wiki:PombasePlanningMeetingAgenda20110418

Planning meeting Mon 18th April 2011 - Agenda


Minutes from this meeting


1. Review of action items

completed action items

  • Val to identify edge cases for Mark
  • All, identify any issues which my be problematic using proposed update strategy (none reported)
  • Val Import and annotate new genes and gene structure changes from Broad data. Needed to be done before sequence update (which needs to be done ideally before beta release)
  • Val GO update
  • Midori will write a proposal for the phenotype ontology and start development...well underway

http://pombase.svn.sourceforge.net/viewvc/pombase/phenotype_ontology/fypo.obo?view=log

  • Jurg to send sample variation data to Dan Staines (done?)
  • Midori arrange obo edit training (me and Flora Logan-Klumpler who is based a the Sanger curating T. Brucie but wirks for Mark Carrington at the university). Flora wants will be setting up the community curation tool, and is create a phenotype ontology for T. brucei
  • Kim will do a bit more work on the curation tool this month so we can start to use it...Most major features are in place and we can now use for most types of curation (HO, genetic interactions, physical interactions, modifications, phenotype), can also transfer annotations to multiple genes.....ADD MORE
  • to arrange training at Cambridge (need to book space)..Kathryn Lilley's room at Jesus College will be borrowed in July
  • BYG Val and Midori attended, preparing a poster about community curation
  • Val needs to discuss 6-7 April Ruth's annotation workshop UCL this with Jurg (Did not attend in the end as Antonia was not available)
  • NAR issue Val mailed Micheal Galperin to book a slot. August 15th deadline, with the understanding that a delay of 1-2 weeks would be OK, but probably not much more.

ongoing items moved to tracker

  • Val to identify potential sanity checks for Kim - PART DONE, remaining list on the tracker
  • Val Ortholog table update (new genes and missing genes)
  • Specific phenotype ontology changes

outstanding action items

  • Mark to implement requested content changes,  send around URL to main site screenshots of prototype gene page (part done)
  • All, Have a look sites and suggest any revisions (only for the structure and functionality, Midori and I will revise the content) (part done, and more comments anyone)
  • Val Finishing phenotype analysis for the Nurse lab (in progress)
  • Val Write training session for new curator/ Mark and Midori (Hope to run this in about a month…..) (in progress)
  • Val Finish tidying data for migration (in progress)
  • Val and Midori Refine and describe annotation extensions (now urgent for curation tool and GO)
  • Val EMBL resubmission. This will allow all of the new genes/ gene structure changes to propagate through o Uniprot/Pfam/Interpro? etc (At present UniProt? are missing a number of protein coding genes and the Gp2GO file is very out of date) was dependent on the Broad data update, has now moved up the list
  • 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. GeneDB files need backwardly naming: GeneDB 1_date GeneDB 2_date
  • Midori and I will scope out a proposal for the phenotype model in the next few weeks
  • Val circulate “names ideas”  list
  • Pombeclub 10 May 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
  • Pombe 2011 June 27-30 Val, Midori, Mark Prepare 3 poster abstracts and posters
    • Val/Midori? community curation
    • Midori phenotype ontology and phenotype curation
    • Mark "PomBase" as "un-techy" as possible; try to show some of the displays/features
  • Val will also try to arrange talk/demo/workshop but will probably be selected for a workshop talk from the abstracts

2. Tracking

i. Community queries

https://rt.sanger.ac.uk/Search/Simple.html?q=ebi-pombase

ii. Curation and ontology development

PomBase SourceForge page https://sourceforge.net/projects/pombase/

Trackers: https://sourceforge.net/tracker/?group_id=65526

  • Chado 23 Open/ 0 Closed
  • Controlled vocabularies 3 Open/ 0 Closed
  • Curation tasks 11 Open / 0 Closed
  • Documentation 1 Open / 1 Closed
  • Fission yeast phenotype 6 Open / 3 Closed
  • GO annotation 15 Open / 1 Closed
  • Sequence analysis 12 Open/ 0 Closed

iii. Curation tool tracking

SourceForge PomBase Curation Tool tracker

iv. Ensembl tracking

http://www.ebi.ac.uk/panda/jira/browse/PB

v. Project Wiki

(Which you found if you are reading this) https://sourceforge.net/apps/trac/pombase/wiki/CurationTool and a wiki used for brainstorming and documentation which can be transferred to the website if it needs to be visible under PomBase

3. Timelines

  • Target for the Beta release is now Mid-May  (lets say Monday 16th) running in parallel to GeneDB
  • For GO meeting - need curation tool improvements, annotation extension documentation
  • Still aiming for "PomBase" launch at fission yeast in international meeting in Boston 27-30 June 2011  
    • need for release - data, web pages including gene pages (good for poster/slide snapshots)
      • data equivalent to geneDB pages
      • search
      • static content
    • community curation launch - need workflow, literature triage, view of existing annotations by paper; may have more specifics to fill in
    • should have high-level terms available in phenotype ontology (subsequent refinements post-launch OK)
  • What still needs to be done?

PomBase web pages

  • demo site

http://demo1.ensemblgenomes.org/Schizosaccharomyces_pombe

  • Prototype Gene page links

http://dev.pombase.org/ensembl/result/SPBC409.20c/gene

  • Query Builder will be under "find tab" on Monday
  • Need a tracker for curators to request web page additions/changes - within Jira?

4. Upcoming meetings

  • Val attending GO consortium meeting 19-21 May will demo community curation tool, potential collaboration
  • Val, Midori, Mark and Antonia attending Fission yeast International meeting

5. AOB


Minutes from this meeting


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Last modified 9 years ago Last modified on Dec 16, 2011, 5:20:14 PM