Managers 27Jan10

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Participants: Pascale, Midori, Jen, Suzi, Judy, Mike, Jane

Agenda: Pascale

Minutes: Midori

Action items from previous calls

  • David, Tanya, Jane: Compose wiki documentation for ontology editors, with step-by-step instructions on making cross-products - DONE.
  • Jen: Draft wiki page to summarize motivation for MF-BP links - in progress
  • Jane: will send another email to clarify that not everyone has to start using ext GO file - we're only interested in inter-ontology links DONE.
  • Midori: release first set of cross products, Jan 18 (regulation) DONE.
  • Midori: add this to GO news on Monday. DONE.
  • Midori: will create a new section in the Ontology development page for proposed content dev projects. DONE.

Discussion items

TCDB into GO

Asking for support letter [Jen]

Jen and Milton Saier have drafted letters; Judy will bring to GO-top call, and then they'll send it.

Term changes and term provenance issues cont.

I've been making a list of the types of changes I've been making over the last couple of weeks, to see how we might want to track changes/history/rationale [Jane]

needs Chris, so carry over to next meeting

Date for GAF2.0 switch

Could the managers agree on a date for switching the primary GAF format from GAF1.0 to GAF2.0? It was originally going to be January. How about 1st of May for the new date? This would give a 4 month alert for users to update parsers (Emily)

Emily will compose and send an announcement, with May 1, 2010, as the date.

GOA to create Gene Product information file to supplement GOA GAFs

Would the managers be happy if GOA were to start creating a supplementary file for UniProt GAFs (primarily to store Swiss-Prot/TrEMBL DB subset information), this would fix AmiGO's issue with GOA's usage of column 1. The file would supply all information that the proposed gene product information file (suggested by Amelia) would have. However in addition to the DB subset information, GOA would also like to use this file to indicate when proteins were annotation targets of the Reference Genome project and where protein annotation is complete (Emily)

Discussion of
  • what would be in the file;
  • how it would solve the AmiGO problem;
  • whether GOA should submit jut SwissProt subset, separate files for the subsets,
Going further requires discussion among Chris, Emily, Mike, perhaps others (e.g. Dan or Tony)
Chris to get in touch with Emily, Mike, et al.

Reference genome goals for Jan-June 2010

(Pascale) File:2010-RG-plan-V2.pdf

Enthusiastically received
Pascale summarizes content, and also suggests tree annotation meeting before annotation camp


New management organization

Proposal circulated by Suzi:

  • Ontology Development (David Hill, Jane Lomax)
  • Reference Genome Project (Pascale Gaudet, Kara Dolinski)
  • Annotation & Curation (Rama Balakrishnan, Emily Dimmer)
  • Software Infrastructure (Chris Mungall)
Jane: how will web presence, helpdesk, etc. fit in?
These are among topics that can be raised among managers whether there's a dedicated manager or not.
For now, Jane will continue to act in a manager-like capacity; review
Unfortunately, we don't have anyone well placed to share software management with Chris, although Suzi and Mike will chip in
GO-tops will contact prospective new managers confirm roles, start planning, etc.

GOC and SAB meetings

Managers should discuss what to present to SAB; what plans and goals are (long- and short-range, 5 years and ~6-8 months respectively); which of our funded objectives have been accomplished

Visualization as in Pascale's RefG plan is very helpful

Kidney development meeting

Went very well; experts got very involved; Yasmin has sent comments to Judy

Action items

  • GO-tops: Send TCDB/GO support letter
  • Emily: Send email announcing GAF2.0 on May 1
  • Chris: Discuss UniProtKB etc. issue with Emily, Mike, et al.
  • GO-tops: Contact prospective new managers
  • All managers: Prepare materials for SAB as described above

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