Managers 18June08

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GO Managers, Weds. June 18th, 2008 8a.m. PDT, 9a.m. MDT, 10a.m. CDT, 11a.m. EDT, 4p.m. BST

Agenda/chair: David

Minutes: Midori

Present: Jennifer, Judy, Midori, David, Pascale, Michael, Jane, Chris

Current items

MF-BP links

Discussion of mf-bp links started last meeting. See details at

Judy - adding more specific processes should work; connect function to specific term or parent as appropriate [paraphrase by MAH]. After some discussion, all agreed on this point.

A few discussion highlights:

  • Basically have 'photosynthetic electron transport' as a parentt term to these 5 specific sub-types
  • Links would then be between sub-type terms and the function terms; i.e., BP:photosynthetic electron transport transferring from P700 to Ferrodoxin Sulphur protein ['photosystem I'as synonym?] would then link to MF:electron transport: transferring from P700 (photosystem I) to Ferrodoxin Sulphur protein (judy)
  • We already have some unwieldy term names. (Midori)
  • We can fall back on "taxon-type" names as a last resort, as we did for some formerly-sensu term. (David)
  • Definitions and names must mention the steps that distinguish one (e.g.) photosynthetic electron transport pathway from another. (David et al.)
  • Most important to get biology right first, then worry about term names. (David, to general agreement)

Agreed to create specific process terms where necessary (option 1 from June 4 minutes).

Chris also noted that a discussion yesterday was prompted by worry that ontology group hadn't discussed the concerns among themselves before bringing to managers.

Action: Ontology developers (mainly Jen and Harold at present) to continue collecting MF-BP links, creating new process terms as needed. Worry about making up nice term names later.

Regulates links, MF/BP and MF/MF

Email to gofriends about impending MF-BP, MF-MF regulates links.

Last time, we left the email draft in Chris' hands, to add details of technical implications.

Chris - more email in meantime about implied relationships; deserves serious consideration. [general agreement]

We have announced an implementation date, Nov. 30, in the last newsletter, but could delay implementation (MA notes that there will be one more newsletter before then).

After some discussion about what we should and shouldn't include in the next announcement, we decided that Chris should put more content into the latest draft of the email; others (e.g. David, Tanya) can then work on its organization.

Action: Chris to add content to existing email draft.

Next GO meeting

Montreal, October 21-23 (GOC 21st-22nd; SAB 23rd)

Action: Pascale will sign contract this week.

Decided not to add annotation meeting (RefGen or more general), since we already have a full GOC meeting and SAB. Also, Mike C has scheduled first virtual annotation meeting for July 18th (just before ISMB Bio-Ontologies SIG).

Reference genomes progress report

Available at RefGenProgress_2008-06-18

Report on Avian Annotation Meeting

Organized by Fiona McCarthy; the meeting was a resounding success. Minutes available in Outreach_May_2008_Report

Participants would like to see something similar at PAG.

Any other business

Ontology development report from Jen

  • Jen will chat with Chris about taxon work
  • Review in Nature on drug transporters - Jen has supplementary material from author Paul Dobson to trawl for terms and annotations; sent to Emily; Judy also interested
    • Action: Jen to send supplementary data to Judy
  • Manchester group also interested in another Aspergillus annotation meeting at EBI (Steve Oliver organizing)

Muscle paper

  • Barry Smith wanted more detail on ontology development methods (added)
  • 2nd reviewer expected research article; responded to editors that paper should be short communication

Chris - ontology development papers should have research slant: demonstrate practical value of ontology work, e.g. annotations before and after (but David notes that annotations trickle in after ontology work done).

Next call

July 2, 2008, 8 AM PDT/11 AM EDT/4 PM BST

Agenda: Midori; Minutes: Pascale

Summary of Action items

  • Ontology developers (mainly Jen and Harold at present): Continue collecting MF-BP links, creating new process terms as needed, and postponing worry about nice term names
  • Chris: Add technical content to MF-BP link announcement email draft
  • Pascale: Confirm bookings for GOC and SAB meetings
  • Jen: Send supplementary data from Paul Dobson drug transporter review to Judy

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