Signaling to do list
Logical definitions
Project from Chris Mungall:
>> (4) 'signal transmission' is defined as: >> "The process whereby a signal is released and/or conveyed from one location to another. The process terminates at the end of the sub-process of signal transduction, when the function of the cell has been altered as a consequence of receipt of the signal." >> So, the definition says that signal transduction is a sub-process of signal transmission. This implies that signal transduction is part_of signal transmission. Yet 'signal transduction' is an is_a child of signal transmission. Which is correct? > > I think they are both correct. I am going to leave the relationship as is_a. We could follow this up in a separate thread if you'd like to discuss it. This is a bit worrying. What I would really appreciate is a simple diagram showing the flow of time on the x axis, with the processes arranged according to the allen interval relations (http://www.ics.uci.edu/~alspaugh/cls/shr/allen.html ). Looking at signaling3.obo doesn't really tell me the changes. for example, is a receptor binding pathway always immediately preceded by receptor binding? (Reactome doesn't appear to be consistent here) I think we should get the logical definition template correct first. I have set up a file biological_process_xp_signaling.obo I used starts_with, which implies part_of, but I think this should really be initiated_by
Chris's Reactome2GO analysis
3 cols of 3:
Pathway/Process
Initiating event
Initial Event
Each is split into 3 - reactome label, GO ID, GO label
(Jen: I have checked this into cvs go/scratch/xps/r2go-signaling.txt)
Here initial event is a reactome leaf node in P that has no preceding event in P. initiation event is the event preceding this one.
I would expect that for any pathway that has the GO def "..generated as a consequence of a X receptor binding to..." to have something like "X receptor binding" (or something that entails this) as an initiating event and perhaps something like "X receptor activity" as the first event in the process. Is this too simplistic?
Cross-references to Reactome
Peter D'Eustachio is making a list of GO terms and Reactome terms that could be cross referenced. Once he has completed this he will pass the list along to be intergrated into the GO ontology file.
Glutamate pathway
Invite Anita Bandrowski to meet with the signaling working group to make new terms for the glutamate pathway and related areas. (abandrowski at ucsd.edu)
Documentation
Work with the signaling working group to try to produce the kind of docs that Chris is interested to see: