Signaling Meeting Minutes April 2008 -

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Meeting time: 3pm Monday afternoon UK time. 10 am MGI time.

March 2008

Participants: Jennifer Deegan and David Hill

David and Jen met to review Jen's initial structure. David suggested that the general grouping terms could be done along the lines of pre-existing terms in GO. Chemical properties might follow Chebi and location and distance might follow the development model.

Action: Jen will work on this before next meeting.

30th April 2008

Jen and David have agreed to have a 1 hour meeting once a week to get David's input into what Jen has done during the week. Jen will carry out action items in between. One important part is to align this with the regulates work.

One first step is to make a list of the signaling pathways already in the ontology and what they regulate.
Action: Jen is to make a table of signaling pathways and the things they regulate and put them in a table.

2nd May 2008

Participants: Jennifer Deegan, David Hill.

At our previous meeting a couple of weeks ago we realized that we had a big problem with capturing signaling where a signal goes through the blood stream and reaches everywhere in the organism but is not acted upon by all parts of the organism. Physiologists call this long-distance signaling and Jen was keen to capture the fact that the signal goes to all parts of the organism (organismal signaling), whilst David was keen to stick to capturing where the signal comes from and which cells act on the signal (tissue-tissue signaling). Jen discussed this with Tim Deegan who explained the similarities between the signaling in organisms and signaling in computer networks. In computer networking they already have terminology for this, and they are able to describe signals based on both the areas that a signal reaches and the parts of the system that react to the signal. A 'broadcast signal' is one that reaches all points in the system, even though only a selection of parts respond to the signal. A 'directed signal' is one that is sent from one specific place to another, and then there are also 'unicast' and 'multicast' signals.

Jen and David have discussed these ideas and Jen is going to look into making a structure to capture this kind of information, without some more biological words (perhaps systemic signaling?). Jen is taking care of signaling, which is the travel of a signal to the location of action and David is going to deal with signal transduction, which is what cell biologists call the thing that happens when a signal arrives at the cell where it will have its effect. Jen is to look into including all the different kinds of signaling, including light, chemical, mechanical, sound and so on. If she can get the structure down to the level of detail where it will meet up with the signal transductions lever e.g. of retinoid signaling then that will be good as it will set the scene for David to pick up later.

23rd June

Participants: David Hill, Jennifer Deegan.

We discussed the new signaling terms that had been made. We made some rearrangements.

  • Behavioral signaling is now to be included under the top signaling term.
  • The top signaling term is to include all parts of signaling from inception to the end of signal transduction (which is the process whereby the signal is received and acted upon.)
  • We need to be careful of terms that cover only the transport of a signal and that will not involved any gene products at all.
  • We decided to keep the term 'system signaling' as this will involved gene products in ong range nervous system signaling, though it may not in hormone signaling.
  • In old terms that say 'X-mediated signaling pathway' the term means the signal transduction part of that where the signal is received and acted upon.


30th June

Participants: David Hill, Jennifer Deegan.

Worked on top nodes of signaling.

Action item: David will define what he means by 'at the level of'.

21st July

Meeting with David to define the top terms under signaling.

David has defined 'at the level of' such that 'processes occurring at the level of the heart' means 'processes carried out by the heart.


8th August 2008

Some notes for discussion.

Would this be a good standard def for the signal transduction terms?

The series of molecular signals initiated upon sensing of [signal].

Some of the signal transduction terms are oddly defined and need a standard def.

I have put the hormone ones under the new general hormone term.

20th August

Participants: Jennifer Deegan, David Hill.

We have checked the definitions and positions of the top signaling terms and they are fine. Now Jennifer will look for all the child terms that will go under these and next meeting we can work out exactly how they should be related. Particular care will be taken over those parts of the graph mentioned in the many open sourceforge items in this area.

Later:

Now all terms including the words 'hormone' and 'signal' are under 'systemic hormone signaling'. Some other hormone terms without signal in the text have been put under a temporary grouping term that is under 'systemic hormone signaling'.