#49 Reactions and pathways

[Sandra Orchard]

In the provided example xml file, the example where an enzyme joins two RNA molecules there is no explicit product defined. This may be intuitive for a human to conclude that the combined RNA molecules are the product, but it requires context specific rules to computationally reconstruct this pathway. It would be
better to require any reaction to have at least one product and a substrate. Enforcing this in the XSD is not possible in the given Schema but validation tests could be preformed against the ontology. If the ontology specified the minimum required types involved in a given interaction type, this would make the data format much more robust. It also supports the need for a API that uses the ontology during processing.

PSI-MI2.5 reviewer comment