Managers 04June08: Difference between revisions
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{| border="1" cellpadding="5" cellspacing="0" | {| border="1" cellpadding="5" cellspacing="0" | ||
!Process||relationship||function||taxon | !Process||relationship||function||taxon restriction | ||
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|photosynthetic electron transport||has_part||electron transport, transferring from P700 (photosystem I) to Ferrodoxin Sulphur protein||in organisms with | |photosynthetic electron transport||has_part||electron transport, transferring from P700 (photosystem I) to Ferrodoxin Sulphur protein||in organisms with chloroplasts and cyanobacteria | ||
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|photosynthetic electron transport||has_part||electron transport, transferring from P680 (photosystem II) to plastoquinone||in organisms with | |photosynthetic electron transport||has_part||electron transport, transferring from P680 (photosystem II) to plastoquinone||in organisms with chloroplasts and cyanobacteria | ||
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|photosynthetic electron transport||has_part||electron transport, transferring from cytochrome complex to plastocyanin||in organisms with | |photosynthetic electron transport||has_part||electron transport, transferring from cytochrome complex to plastocyanin||in organisms with chloroplasts and cyanobacteria | ||
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|photosynthetic electron transport||has_part||electron transport, transferring from plastoquinone to cytochrome b6/f||in organisms with | |photosynthetic electron transport||has_part||electron transport, transferring from plastoquinone to cytochrome b6/f||in organisms with chloroplasts and cyanobacteria | ||
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|photosynthetic electron transport||has_part||electron transport, transferring from plastocyanin to photosystem I||in organisms with | |photosynthetic electron transport||has_part||electron transport, transferring from plastocyanin to photosystem I||in organisms with chloroplasts and cyanobacteria | ||
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Revision as of 09:31, 3 June 2008
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 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: