Managers 04June08

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


Minutes: David


Jen Midori David Pascale Jane Mike

Action items from last meeting

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

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

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

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

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

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

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

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

Jen:Put together bigger picture of function – process task SEE BELOW

Agenda items

Hot Topics and Concerns

  • Montreal GO Meeting (Pascale):

Found a nice place for Oct 21-23 (21, 22: GOC; 23: GO SAB). We could extend 1-2 days for an annotation meeting? I don't need to confirm this until some time in July but it may be easier to reserve dates now, even if we cancel later.


Are we going to tack another meeting onto Montreal? Discuss virtual meeting vs. travel in general 1) Annotation camp: Pascale wants to add another day to the meeting. David is concerned that this will make the meeting too long and people will be burned out. For annotation we need a lot of people to be present. 2) Documentation Meeting?: Maybe only a few people needed. Midori, the face-to-face meetings are nice, but sometimes we just can’t do that. In these cases the virtual meetings are the next best thing.

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.


  • 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).

Proposal 1

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

Proposal 2

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.

Proposal 3 (Pascale) Maybe we could figure out a way to capture that at the level of annotation. If there was a way to link F and P annotations, that link itself could be an alternative to the relationship we are looking for between function and process. For example:


I would like to hear people's views generally. The scientists that I have been working with are concerned, as am I, that this project is just infeasible. We would like to discuss the issues frankly before we use any more time on the pilot project.

Specific 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. All thoughts much appreciated.


Comments on Jen’s proposal for F-P links Jane’s idea use has_part relationship. Delineate the processes by using has_part. Only put links between the common function. Problem is some taxa will be missing functions. Pascale will write a proposal about linking MF and BP in annotations. Jane will also write a proposal and add it to the wiki.

Summary of RO meeting

2 things relevant to GO 
1) OBO wants a firmer more axiomatic def of regulates. Tanya, Chris and David will work on this.
2) We will begin to promote the idea that the relationship between a gene product and the 
molecular function is that the gene product has the potential to execute the function and 
the function ontology represents the execution.

Progress of note

Next call

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

Agenda: ; Minutes:

Summary of Action items

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