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feat: enable I/O of SBO terms from SBML file #235

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merged 7 commits into from
Sep 19, 2019
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@JonathanRob JonathanRob commented Aug 17, 2019

Main improvements in this PR:

The exportModel, importModel, and ravenCobraWrapper functions were updated to enable writing and reading of gene, reaction, and metabolite SBO terms to and from an SBML file. This PR addresses Issue #196.

  1. exportModel writes SBO terms from .xyzMiriams model fields to SBML .sboTerm fields.

  2. The default gene SBO term assigned in exportModel was changed from SBO:0000252 ("polypeptide chain") to SBO:0000243 ("gene"), the latter of which is consistent with memote.

  3. importModel reads SBO terms from the SBML .sboTerm fields, and adds them to the corresponding .xyzMiriams model fields.

  4. A check was implemented in importModel to prevent importing SBO terms if they are all identical for a given entity (e.g., if all metabolites have the same SBO term, it will not be imported into the model structure).

  5. ravenCobraWrapper was updated to enable conversion of gene SBO terms between the .geneMiriams and .geneSBOTerms fields of RAVEN and COBRA model structures, respectively.

I hereby confirm that I have:

@edkerk edkerk self-requested a review September 5, 2019 08:43
@edkerk edkerk merged commit ce906d5 into devel Sep 19, 2019
@edkerk edkerk deleted the feat/SBO_SBML_IO branch September 19, 2019 17:50
@simas232 simas232 mentioned this pull request Nov 7, 2019
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@simas232 simas232 added this to the v2.3.0 milestone Nov 7, 2019
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4 participants