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ChEBI prefix #113

Closed mihai-sysbio closed 3 years ago

mihai-sysbio commented 4 years ago

I am a bit confused by the prefix used in the ChEBI identifier. When comparing the documentation pages for MetaNetX chemical and ChEBI side by side, the difference is more obvious:

ChEBI MetaNetX chemical
Local Unique Identifier (LUI) pattern ^CHEBI:\d+$ ^(MNXM\d+|BIOMASS)$
Prefix CHEBI metanetx.chemical
Sample URL https://identifiers.org/CHEBI:36927 https://identifiers.org/metanetx.chemical:MNXM1723
Sample Compact identifier CHEBI:36927 metanetx.chemical:MNXM1723
Sample ID (LUI) 36927 MNXM1723

The chebi: prefix is not being used in the sample url.

I'm seeing explanations in #65 and #93 as to why https://identifiers.org/CHEBI:36927 has been allowed, and I would not advocate for changing that. What I am puzzled by is why the more standard https://identifiers.org/chebi:CHEBI:36927 is not allowed in addition to the above - most likely it was down to technical difficulties.

Would it be acceptable to remove the misleading CHEBI prefix from the documentation page?

mbdebian commented 4 years ago

Dear @mihai-sysbio ,

I'd like to thank you for reaching out on this matter, I really appreciate the time you've taken to explain the issue so nicely, as well as the investment in reading the explanations by the linked issues.

This is a controversial part of how the concepts of LUIs (Locally Unique Identifiers) and Compact Identifiers were a little bit bent over their backs to accommodate some particular requirements from the ontology communities.

Hopefully, the Sample Compact Identifier field gives users useful information on how to create compact identifiers for a particular namespace.

I'm afraid removing the prefix information for those namespaces like CHEBI, VariO, GO... etc. may contribute to the confusion among the community, but, what we could probably do, is to implement a mechanism that highlights this special case, when applicable, in our landing pages.

I'll leave this issue open, to take it into account for the next iterations on the interface.

Thanks again for your feedback, @mihai-sysbio

Kind Regards, Manuel

mihai-sysbio commented 4 years ago

Thank you for the explanation @mbdebian . May I suggest moving the row with the prefix lower down in the documentation, so that it is less observed? Or perhaps adding a separate section called Usage with only the Sample Compact identifier and the Sample URL would be useful. I'm not sure what most people want to see in the documentation, but my intuition is that understanding how to convert an ID into a URL is would be a very popular need, and for that I gather those two fields are sufficient.

mbdebian commented 3 years ago

Hi @mihai-sysbio ,

I just wanted to let you know that we'll move these suggestions to our backlog, and I'll proceed on closing this ticket.

Thanks, Manuel