View source for Managers 04June08

GO Managers, Weds. June 4th, 2008 8 AM PDT, 9 AM MDT, 10 AM CDT, 11 AM EDT, 4 PM BST<br>

Agenda/chair: <br>

Minutes: 

Present: 

== Action items from last meeting ==

'''Managers (especially call chair):''' Meeting agenda should be available on Monday (48 hours in advance)

'''Managers:''' Post progress reports on Wiki with links back and forth (e.g. from call agenda to report); refer to wiki during call

'''Managers (especially call chair):''' ‘Hot topics and Concerns’ should be at the top of the agenda

'''Managers (especially call chair):''' The chair is empowered to manage the call; "Chair trumps PI".

'''Managers:''' Digressions become an action item, not to consume the time of the manager’s meeting

'''All:''' GO-paid staff should check with PIs before writing papers or going to meetings.

'''GO-top:''' Discuss meeting frequency, who should come, etc.

'''GO-top:''' Discuss Jane’s letter about review for Human Genetics

'''Jen:'''Put together bigger picture of function – process task (Jen is on holiday this week but will do this for the next meeting.)

==Agenda items==

===Hot Topics and Concerns===


==mf-bp links==

===Report on current status by Jennifer Deegan.===


The biological process "photosynthetic electron transport" is to be connected to all its consistuent molecular functions in the function ontology.
http://www.life.uiuc.edu/govindjee/photoweb/art/electron-transfer.jpg

Problem: The same process has different constituent functions when it happens in different taxonomic groups. For example photosynthesis in chloroplast-containing organisms and cyanobacteria is a bit different from photosynthesis in other photosynthetic organisms (e.g. purple bacteria).

As I understand it Chris has an idea of how we could manage still to make the mf-bp links without putting taxon information into the actual ontology file. I think his idea is to make a separate file that would contain the mf-bp links and the taxon constraint information. I guess it would be something like:

{| border="1" cellpadding="5" cellspacing="0"

!Process||relationship||function||taxon||restriction
|-

|photosynthetic electron transport||has_part||electron transport, transferring from P700 (photosystem I) to Ferrodoxin Sulphur protein||in organisms with|| chloroplasts and cyanobacteria
|-
|photosynthetic electron transport||has_part||electron transport, transferring from P680 (photosystem II) to plastoquinone||in organisms with ||chloroplasts and cyanobacteria
|-
|photosynthetic electron transport||has_part||electron transport, transferring from cytochrome complex to plastocyanin||in organisms with|| chloroplasts and cyanobacteria
|-
|photosynthetic electron transport||has_part||electron transport, transferring from plastoquinone to cytochrome b6/f||in organisms with ||chloroplasts and cyanobacteria
|-
|photosynthetic electron transport||has_part||electron transport, transferring from plastocyanin to photosystem I||in organisms with ||chloroplasts and cyanobacteria
|-

|}

His alternative idea is to  subclass the process term  using non-taxon differentia as we do now with the old sensu terms. For example "chloroplast-based  photosynthetic electron transport" however, I can't see how this could be done across the board without making really unusable clunky names. This does not seem a viable option to me. 

I would like to hear people's views.

Two further questions:

*Can we make these kinds of generalization when scientists have not checked all taxonomic subgroups? 

* Are we prepared to take on the amount of work that would be involved in situations where there may be many many different variations in different taxonomic groupings.

*Are we instead proposing only to cover a small number of well known and researched species, and are we sure that the information is fully available in those cases?

or as Chris says: 

- how much time should we spend on each process term in GO?
- how important is it to get each individual function step as the  process is instantiated in a given cell? i.e. are gaps a problem
- how important is it to get broad coverage across different  organisms or variations of a process? i.e are "representatives" enough? 

It may be that we are just not able to make the bp-mf links because of the complexity involved, but I think we have now reached a place where it makes sense to stop and discuss it before using more time on the pilot project. 













===Progress of note===

==Next call==
June 18, 2008, 8 AM PDT/11 AM EDT/4 PM BST

Agenda: ; Minutes: 

== Summary of Action items ==

[[GO_Managers_conference_call_minutes|Back to minutes list]]