Managers 4Nov09

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Participants: David, Pascale, Jane, Jennifer, Mike, Midori, Suzi

Agenda: Pascale

Minutes: Midori

Action items from previous calls

  • David, Chris: organize the xp webex. (There has been a great tutorial by David OS at the Buffalo Ontology meeting)
    • Took place Monday (Nov. 2); went pretty well. David will check with Tanya to make sure Donghui is up to speed; we think we've covered everyone else before and/or during Monday's session.
  • Jane: email Amelia to put xp documentation (for GO users): DONE see GO Structure and XPs
    • Suggestion: add step-by-step instructions for curators on how to make XPs - start with regulation; also include CC-xp-self. Action: David & Tanya (regulation); Jane (cc-xp-self)
  • Midori awaiting webex on XPs before sending announcement mail.
    • Will do now that webex session has happened. Implementation date discussed; decided on two months from now -- January 5, 2010 -- with a reminder two weeks in advance. Also do news item. DONE. Announced release date January 18, 2010, to allow two-week reminder to go out just after New Year.

Discussion items

Function-process proposal

[David, Tanya, Chris and Jane] - in progress. 

Jane - concerned that people don't understand implications

Pascale - would be good to have more formal presentation for annotators

David - annotators shouldn't change their current practices

Pascale, Suzi - GAF inference does have potential to change annotation practice -- annotate only to MF because BP annotation is implied by MF annotation plus MF-BP link

Some DBs, e.g. SGD, MGI, not ready to import inference GAF file. (This is the file that instantiates BP annotations inferred from MF plus links.)

Some discussion of loading files into GO DB and MODs ... which groups can take GAF(s) from external source and incorporate it?

Mike - using the file, not just loading, is the issue. MODs already take GOA annotations for their organisms.

More discussion of timing, priority for MODs, etc. Need a MOD group to test inferred-GAF loading. David will check whether MGI can test.

David & Tanya have added about 500 MF-BP links. The work isn't trivial, so they want to confirm that it is where they should focus effort (there's plenty of other stuff to do!). Only one BP-specific MF term so far.

Implications for annotation discussed again. MF-BP links made on basis of biology, not annotation; no different from any other ontology changes. (Annotations can help us spot ontology problems, and vice versa.)

Jen - we need a coherent summary of where we are now and what the MF-BP plan is (and that it's not to merge MF into BP any time soon).

Write a paper? Describe advantages of MF-BP links. Makes ontology development more logical (better error detection, etc.); annotation more intuitive and efficient; more consistency with other pathway resources such as Reactome. Also define processes w.r.t. the functions that occur.

Decision: Continue adding MF-BP links. Action: create and maintain documentation of motivation -- also useful as basis of paper. Jen will circulate some email she's saved, and convert to wiki page.

Renal development meeting

Judy said there are funds for those content meetings; what next?

David and Yasmin have discussed further. Yasmin has emailed experts in Edinburgh, trying to arrange meeting for January or February. Doug, David, and probably Tanya will attend.

Suzi - could Pascale, Kara, or Mike Livstone also join? Not much annotation done at these meetings, but could try it ... [some discussion] Remember that many terms actually get added after, not during, the meeting.

More discussion on possible ways to get expert input into annotations as well as ontology, e.g. two-stage meeting, or annotation follow-up meeting 1-2 months later. People like the follow-up idea.

Annotation camp in Geneva

Swiss-Prot wants to do it; we're looking at dates around mid-April but that still needs to be confirmed. It may be easier after May 21 (end of the classes). They are suggesting June 14-18 to join with 'la fete de la musique'

They may be able to get about 10,000 CHF from the KGF ( This requires to open the meeting to the industry - maybe we can add a day or half a day of training?

Pascale will continue looking into this, and report back to managers.

EBI GO MySQL mirror

This was never supposed to be the main server and has had lots of outages. Dan will try and reduce downtime - but what is the longer term plan for the MySQL server? [Jane]

Mirrors at Berkeley, Princeton, and Northwestern under discussion. Berkeley has firewall issues; can use GOOSE or PAINT but not command-line or programmatic access there. Princeton motivated by PAINT bandwidth. Pascale - NU may also have firewall issue.

Try to keep EBI mirror up in the meantime! Jane will discuss with Dan.

Jennifer Deegan - Maternity leave

I am planning to go on 1 year of maternity leave on 1st March 2010.

I would like to prioritize my last last four months of work to round off the current set of big projects as far as possible:

Proposal for comments:

  • Put the 500 fully vetted terms from biological_process_self_xp set in the queue for release. The remaining difficult terms can be worked on and added later on.
  • Signaling group would like to polish the top terms, and put in just one or two signaling pathways to completion as an example of how others might be done. We hope to finish this and commit before March.
  • Taxon checking system final details were agreed at the Consortium meeting in a break time amongst Judy, Emily, Chris and me. I would like to prepare and send off a manuscript for publication of this system before I go.


Regulates paper - needs biology-perspective introduction, with reasons why we did the work and how it benefits biologists (as well as ontology developers).

Action items

  • Midori: Send cross-products announcement (GOfriends email, news item) - DONE
  • David, Tanya, Jane: Compose wiki documentation for ontology editors, with step-by-step instructions on making cross-products
  • David: Check whether MGI can act as the "beta-tester" for incorporating GAFs inferred from MF-BP links
  • Jen: Draft wiki page to summarize motivation for MF-BP links
  • Managers: Comment on draft proposal that Suzi will circulate (content meetings, RefGen annotations, etc.)
  • Pascale: Continue organizing Geneva annotation camp
  • David, Tanya, Chris: Get back to the regulates paper draft; compose introduction. (Also Midori & Jane)

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