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feat: I/O of SBO terms from SBML file #196
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COBRA deals with SBO terms in a different way by using |
@Hao-Chalmers For merging the model fields, it was proposed to use the COBRA version, taking advantage of their new |
This feature is currently of interest to me, so I implemented the changes into Regarding changes to This seemed unnecessary to me, so I left the original formulation which will only import SBO terms from the SBML if it is part of the I also have a quick question: The default SBO term assigned to genes by |
@JonathanRob, feel three to change the default SBO terms in |
Perhaps check if particular SBO terms are part of a test in memote. If we'd like to use different SBO terms, we should then also advocate this with memote people (and COBRA?). Regarding the I/O function you introduced, I'll check it out. I think it's also important that it can deal with non-RAVEN models, so where do COBRA- and cobrapy-exported models store the SBO terms in the XML file? |
@edkerk Ah, I should have mentioned, memote uses But good point regarding functionality with COBRA-exported models, I will probably need to add a few things for that. |
@JonathanRob In that case, definitely use |
@JonathanRob, regarding SBO terms parsing in On the other hand, if we agree to implement this check, the changes would be made to |
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@simas232 I think a check for uniqueness of SBO terms when importing could be a good option, since the user probably doesn't really need the terms if they're identical for every entry of a particular entity. As for the Regarding the duplication of SBO term information in the SBML file (present in both |
Nice! Okay, then we should try to implement these changes to |
I'll soon make a PR to implement these changes. |
Description of the issue:
Reproducing this issue:
SBO terms are included in the SBML file as following (similar for metabolites and reactions):
When loaded in Matlab using
TranslateSBML
, SBO terms are easily accessible at (similar for metabolites and reactions):Parsing this in
exportModel
andimportModel
should be relatively straight forward, and should be stored in themetMiriams
andrxnMiriams
structures.Note that
ravenCobraWrapper
does already have the option to parse SBO terms from the MIRIAMS structures to their COBRA counterpart fields (metSBOTerms
).System information
I hereby confirm that I have:
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