validate consistency of reactome location curation about pathways2go HOT 6 CLOSED

Processes in GO now use the 'has primary input' relation in their definitions. Reactome doesn't distinguish something as primary, hence we will not be matching the GO logical definitions very often any more. We can still use this as a curation check on Reactome. e.g. glycolysis should have glucose as an input.

from pathways2go.

Note that the the 'primary' relations are only used for GO metabolic processes at this time.

from pathways2go.

Later thought after the discussion yesterday: Perhaps Reactome could annotate primary inputs and outputs, by creating primary input and output attributes for its pathway class, that would take one or more physical entities as values. And perhaps a GO QA script could retrieve the GO biological process term, if any, associated with a Reactome pathway, retrieve the primary inputs and outputs named in the logical definition of that term, if any, check the Reactome pathway for the presence of the inputs in its first reaction and outputs in its last one, and complain if they are missing. Note the substantial maintenance overhead caused because both Reactome pathway makeup and GO biological process definitions can change substantially over time, so continued checking and patching will be needed.

from pathways2go.

Note that the the 'primary' relations are only used for GO metabolic processes at this time.

But it looks like a really good way of formalizing pathway boundaries and should be easy to extend to signaling cascades, and to localization processes involving individual proteins and complexes.

from pathways2go.

Thus the 'at this time qualifier'. We think alike.

from pathways2go.

Closing this one. QC will be done on the Reactome side where they will be able to highlight inconsistencies to their curators.

from pathways2go.