alanbridge
commented
5 years ago I think we need to start curating the location explicitly in Rhea when we have that information, and replace the "in" and "out" (conventions left over from IUBMB) with actual GO terms for subcellular locations. Actually IUBMB use a range of terms now like side 1 and side 2 which is creating even more trouble.
This would give us a reaction hierarchy that would be much easier for users to understand and exploit.
- A (in) = A (out) [moving from here to there but no real idea as to where...]
and "child" terms like
-
A (cytosol) = A (extracellular space) [crossing a membrane...]
-
A (cytosolic leaflet of plasma membrane) = A (extracellular leaflet of plasma membrane) [flipping within a membrane]
-
A (cytosolic leaflet of plasma membrane) = A (cytosolic leaflet of golgi membrane) [moving from one membrane to another, but staying on the cytosolic face]
(apologies for not using real GO terms here for the sake of speed)
the transport hierarchy could then be inferred based on i) ChEBI classes and ii) GO cell components:
- lipid (in) = lipid (out)
- lipid (cytosol) = lipid (extracellular space)
- phospholipid (cytosol) = phospholipid (extracellular space)
cmungall
goodb
pgaudet
Right now, there is no OWL representation in the axioms I have generated for the "in" and "out" you see in the RHEA transport reactions. The definition for A (in) = A (out) is the same as it is for A = A. I suspect this is something we could improve on with some more thought.
A related issue came up before for the translocation reactions coming into Noctua from Reactome, many of which are currently not classified in GO. The idea there was to use the occurs_in information in Reactome to generate 'has target start/end location' statements on the reaction entities that would then work with existing axioms to get classifications into biological process terms. E.g.,
R instance_of ‘establishment of protein localization’ R has_target_end_location location2 R has_target_start_location location1 <= R has output P2, P2 occurs_in location2, R has input P1 P1 occurs_in location1 P1 = P2 location1 != location2
Then the OWL reasoner should add more specific biological process - e.g. R instance_of ‘establishment of protein localization to mitochondrial membrane’ Based on its definition: 'establishment of protein localization' and ('has target end location' some 'mitochondrial membrane')
I think the transporter / translocation area could be a really nice result from the rhea/reactome/go integration. We get the more specific information about locations from Reactome, the class structure with extant OWL definitions from GO, and the expanded set of transport reactions from rhea. I think worthy of another ticket @ukemi .