bridgedb / bridgedb/Goliath

Unify Mapping results

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#11 1 comment 0 reactions 3 assignees Assigned to @Chris-Evelo View on GitHub
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Description

See also #4 for the long discussion on this topic.

I would prefer to use CHEBI:1234 ; simply because then people see where the identifier comes from with more ease. HMDB also includes their database name in the identifier, and Ensembl does this too (even with a code to see which species the ID belongs too). And Pathvisio can handle both ChEBIs (so CHEBI:1234 and 1234). About the secondary IDs: it would be great if we could do such a mapping at some point (as well as for outdated IDs from other databases), however these are very specific use cases, so I wouldn't bother with it now. Therefore, I believe the correct format for metabolite IDs should be:

- [ ] ChEBI CHEBI:1234
- [ ] HMDB HMDB0012345 (so with a length of 11, not 9, that was the old structure of the ID).
- [ ] Inchi+InchiKey Not sure about these, what do you think @egonw ... At Wikidata the Inchi is not given with the prefix "InChI=", at wikipedia this is given (because they add the InchiKey under the same database (and given a prefix "Key"); we do not do that in BridgeDb right?).
- [ ] please add other specific examples if needed.

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