March 15th 2010

GO signaling group conference call

Monday March 15th 2010

• 4pm GMT
• 11am US East coast
• 8am US West coast

• US: 1 866 953 9688
• UK: 0808 238 6001
• pin: 801561

Minutes: Becky

Agenda

1/ Check everyone is happy with the placement and definitions of the high level terms:

• • signaling ; GO:0023052
  • signaling pathway ; GO:0023033
  • signaling process ; GO:0023046
  • signal transmission ; GO:0023060
  • signal transduction ; GO:0007165

2/ intracellular signaling cascade ; GO:0007242 vs intracellular signaling pathway ; GO:0023034. Should these terms be merged? [1]

3/ Placement of the regulation of signaling terms. They're currently under 'regulation of signal transduction ; GO:0009966' but the pathways themselves are under signaling pathway ; GO:0023033 [2]

4/ Checking the signaling terms that are children of both intracellular signaling and cell-surface receptor linked signaling pathway. Is it correct that terms such as Notch signaling pathway ; GO:0007219 are under both?

5 /Defining initiation and termination terms- where does initiation start and termination finish?

6 /Should the whole of the cytokine-mediated signaling pathway really be under a signal initiation term? currently, we have:

%signal initiation by protein/peptide mediator; GO:0023049

---%cytokine-mediated signaling pathway; GO:0019221 [3]

7/ Signal transduction as a child of reg of cellular process.

regulation of cellular process ; GO:0050794

--%signal transduction ; GO:0007165

looks like an odd relationship to me. Is it deliberate, or can it be moved up to be a direct child of 'cellular process ; GO:0009987'? [4]

• 8/ Should response terms be children of signaling? [5]

The definition of signaling is: The entirety of a process whereby information is transmitted. This process begins with the initiation of the signal and ends when a response has been triggered. Yet we have response terms under signaling which as Val pointed out, is a TPV.

• 9/ Should all response to x terms be a parent of signaling? Some are, some aren't [6]

cellular response to auxin stimulus ; GO:0071365

--%auxin mediated signaling pathway ; GO:0009734

but some are missing:

fibroblast growth factor receptor signaling pathway ; GO:0008544 and cellular response to growth factor stimulus ; GO:0071363 are unconnected

cellular response to epidermal growth factor stimulus ; GO:0071364 and epidermal growth factor receptor signaling pathway are unconnected