Planning Meeting Mon 15th August 2011 - Minutes

Agenda for this meeting


  • Mark will let us know when minor fixes are done, and current dataset is on Dev so we can do thorough site testing

This will enable us to submit final requests/fixes before encouraging community use (without geneDB redirecting) but at this stage we will:

  • i) Announce to community for feedback
  • ii) Add links from GeneDB for people to try new site
  • iii) Send out a request for HTP datasets from the community in defined formats (current assembly only at first, this covers most HTP data)
  • Discussed representation of phenotypes, will have a meeting to describe plans
  • Discussed replacement for RT, nobody could think of a better solution so we will persevere for a while
  • Discussed "Gene Page name" We will think about better names for pages
  • Discussed annotation extension ( a heads up that these are in the pipeline) Attempted to demonstrate how annotation extensions might be presented on gene page (under drop down for relation type)
  • Gene Pages, will be viewable on iphones and Androids
  • Access statistics, will be available to monitor page access during and after transition
  • Discussed interaction display in Ensembl, will revisit later (need to evaluate pros and cons of pulling BioGrid? format data from Chado vs Intact)
  • Discussed Ontology Browsing in Ensembl Various Pros and Cons of
    • AmiGO (GO only)
    • QuickGO (GO only, no ncRNA's, large proportion of fission yeast annotation missing, No pombe systematic IDs? (check))
    • OLS ( no ability to show annotations)
    • Ensembl "custom view" (not user friendly, does not provide required functionality) Will revisit later. If there is any opportunity for Val and Midori to contribute to specification for Ontology viewing within Ensembl

Action items

  • CC Midori and Val on all Jira items (Dan/Mark??)
  • Alert curators when current dataset ready for testing (Mark)
  • Set up a phenotype meeting to describe phenotype model (input from Val/ Midori/Kim?)
    • i) how phenotypes will be curated, including
      • what information will be stored in the allele record
      • annotation genotypes (we can currently capture information for single deletions only)
    • ii) describe data model
    • iii) how this will be stored in Chado
    • iv) How this will fit into workflow in curation tool

(this will probably not happen until November but in the meantime we can document current progress/ brainstorming on wiki)

  • Need to coordinate dataset for public release with Ensembl genomes release (Kim/Mark/Dan?)
  • FYPO will be submitted to OBO foundry shortly which should trickle through to OLS in due course (Midori)
  • Ensembl group tell us which format specification for various HTP datasets (Dan/Paul/Mark??)
  • Load external GO data into Chado as a priority (Kim)
  • Annotate telomere features (Curation group)
  • Follow up desktop sharing software (circulate possibilities, do free trial?) (MIdori)
  • check university standard providers of conference lines etc with Gos (Val)

(DONE) Gos has a BT MeetMe? account

  • Organise fortnightly conference call (DONE)
  • Ask Henning Hermjakob about possibility of OLS as webservice to attach annotations to (?)
  • Finish NAR paper (All)

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Last modified 10 years ago Last modified on Sep 10, 2011, 6:52:43 PM