2016 Advisory Board Meeting

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The 2016 edition of the WormBase Scientific Advisory Board meeting will take place at Caltech on 4/5 Feb 2016.

Logistics

Attending

  • Hinxton
    • Paul Kersey, Matt Berriman, Kevin Howe, Bruce Bolt, Jane Lomax, Michael Paulini, Paul Davis, Gary Williams
  • OICR
    • Lincoln Stein, Todd Harris, Sibyl Gao, Adam Wright

Travel

  • Hinxton
    • Will fly out on the 2nd of Feb, and return on Sun 7th Feb (cheap flights)
  • OICR
    • Arrive 3rd Feb, depart 6th Feb
  • Remote workers
    • Mary Ann - arrive 2nd Feb (evening), leave 7th Feb (evening)

Advisors

Discussion topics

Organisation of SAB talks

Agenda for the SAB itself will be organised into 4 main sections. Each section will have a short overview/scene-setting talk, followed by selected specfic talks. Each section will end with a time-tabled open discussion, which we should use to discuss strategy in that area, and put any specfic questions we have to the advisory board. Please add suggested questions/discussion topics for each section below.

  • Curation
    • How can we work with other MODs on curation strategy?
    • Are our priorities for curation appropriate?
    • How can we best make use of LEGO annotation?
  • Genomics
    • C. elegans
      • Should we update the reference genome with data from Li et al?
      • What is the status of the initiative to select (and sequence) a new reference strain?
      • Should we curate gene models in key strain genomes (e.g. Hawaiian)?
      • A graph genome for C. elegans?
      • Is curation/processing/display of all RNASeq data sets for C. elegans valuable? Sustainable?
    • Other species
      • What criteria should be used to assess whether a genome is elevated to "core" status?
      • Is special treatment of C. briggsae, C. remanei, C. brenneri and C. japonica still justified in light of the Caenorhabditis genome project?
      • Would a community curation system for gene models be successful for nematodes?
      • Where to focus curation effort for other nematodes?
      • Integration between WormBase and WB ParaSite - to what extent is this required?
  • User interface
    • How best to measure the utility of WormBase (and similar resources)?
    • What new tools / views should we have (e.g. enrichment tool, RNASeq querying)
  • Infrastructure and interoperability
    • How important is it that our infrastructure solution is reusable by other MODs (or genomics data management projects)
    • Is the amount of effort we invest in maintaining/extending wormMine typical for other *Mine deployments?
    • Is use of non-open-source software for core data management an acceptable risk?

Specific topics for project meeting / working groups

  • Cross-site communication
    • Unification of documentation and code; what are our standards for documentation? For code?
  • Database migration
    • Specific plans for the next 6-12 months
    • extending use to non-Caenorhabiditis sp
  • WormBase and human disease
    • Linking C. elegans alelles to human pathogenic variants, or variants of unknown significance
    • What about a disease portal? Could be as simple as having a separate tab, this serves to increase visibility
    • Increasing number of papers on therapeutics for disease (drugs, small molecules, herbals)
    • Increasing number of papers on disease exacerbating metals and compounds (falls into two broad areas-disease and toxicity)
  • How to better integrate WormBase services (i.e. WB and WBPS)
    • Integrated search - what do we need to do to make this work?
    • Cross-site tools
      • Enrichment tool
      • Data mining
        • ParaSite has provision to replace BioMart with a system that supports "biologist friendly" queries, e.g. using set operation (a la EuPathDB, PomBase)
        • Is this on the InterMine road map?
        • If not, can we develop something that can be used in both WB and WBPS that complements (rather than competes with) WormMine?
  • Texpresso for parasitic worms
    • Discussions already started on this
  • Gene summaries, one too many: legacy manual descriptions, the automatic gene descriptions, and community contributions
    • A plan to phase out the un-maintainable manual descriptions: Start with the oldest (by last_updated date) descriptions
    • Currently community contributions could be to a manual description, to an automated one or could be entirely new
    • With the automated descriptions being amenable to updates and the addition of new data (as and when they get curated in WB), should we even solicit community contributions?
    • How do we merge the community contributions and the automated descriptions? Should we display them as one or separate them?

Agenda (preliminary)

Google drive with useful docs in https://drive.google.com/drive/u/0/folders/0BwFG0nRdT4ZGVjM1REpNT0Q5YXM

Wed 3rd Feb

  • 1400 : Project meeting (part one). Morgan Library (Kerckhoff 2nd fl)

Thu 4th Feb

Keck Conference Center (Building 127, Room 155, Head towards the Broad cafe, past the gene pool)

  • 0900-0915 - Arrivals and discussion
  • 0915-0930 - Introduction - Paul Sternberg
  • 0930 : Literature curation
    • 0930-0935 - Overview - status and priorities - Chris Grove
    • 0935-0945 - Automated identification of data - Karen Yook
    • 0945-0955 - Automated writing of gene summaries - Ranjana Kishore
    • 0955-1005 - Community curation - overview, status, tracking - Mary Ann & Chris
    • 1005-1015 - Micropublications - an incentive for community participation - Daniela Raciti
    • 1015-1025 - LEGO - Kimberly Van Auken
    • 1025-1045 - Discussion (+ specific questions for SAB)
  • 1045 - 1100 : BREAK
  • 1100 : Genomics
    • 1100-1120 - Overview - genomics at WormBase - Kevin
    • 1120-1140 - Curation and analysis of all RNASeq gene expression data - Gary
    • 1140-1200 - WormBase and parasitic worms - Jane
    • 1200-1230 - Discussion (+ specific questions for SAB)
  • 1230-1330  : LUNCH
  • 1330 : User interface
    • 1330-1345 - Website - architecture, structure, usage, outreach - Todd
    • 1345-1350 - JBrowse - A new genome browser for WormBase - Todd
    • 1350-1400 - Focus on new website features - Sibyl
    • 1400-1410 - Visualisation of Ontology annotations (incl WOBr, SObA) - Raymond
    • 1410-1425 - WormMine - Todd
    • 1425-1500 - Discussion (+ specific questions for SAB)
  • 1500-1515 : BREAK
  • 1515: Infrastructure and interoperability
    • 1515-1530 - Overview of current data management strategy and vision for future - Kevin
    • 1530-1545 - Database migration - status and roadmap - Adam
    • 1545-1600 - The InterMOD project and cross-MOD interoperability - Todd
    • 1600-1630 - Discussion (+ specific questions for SAB)

1630-1645 : BREAK

  • 1645-1800: General discussion
    • Threat to NIH funding and alternative funding strategies
    • Working more closely with other MODs
    • How to make WormBase more useful/appealing to biomedical scientists

Fri 5th Feb

Millikan Library Board room

  • 0800-0900 : Advisors breakfast
  • 0900-1130 : Advisors report back to whole group
  • 1400-whenever : Project meeting (part two)