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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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Annotations in the notes #15

Closed silviamorins closed 5 years ago

silviamorins commented 6 years ago

Hi, I was wondering why in the SBML output file many attributes of reactions and compound are written in the notes - would it maybe be a better idea to have them written as annotations?

cdanielmachado commented 6 years ago

Yes, this would be the right way to do it. There is currently some debate on how to properly encode different model attributes: https://github.com/opencobra/schema/issues/4

So I think we will probably first let the debate settle, and then make modifications accordingly. But thanks for pointing that out.

lottewitjes commented 5 years ago

Hi, Do you know if any parser is available that incorporates RDF based annotations (MIRIAM) in the output models of CarveMe, so that I can use it together with memote ,as in: the metabolite annotations are recognized by MeMote?

cdanielmachado commented 5 years ago

HI @lottewitjes,

It seems that libSBML has an RDF parser:

http://sbml.org/Software/libSBML/5.16.0/docs/python-api/classlibsbml_1_1_r_d_f_annotation_parser.html

But I haven't tried it yet.

We do plan to move from storing metadata in the <Notes> field to the <Annotations> field in a future release.