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identifiers-org / identifiers-org.github.io

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NCBI Taxonomy update at identifiers.org #218

Closed cls44 closed 1 year ago

cls44 commented 1 year ago

I am the product owner for NCBI Taxonomy and I am interested in improving our own recommendations for the formatting of Taxonomy IDs. We are currently recommending an unspecific prefix followed by text and numbers, for example, referring to Homo sapiens: NCBI:txid9606 identifiers.org resolves with another generic prefix; taxonomy:9606

I am still considering the best way to improve our recommended format, but it may also involve a registry update at identifiers.org. How could we proceed?

renatocjn commented 1 year ago

Right now the taxonomy namespace resolves to other resources besides the ones hosted by NCBI. For example, it resolves to bioportal and ENA. Some of these resources also use the "taxonomy" prefix. If NCBI does change the format we may keep the namespace as is and change the URL pattern for the NCBI resource or we may create a new namespace depending on the needs of users.

In general, if you need to update an entry, just write here and I can help. Or send an e-mail to identifiers-org@ebi.ac.uk. At any rate, it would be nice if you could fill in your GitHub profile so that we can verify your identity.

cls44 commented 1 year ago

Ok, makes sense. Not clear then what, if anything, should change at identifiers.org if we adapt our own formatting recommendations to something like "ncbi.txid:9606" ? Regardless, I will send an update email when it happens.

renatocjn commented 1 year ago

Great, I wait for your contact then.

cthoyt commented 1 year ago

Ok, makes sense. Not clear then what, if anything, should change at identifiers.org if we adapt our own formatting recommendations to something like "ncbi.txid:9606" ? Regardless, I will send an update email when it happens.

Ok, makes sense. Not clear then what, if anything, should change at identifiers.org if we adapt our own formatting recommendations to something like "ncbi.txid:9606" ? Regardless, I will send an update email when it happens.

@cls44 this would be an incredible improvement for the biomedical community for NCBI to adopt more standard CURIEs, however, I would suggest doing ncbi.taxon or directly ncbitaxon since this is how everyone is already referring to NCBI Taxonomy entries in most ontology and FAIR data settings.

Can you additionally identify yourself? What is your name so we can cross-reference that you're the NCBI Taxonomy data owner?