wiki:PombasePlanningMeetingMinutes20110301

March Pombase planning meeting 3 pm Tuesday 1st March

Sanger Seminar Room, Sanger Building, Tennis Court Rd

Present VW, SGO, MAH, KRM, JB, PK, DS, MMcD

  • 1. Review of Jan action items
    • i) AI Val to provide feedback on front-page mock-ups (I will suggest some style changes but run them by you all first)
    • ii) AI Val provide feedback on front page content directly to Mark
    • iii) AI Val to meet with Mark to discuss mock-up content and take over maintenance of static content
    • (i) – (iii) in progress (see 2 below) except taking over content maintenance which may wait until all curators can be trained simultaneously
    • iv) AI Kim to prioritise full Chado load, In progress see 3 below
    • v) AI Val to discuss phenotype model with Jurg, In progress see 5 below
    • vi) AI Val follow up use of tool by GO consortium
    • vii) AI Val follow up potential use of tool by Dictybase
    • vi and viii Done, but will report responses at next meeting
  • 2. Mark demo website static content
    • AI Mark to implement requested content changes, send around URL to main site screenshots of prototype gene page
    • AI All, Have a look sites and suggest any revisions (only for the structure and functionalitly, Midori and I will revise the content)
  • 3. Chado and Ensembl loading progess (Kim & Mark update)
    • In progress
    • AI Val to identify edge cases
    • AI Val to identify potential sanity checks for Kim
  • 5. Specific plans for curation group for next month
    • AI Val Finishing phenotype analysis for the Nurse lab
    • AI ValWrite? training session for new curator/ Mark and Midori Hope to run this in about a month…..
    • AI Finish tidying data for migration
    • AI Refine and describe annotation extensions
    • AI Val Import and annotate new genes and gene structure changes from Broad data, Need to do this once the Broad provide the reduced set of changes. Needs to be done before a sequence update, and before the beta realease
    • AI Val EMBL resubmission. This will allow all of the new genes/ gene structure changes to propagate through to Uniprot/Pfam/Interpro? etc (At present UniProt are missing a number of protein coding genes and the gp2protein file is very out of date)
    • AI Val/Kim? identify edge cases for Mark
    • AI Val GO update (not updates since OCT)
    • AI Val Ortholog table update (new genes and missing genes)
    • AI Val Sequence update and versioning Versioning for Ensembl will start Pombase 1.1 where 1. Is the sequence assembly version and .1 is the annotation version. We will backwardly name the GeneDB files GeneDB 1_date GeneDB 2_date (it will be impossible to figure out all of the annotation versions (almost 1 a week for the past 6 years)
    • AI Midori and I will scope out a proposal for the phenotype model in the next few weeks
    • AI Midori will write a proposal for the phenotype ontology and start development
    • AI Midori provide obo edit training (me and Flora Logan-Klumpler who is based at the Sanger curating T. brucei but works for Mark Carrington at the university) She wants to use the curation tool, and create a phenotype ontology for T. brucei
  • 6. Timelines
    • Target for the Beta release is now Mid-May (let's say Monday 16th) running in parallel to GeneDB
    • Still aiming for "PomBase" launch at fission yeast in international meeting in Boston 25-30 June 2011
  • 7. Curation tool update, (name?)
    • AI Val circulate “names ideas” list
    • AI Kim will do a bit more work on the curation tool this month so we can start to use it
  • 8. Variation data
    • AI Jurg to send sample data to Dan
  • 9. Appointments (Jurg)
    • Antonia Nilsson to start at UCL 1st July
    • AI Val to arrange training at Cambridge (need to book space)
  • 10. Liftover
    • We may provide a “liftover” tool in the long term but it’s low priority. We revisit this later.
  • 11. Upcoming meetings
    • BYG 23-25 March
    • AI Val and Midori to attend, preparing a poster about community curation
    • 6-7 April Ruth's annotation workshop UCL
    • AI. Val needs to discuss this with Jurg
    • Pombeclub 10 May AI Val presenting, will talk about the using ontologies for curation and the new phenotype ontology (probably), or just an overview of what we are doing
    • GO consortium 19-23 May
    • Val and Antonia may attend if GO will pay. Otherwise I will attend remotely and we will go to the next meeting in person
    • Pombe 2011 June 27-30
    • AI Val Midori Mark and Antonia will attend Prepare 3 poster abstracts/posters:
      • Val/Midori? Community Curation
      • Midori The phenotype ontology and Curation
      • Mark Computational infrastructure (Chado/Ensembl?) make this as “un-techy” as possible And try to show some of the display features
      • AI Val will also try to arrange talk/demo/workshop but will probably be selected for a workshop talk from the abstracts
  • 12. Publications
    • NAR issue
    • AI Val mail Micheal Galperin to book a slot
    • 10th anniversary of genome (Feb 2012)
    • AI Val Think about review/update for yeast phenotype ontology/annotations
    • AI Midori is already planning this
  • 13. Access statistics Will be available
  • 14. AOB Artemis course April, a little early for Antonia, consider next course
  • 15. Date for next meeting
    • AI Hayley to set up doodle pole for April
Last modified 9 years ago Last modified on Jun 16, 2011, 10:56:35 AM