Managers 10Mar10

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Participants: David, Pascale, Midori, Kara, Jane, Chris, Suzi

Agenda: David

Minutes: Kara

Phone passCode: 801-561


Action items from previous calls

  • All managers: Prepare materials for SAB
    • Funded deliverables can be found in the agenda of the GOC meeting in Cambridge 2009: some questions for PIs (e.g. OboEdit/AmiGO, are cross links: cross products?)
    • 4-10 slides describing our goals and accomplishments

Discussion items

  • Brief report on the Chemical workshop that we held at the EBI last week (David, Jane, Midori, Tanya + Harold-remotely): align chemicals in GO with chemicals in ChEBI so that we can eventually rely on an external source of this information. Chris created GO-ch, which does an initial mapping of ChEBI to GO. 400 chemicals were reviewed so far by David, Jane, Midori, Tanya, Harold. They will clean the GO representation and also work with ChEBI to improve definitions, etc.
  • Jane forwarded an email from Vinod Scaria from the Mycobacterium tuberculosis annotation project. I think he has been in touch with Michelle et al (someone needs to check). The annotation group will be responsible for following up on this.
  • What is the hiring procedure for the new person at the EBI? Advert is now out. The post stays open for applications until April 11.
  • The upcoming GOC meeting:
    • Prioritization of some things Chris would like to discuss/present at the GO meeting. Including estimates for ideal length of time, but we can discuss these. We should be sure to see which topics that people who phone into the meeting are most interested in so we can plan the agenda accordingly.
      • Cross-product / logical definitions update, go/chebi xps (15 - David says longer)
      • GO-pathway database integration (15 - Chris, Harold)
      • GAF inference and Evidence codes for automated inference (5-10 - Chris, Rama)
      • Proposal for more streamlined addition of compositional terms (5)
      • GAF2 update (5-10) CJM/Rama
      • Tighter obo-edit/protege/owl integration in CL and GO (5)
      • AmiGO new features
        • New search features in AmiGO (5)
        • PAINT-style displays in AmiGO (5)
        • Improved tree view (5)
    • Wish list for discussion items at the meeting
      • linkages between GO complex and PRO classes
      • signaling

Funded Deliverables

  • Aim 1: We will maintain comprehensive, logically rigorous and biologically accurate ontologies
Year Task Status
1 Completing is_a relations Done
1 Completing part_of relations Done
3 Substitution of regulates relationships Done
3 Produce slim versions excluding specified relationship classes Done?
1 Parse implicit Cell terms from GO and resolve Parse done, waiting on cell ontology
2 Parse implicit Chemical terms from GO and resolve Parse done, alignment in progress
5 Parse implicit Anatomical terms from GO and resolve Parse done, alignment in progress
2 OBO-Edit that enables cross-links Done
3 AmiGO that supports cross-links
5 Automate inconsistency checking Done, ongoing
3 Inclusion of specialized part_of & contained_in relationships in CC Still to do
3 Inclusion of located_in & has_part relationships in BP has_part-done and ongoing. located_in-still to do
1 Programmable access to retrieve annotations Done
5 Add relationships between BP, MF, and CC Done, ongoing
5 Develop tools and protocols to maintain pathways congruency In Progress
3 OBO-Edit support for tracking changes to the ontology Done
5 OBO-Edit interoperability support Done?
5 Implementation of faster querying techniques In progress

Reference genome report

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