July 19th 2010

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MINUTES

Present: Becky, Ruth, Pascale, Varsha, Peter, Alex.


1. Wnt signaling

It was agreed that although it's not good ontology development to have non-canonical as a term, biology, authors and the reference genome project need these terms so we'll create them. Just don't highlight it as an example in a paper!!

Ruth said it was needed because some authors didn't say what it signalled through, they just said it DIDN'T signal through beta-catenin.

Varsha pointed out that annotators could use NOT canonical wnt signaling | annotations instead. But the trouble comes when a protein is involved in both canonical and non-canonical signaling.

2. Cleaning up intracellular signaling

AI: Becky to move a number of terms from intracellular signaling, to be direct children of signaling cascade:

  • jasmomic acid mediated signaling pathway
  • nitric oxide mediated signal transduction
  • salicylic acid mediated signaling pathway
  • red/far red light signaling pathway
  • chemoreceptor signaling pathway involved in regulation of blood pressure
  • sphingolipid signaling pathway
  • hydrogen peroxide mediated signaling pathway

AI: Rename children of intracellular signal transduction from pathway to 'cascade'. These are terms where they are called pathway but don't begin with a receptor, and are really 'bits of pathways'.


3. Naming for terms connecting the receptors with their downstream cassettes.

It was unanimously agreed to go with the wording of:

  • insulin receptor signaling via the phosphoinositide 3-kinase cascade


4. Discrepancy in definitions of receptors vs receptor signaling pathways

Alex: This is probably ok because in the process you're talking about the EGFR protein, but in the function, you're talking about a specific activity.

Becky: There's still discrepancy as to whether we talk about:

  • A ligand binding to a(ny) receptor
  • A ligand binding to a specific receptor
  • A receptor binding to a(ny) ligand.

Becky emailed Chris M about the problem. He came up with a diagram that would involve terms for signaling via the receptor, terms for signaling via the ligand, and terms for signaling via a particular ligand/receptor combination.

AI: Becky will generate a list of all pathway process terms and their definitions. Same for the receptor function terms. We will go through them and see if the discrepancy is ok or needs to be standardised.


5. Morphogen activity

Ruth would like a term for ligand/signal/signal initiator activity/morphogen that distinguishes it from the other receptor binding terms. It was decided in the last RefGenome call that 'receptor binding' was sufficient.

Alex says the wnts could be annotated to cytokine activity, because it's a broad term.

AI: Ruth will send Alex some papers to ask his opinion on whether cytokine activity is a suitable term.

There was no conclusion on either defining morphogen activity, or obsoleting it. But it was decided that it's current placement as a child of transducer activity is incorrect and it needs to be moved up, possibly as a child of receptor binding.


FUTURE ISSUES

There's alot of FUNCTION terms in signaling that need defining or getting rid of:

  • receptor signaling protein activity ; GO:0005057
  • receptor signaling protein serine/threonine kinase activity ; GO:0004702
  • receptor signaling protein tyrosine kinase activity ; GO:0004716
  • receptor signaling protein serine/threonine phosphatase activity ; GO:0009400
  • receptor signaling protein serine/threonine kinase signaling protein activity ; GO:0005067
  • receptor signaling protein tyrosine kinase signaling protein activity ; GO:0008268
  • receptor signaling protein serine/threonine phosphatase signaling protein activity ; GO:0005081

etc etc

AGENDA

  • 1. Wnt signaling- is it ok to split into canonical and non-canonical, and how do we divide up existing terms if so?

http://sourceforge.net/tracker/?func=detail&aid=3023417&group_id=36855&atid=440764


  • 2. intracellular signaling is still a mixed bag. How can we clean it up? Can we go through each child during the conference call and decide whether it should stay or have a new parent, or be modified.


  • 3. naming for terms connecting the receptor and intracellular components- we need to agree on naming before I add in any more terms. It currently stands at, E.g.

phosphoinositide 3-kinase cascade involved in insulin receptor signaling | GO:0035558. The process whereby a signal is passed from the insulin receptor to components of the phosphoinositide 3-kinase (PI3K) cascade, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.

Current suggestions for rewording (open to further suggestions):

  • insulin receptor signaling through the phosphoinositide 3-kinase cascade
  • insulin receptor signaling via the phosphoinositide 3-kinase cascade
  • insulin receptor signaling pathway through the phosphoinositide 3-kinase cascade
  • insulin receptor signaling pathway via the phosphoinositide 3-kinase cascade
  • phosphoinositide 3-kinase cascade downstream of the insulin receptor


  • 4. definition of receptor (FUNCTION) vs receptor signaling pathway (PROCESS)- we're not consistent at the moment. The receptor is defined as 'combining with x to initiate a change in function. But the signaling pathway terms are described as 'the x receptor combining with any of its physiological ligands....'. I've written to Chris M to see if he has any inspiration. They're not consistent at the moment either.


  • 5. morphogen activity. It needs a definition and a new parent. It's currently a child of 'signal transducer activity' which is defined as 'Mediates the transfer of a signal from the outside to the inside of a cell by means other than the introduction of the signal molecule itself into the cell', which is clearly wrong parentage. Should the term even be kept?

See https://sourceforge.net/tracker/index.php?func=detail&aid=3026415&group_id=36855&atid=440764.

    • One suggestion is to create a new term 'signal ; GO:NEW'.


  • 6. Go through existing signaling SF items to get a resolution/AI.

http://sourceforge.net/tracker/?func=detail&aid=3026790&group_id=36855&atid=440764 (neg reg of apoptosis via canonical Wnt signaling)

http://sourceforge.net/tracker/?func=detail&aid=3025823&group_id=36855&atid=440764 (receptor internalization involved in Wnt receptor signaling pathway through beta-catenin)

http://sourceforge.net/tracker/?func=detail&aid=3025898&group_id=36855&atid=440764 (Wnt receptor signaling pathway through beta-catenin involved in...)

http://sourceforge.net/tracker/?func=detail&aid=3023417&group_id=36855&atid=440764 (canonical/non-canonical)

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