic databases and each time new fields. If something is missing from the Bioregistry, then the request will be added there so that the whole community benefits from it.

For more background, see also https://github.com/biopragmatics/bioregistry/pull/398.

Happy to develop if needed, especially on the Wikidata part!

mwang87 commented 2 years ago

That sounds exciting. Do you know if for the bioregistry, if we can resolve back to NCBI if an accession is available? I first just want to avoid white listing a million NCBI entries, but also one important thing is that we can place any organisms on a tree of life.

Best,

Ming

Adafede commented 2 years ago

Not sure to get your question, any case:

https://bioregistry.io/registry/ncbitaxon