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'.

22nd September

Participants: David Hill, Jennifer Deegan.

Lots of 'response to hormone' terms have been moved under 'system hormone signaling'. We started by looking at those. We had a good discussion about standardization of these terms. There are some problems with the 'response to X' and 'detection of X' terms that are quite fundamental and need to be worked out before we can proceed.

We started with this:

[i]systemic hormone signaling
---[p]response to hormone stimulus
------[i]detection of hormone stimulus
------[i]response to auxin stimulus

Generic signaling

1) The signal is sent.
2) The signal travels to its destination.
3) The signal arrives at its destination in such a way that the receiving organism or cell is now aware 
   of the presence of the signal. This may mean that a signal protein has bound to a receptor, or an 
   electromagnetic (light) wave has been absorbed by a photoreceptor, or there may be some other mechanism. 
4) The point of first contact usually sends a further message via some other mechanism, down a chain to 
   the place or process where the signal will be acted upon. 
5) The signal message arrives at its final destination, which is the place where changes need to be made 
   to cause an appropriate response in the organism. 
6) The organism responds. 

A real example

In the effect of light approaching a plant shoot from the side and causing bending.

1) Light exits the sun or a light bulb.
2) The light travels through space and hits one side of a plant. 
3) The light is absorbed by a photoreceptor at the tip of the plant, on only one side of the plant.
4) A message is sent from the photoreceptor via auxin to a place a centimetre down from the tip of the shoot, 
   on the other side of the shoot from where the light was absorbed. 
5) The auxin signal arrives at its destination and is registered in the region that will respond. 
6) Cells on the side of the shoot away from the light that have received the auxin signal elongate 
   to make the shoot bend toward the light. 

Some language questions

The question that we were considering was to do with 'response to signal', 'detection of signal', and 'reception of signal'.

Q/ Does response to signal only include step 6 or does it include everything between step 3 and 6?
Q/ Is detection of the signal a type of or part of the response. In other areas of the graph Alex has suggested that detection is a type of response, in that steps 3 and 4 together can be considered to be a response in their own right.
Q/ Does step 3 constitute the entirety of detection, or does detection require steps 3 and 4.

We got rid of the term 'response to signal'.

Should we say 'response to signal?'

Example - ethylene and ferns

Fern gametophytes are thought to grow taller and thinner when they are planted closer together. They do not detect proximity by the amount of shade falling on them, as they are not so close together as to be shaded. Instead they are thought to detect it by the concentration of ethylene in the surrounding environment. Ethylene is produced by all the individuals and so builds up more in areas of high population density.

To describe this in GO we could make the following terms:

[i]response to population density
---[p]hormone signaling involved in population density
------[p]ethylene signal transmission involved in response to population density
------[p]ethylene signal reception involved in response to population density
[i]hormone signaling
---[p]hormone signaling involved in population density

Things to note here include the idea that the elongation of the ferns is not really a response to ethylene, but a response to population density. So we should not have 'response to hormone' or 'response to signal' terms. Instead we just have 'response to population density'.

As stop-gap we have decided to rename the 'response to signal' terms to 'reception of a signal' where 'reception' is intended to mean the sum of 'detection' and 'reaction'. In other words it represents everything between steps 3 and 6 in the first example. We may need to come back and change the word 'reception' but the new def is fine so we will make the change and retrofit the name.

Action item: Implement the new reception name and standard def on the signaling terms.

New standard definition for 'reception of a signal' terms:
Def: The process whereby the cell or organism changes its state or activity as a result of a signal. A signal is an entity that conveys information.

Action item: Put in the second sentence for the 'reception of hormone' defs. 'Abcissic acid is a hormone that does this and has that structure.'

We also need to make slides for the consortium meeting to show the decisions we have made about the top signaling terms, and the questions that we have raised.