Signaling to do list: Difference between revisions
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Project from Chris: | ==Logical definitions== | ||
Project from Chris Mungall: | |||
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==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. |
Revision as of 05:57, 1 February 2010
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
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.