Managers 04June08

From GO Wiki
Revision as of 06:33, 3 June 2008 by Jdeegan (talk | contribs)

Jump to: navigation, search

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

Agenda/chair:

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:

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 (Viridiplantae) and cyanobacteria
photosynthetic electron transport has_part electron transport, transferring from P680 (photosystem II) to plastoquinone in organisms with chloroplasts (Viridiplantae) and cyanobacteria
photosynthetic electron transport has_part electron transport, transferring from cytochrome complex to plastocyanin in organisms with chloroplasts (Viridiplantae) and cyanobacteria
photosynthetic electron transport has_part electron transport, transferring from plastoquinone to cytochrome b6/f in organisms with chloroplasts (Viridiplantae) and cyanobacteria
photosynthetic electron transport has_part electron transport, transferring from plastocyanin to photosystem I in organisms with chloroplasts (Viridiplantae) 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

Back to minutes list