search

SBRG / bigg_models

The BiGG Models website server
http://bigg.ucsd.edu
Other
75 stars 18 forks source link

Metabolite annotation with InChI Key #363

Open Midnighter opened 4 years ago

Midnighter commented 4 years ago

Metabolites in BiGG, where available, are annotated with InChI Keys. That is super useful. Unfortunately, the keyword does not follow the Identifiers.org standard. It describes the namespace/collection/registry as inchi_key but it should be inchikey.

Here is an SBML example for pyruvate.

<rdf:li rdf:resource="http://identifiers.org/inchi_key/LCTONWCANYUPML-UHFFFAOYSA-M"/>
draeger commented 4 years ago

@mephenor and I will check if this problem comes from ModelPolisher.

mephenor commented 4 years ago

Seems to be an issue with ModelPolisher, might have to do with the way how the annotation URIs are constructed. URL_Prefix is correct, but we somehow use the bigg_id inchi_key instead for the collection part. This will be fixed when I refactor the code dealing with annotations.

Midnighter commented 4 years ago

Sounds good. If you are anyway refactoring that code, can you also switch http://identifiers.org to https://identifiers.org, please?

mephenor commented 4 years ago

Sure, I'll change that.