Managers 05Nov08

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GO Managers, Weds. Nov 5th, 2008 8 a.m. PDT, 9 a.m. MDT, 10 a.m. CDT, 11 a.m. EDT, 4p.m. GMT

Agenda/chair: Pascale
Minutes: Jane

Participants: Suzi, Midori, Jen, Pascale, Amina, Chris, David, Jane (apologies from Michael)

Action items carried over

Suzi: A mail on these UniProt ids was sent today by Henning to the reactome list. Suzi to forward to managers’ list. (Note: she wrote to say that this had been done, but the email did not arrive. Please send again.) DONE
Jennifer: to change the photosynthesis discussion over to this list and inform the GO list. NOT DONE

Chris : New gene association file columns: Can all groups implement? see Managers_24Sep08#New_gene_association_file_columns
NOT DONE :

  • Chris will email developers and annotators


Discussion items

  • Jane: Having read the advisory board's comments, should we stop producing the newsletter? We're due to start putting together the Nov edition now. How about an RSS feed? Pamphlet?
    • Advisors not keen on newsletter. No more newsletters. Announcements should be made via RSS feed and GO friends. Pamphlet - professionally designed? Use EBI agency? Get costing [Jane].
  • Jen/Midori: How much do "we" know about the Animal Trait Ontology (ATO; http://www.animalgenome.org/bioinfo/projects/ATO/)? Hein van der Steen is visiting EBI next week, and Emily has asked whether there's any interaction between this project and PATO. (Emily is also getting in touch with George.)
    • Analogous to the mouse phenotype ontology. George should also be involved, as he's been involved with the mammalian phenotype ontology. Plan to decompose ATO terms to make XPs for PATO.

Other issues

  • When do we need to make a decision about the next GOC meeting? - GO top need to make a decision.
  • Ruth and Varsha have offered to host a GOC meeting at University College London (UCL) in September. Ruth will supply cost estimates and possible dates in the next couple of weeks [Jane].
  • OBO-Edit - process for releases:

Suzi: shouldn't be down to software developers to decide whether release should be made. We need to decide on a SOP for releases.

Midori: feels the only reason the release not out is because there are still a lot of bugs. Developers doing a good job responding to issues, but still some way to go. We probably need more testers to get it out there.

Chris: we're hindered by our restriction for not using beta software for general editing - convert to non-beta version for public file.

Midori: don't think this is the time-limiting step - people don't have time to do proper testing.

Suzi: what do we need to do to get this software out there?

Jane: use model used for OE1 - divide up features amongst WG, sign off on features for release.

(some discussion of of why reloading into OE1 is necessary before committing file and whether we could commit to editors file using OE2)

Chris: proposal: make a more rigorous sanity-checking step between copying from editors file to live release file. Use obo2obo so file automatically saved in OE1 format. Also include additional tests for errors in ontology.

(some discussion for the process of editing xps - in essence Chris can't do it on his own any more and needs uptake from the editors. They agreed to start working with them for real.)

Action Items

  • Jane: to get costing for GO pamphlet from agency EBI used.
  • Emily: to contact George to come over for the meeting with Hein van der Steen about ATO.
  • GO top: make a decision about location of next GO meeting(s).
  • Amina: make list of OE features for testing
  • Midori: take Amina's list and parcel out to WG members
  • Chris: interact with production group about adding sanity checks/obo2obo when going between editors file and public file
  • Ontology developers and Chris: figure out process for using xps live

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