Signaling to do list

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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 analysis

3 cols of 3:

Pathway/Process
Initiating event
Initial Event

Each is split into 3 - reactome label, GO ID, GO label

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.