Electron transport function-process links

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Electron transport meeting 17th September 2008

Participants: Michelle Gwinn-Giglio, Debbie Siegele, Ingrid Keseler, Jennifer Deegan.

We considered two possible ways of making mf-bp links in the photosynthesis area, as below.

Version 1

In version 1, we would have a sensu-style arrangements, where a different process term was made for each different form of the given process. The different forms of the process would be distinguished by the different sets of constituent functions.

[i]photosynthesis chloroplast-type (oxygenic)
---[has_part]this chloroplast-type function
---[has_part]that chloroplast-type function
---[has_part]the other chloroplast-type function
---[xxx]a function that occurs in both types
[i]photosynthesis in bacteria (anoxygenic) 
---[has_part]this bacterial function
---[has_part]that bacterial function
---[has_part]the other bacterial function
---[xxx]a function that occurs in both types

Caveats: halobacterium have a different set of enzymes and are archaea. Different even from the anoxygenic bacteria, so we may need an Archaea type as well.

Would it make more sense to derive this information from the annotations? Putting it together without the annotations would take a long time.

Version 2

In Version 2, a single process term would be made to cover all forms of the given process, and all the functions that make up any form of the process would be placed under that single term.

---[part_of]this chloroplast function
---[part_of]that chloroplast function
---[part_of]the other chloroplast function
---[part_of]this bacterial function
---[part_of]that bacterial function
---[part_of]the other bacterial function
---[part_of]a function that occurs in both types

Version 3

During the meeting a third option was proposed in which the GO Consortium simply provides tools that enable users to derive their own mf-bp links by mining the annotations.

If a protein is annotated to both function and process then it is an indication that the function is part of the process. How often is the protein co-annotated? If it's a lot then that is a clue. Use the amazon model - 'people who bought that also bought this'. We can also show that a function coincides with a process in a given set of organisms. Action: Jennifer to ask Chris is it is possible to try this just for this process using an SQL Query.

We tried to use OBO-Edit to find the functions that would be constituents of the photosynthesis process term, but this proved to be quite difficult, even when looking under just oxidoreductase.

Action: Debbie will try to find the E.C. numbers for the functions so we can find them easily in oboedit.

General thoughts

During the discussion many people felt that version 1 was a very labour intensive plan and that it was not a feasible proposition. Version 2 was thought to be more feasible, and version 3 certainly the simplest approach.

Conversely, it was pointed out that is use in distinguishing between oxygenic and anoxygenic photosynthesis if this could be done. They archaeal processes may complicate this. We need a sometimes_part_of relationship. it's the always or never part_of that is very hard to deal with.

Questions to send back:
What are the use cases?
Who wants these links?
Why do they want them?
(Ask David and Suzi which BRCs and why.)
If it was just the NIAID BRCs then they may no longer want them.
BRC update:
They are all about to have funding reviewed.
JCVI group does GO annotations.
ERIC group does too.
Biohealthbase in texas also do them.
JCVI sends in annotations but the others do not. Some groups do
not do manual annotation at all. This is unlikely to change.

Q/ Can we invite Ingrid to the consortium meeting? She is in Peter Karp's group in ecocyc.

Next meeting: How about thursdays instead of wednesday. Jen to write to list.