Signaling Meeting Minutes November 2009

November 4th 2009

Plan for changes to be made. Preferably able to be completed and made live before March 1st 2009.

Participants: Sandra Orchard, Alex Diehl, Peter D'Eustachio, Jennifer Deegan.

Discussion

We discussed how best to do some really concrete work that can be committed before next March, that will pave the way for future work, but without requiring super-human effort to finish in time.

We all agreed that we have been circling round the same problems with the top terms for some time now. Peter suggested that we should each take a pathway that we are very familiar with and try to put the terms in around the new structure that we have created. Everybody agrees that this is a good idea. It will test the structure we have already, and if we can get some pathways right then they will serve as good examples to be followed in future editing by others.

Everybody is able to to use OBO-Edit at least for browsing the file. Jennifer will send the link to the file and people can either edit the file directly in OBO-Edit or put their new structure up on this wiki page.

Jennifer will also make a doodle poll to set up a meeting for three weeks from now, to discuss what we have done.

Instructions

File

http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/signaling3.obo

CVS version number

If you are going to edit the file in OBO-Edit, please could you note down the cvs version number of the file that you started with, as this will be required for merging the changes in again.

OBO-Edit

This is the place to go to get OBO-Edit: https://sourceforge.net/projects/geneontology/files/

Number range

If you would like to make new terms you will need to set up a new number range. It will be best to number terms from 1-999 and have a prefix corresponding to your initials, so for example my first term would be JID:0000001.

To set a number range you go to the menu 'Metadata' then choose 'ID Manager' and then you click the little cog icon and put this in the box: GO:$sequence(7,0000001,0000999)$
You only need to change 'GO' to your initials.

24th November, 2009

Participants: Ruth Lovering, Alex Diehl, Jennifer Deegan, Stan Lauderkind.

We decided to work on the dopamine pathway during this meeting.

The dopamine pathway

Action: Jen to write to Erika Feltrin and ask if she has time to look over what we have done. (DONE - no response yet)

We took the parts of the dopamine pathway in chronological order and slotted the various processes in.

Dopamine secretion

pre-existing structures:

[i]secretion by cell
---[i]catecholamine secreton
------[i]dopamine secretion (pre-existing term)

[i]dopamine transport
---[i]dopamine secretion

new structure:

[i]signaling
---[p]signaling process
------[i]signal transmission
---------[i]signal release
------------[i]dopamine secretion 

Activation step

New:

[i]dopamine receptor signaling pathway
---[pr]positive regulation of dopamine receptor signaling pathway
------[i]activation of dopamine receptor signaling pathway

[i]signaling process
---[i]initiation of signal transduction
------[i]signal initiation by diffusable mediator
---------[i]signal initiation by neurotransmitter
------------[i]activation of dopamine receptor signaling pathway

We noted that the structure above could be most correctly set up with reference to ChEBI.

Signal transduction step

Moved to cell surface receptor linked signal transduction.

[i]signaling
---[i]signaling pathways
------[i]cell surface receptor linked signal transduction
---------[i]G-protein coupled receptor protein signaling pathway
------------[i]dopamine receptor signaling pathway

Termination step

For this we looked at the pre-existing term "activation of adenylate cyclase activity by dopamine receptor signaling pathway"

Pre-existing:

---[i]dopamine receptor signaling pathway
------[i]activation of adenylate cyclase activity by dopamine receptor signaling pathway 

New:

[i]signaling
---[p]signaling process
------[i]signal transmission
---------[i]conclusion of signal transduction (renamed from signal termination)
------------[i]activation of adenylate cyclase activity by dopamine receptor signaling pathway

Questions: Each pathway may have many many different effects, and each of these could be counted as a type of "conclusion of signal transduction". Should we even by trying to capture these as termination steps? Will it lead to a massive explosion in the graph?

30th November, 2009

Participants: Sandra Orchard, Peter D'Eustachio, Jennifer Deegan, Susan Tweedie, Ruth Lovering.

We discussed whether this is correct:

[i]conclusion of signal transduction (renamed from signal termination)
---[i]activation of adenylate cyclase activity by dopamine receptor signaling pathway

and how we might connect the child term to adenylate cyclase activity and to the effects further downstream. We were not clear on whether the term should be connected to the dopamine signaling at all. We considered asking the GO list for feedback.

There was a general feeling that users should be able to trace the process through from signal to effect using the ontology (or ontologies). However we were not sure of the downstream effects of dopamine, which made it difficult to determine how to do this. To deal with this we switched topic to T cells, since Sandra was present and knows T cell signaling in great detail.

We started to make terms for T cell signaling, but then realised that it might make more sense for the editing work to be done during the week with only Jennifer and Sandra present. This will be done before next week so we can look at the effects of T cell signaling then with everybody present to discuss it.