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[BUG] SBO terms incorrectly handled if multiple exist #1454

Description

@GwennyGit

Is there an existing issue for this?

  • I have searched the existing issues

Problem description

Some reactions can have multiple SBO terms. For example: Nitrate reductase (MetaNetX ID: MNXR102059, BiGG ID: NTR3B)

The nitrate reductase reaction can of course be classified as a biochemical reaction (SBO:0000176). However, if we want to be more precise we can classify it as a redox reaction (SBO:0000200) or as a translocation reaction (SBO:0000185). All these terms are correct for this reaction. Thus, it would make sense to include one of these in the sboTerm tag in the reaction tag and add the others to the annotations. Having said this at the moment if anyone has this setup reaction.sbo returns empty so no SBO term. This causes also issues in other tools like MassChargeCuration when a single SBO term is cast to int() as only one integer is expected.

Possible solution(s):

  • Add code to retrieve a list but return only first entry? -> Might not be the best solution as information gets lost, but could be a quick fix.
  • Get list of SBO terms & return list with reaction.sbo
    -> Could even make two different setups to have reaction.sbos & reacton.sbo

Could maybe be handled together with issue #684

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