There is a bug importing co-transporters and antiporters

[ukemi]

When a transporter transports more than one molecule, only one is imported. For example:

1. In the pathway 'Pyruvate metabolism' (R-HSA-70268), the reaction that transports a proton and lactate from the extracellular region to the cytosol only includes the hydrogen as the transported molecule in the imported model (R-HSA-373875).
2. In the pathway 'Mitochondrial calcium ion transport' (R-HSA-8949215) the reaction that antiports calcium and a proton only shows the calcium being transported (R-HSA-8949687).

E-mail comment from David on possible source of the problem: Ben’s rule was simple. If a chemical was in one place at the beginning of a reaction and in another place at the end of a reaction, the reaction was inferred as a transporter activity and that transported molecule got the 'transports or maintains localization of' relation. In this case though, the MF is asserted as the antiporter activity and takes precedence. Asserted functions always overrule. The process is asserted as ‘mitochondrial calcium ion transmembrane transport’. It looks like for this process, the only molecule that is considered in any of the reactions as being transported is the calcium. Perhaps the transported molecule from the process takes precedence.

But I think this is a red herring. The pyruvate metabolism suggests that the aserted classes are not considered for reasoning or mapping of participants.

[ukemi]

@dustine32 I just double checked this and the first model has been changed at source, but the second example still holds true. NB though, if we implement the has_primary_input fix this bug will go away. The bug is not in current inputs, it has to do with the objects of the transports_or_maintains_localization_of participants.

[ukemi]

• [x] pyruvate metabolism-passes
• [x] Mitochondrial calcium ion transport
• [x] Several other models, just as a passing check and not systematic.

[ukemi]

@dustine32 this one is fixed. We can close it once it goes into production for real.