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Thursday, June 23, 2011; 12-1 PM ET


Grace Stafford, Mike Riben, Riki Ohira, Sherri De Coronado, Larry Wright, tuart Turner, Stuart Bell, Hua Min, Bob Freimuth, Trish Whetzel


Presentation by Stuart Turner


  • Talk about NCRI/NCI meeting
    • NCRI/NCI meeting held last week in London, UK with 5 themes, one of them on standards and vocabularies
    • Goal of the meeting was to discuss efforts of this group towards standards and vocabularies
    • Could have better coordinated with other themes and there are efforts for cross-pollination
    • Q: What did you mean by cross-pollination? A: Using the outcome of this meeting to have further discussions on using of standards and vocabularies
    • Format this year worked and learned a lot about how to make it better next time
    • Presentation by Amnon Shabo on Clinical Genomics (HL7) was very good (worth sharing with VCDE Workspace)
    • Semantic Web experts asked for use cases and problems to solve for them to work on how semantic web can be useful
    • Stuart Turner put together a draft of notes and discussions from the meeting currently avaiable to those who attended
    • Several outcomes of the meeting
      • notes
      • recommendations
      • white paper
      • related paper
      • peer-review journal article
    • Q: Who is doing BioSite map? A: NCBO; this is a joint effort from NCBCs and CTSAs with NCBO
    • There are several resource inventory projects and engaging with
      • Neuroinfomratics Framework project is collaborating with neuroscience resource inventory project
      • Eagle Eye project is also part of the resource inventory project but at a more granular level than other BioSite efforts (who has specific antibody, stored at this specific address, etc)
    • Included Ontology Recommender in the white paper
    • Had discussions about Cross-Community Pollination issues and Profiling
    • There were questions of whether BioPortal could meet everyone's needs
    • Community fragmentation is an issue and although several things were discussed like spidering and message boards, the group probably provide pointers to BioPortal and let that be the place for discussion
      • Tool to help "pitch" funding for a project
      • You need to have a target to say, we will start the project if we get a certain amount
      • There's a community that sets up projects to help solve problems and try to match problem solvers with the problems
      • Community also decides what's important and puts high priorities on the top
      • Provocative questions website could be added to the notes so the community can have a link to that
    • Q: What page are you making changes? A: The ORWG white paper (to be renamed).
  • There is a lot of information on the wiki
    • Plan to restructure the paper and focus on the recommendations
    • To complete the paper by the end of June
    • Reorganize the paper; refine the recommendations section and make it the major focus of the paper
  • Sherri, Stuart Turner and Stuart Bell met last week and those discussions will also be included in the white paper
  • Review major recommendations and see if everyone agrees
    • Executive Summary section has most of the recommendations currently
    • First two recommendations were put there a while ago
      • Publish what the core metadata would be so that we can implement as a test and have community review and provide feedback to know what changes needs to be made
      • Community Input Review; single location be established for community (pointing to BioPortal for discourse about ontologies)
        • If this is effective, then it would bring more people to the BioPortal "watering hole" and we would need to measure efficacy
        • We need to get a critical mass in order to assess usefulness
        • In terms of terminology metadata, Sherri thought the VKC would publish the core metadata and point people for discussion on ontologies to BioPortal
    • Master OMV table
      • Table was updated by Stuart Turner and Sherri
      • Two things to look at are the set of recommendations and the Master OMV table
    • Reuse of existing standards like OMV and Dublin Core
    • Resource metadata could potentially be completed as a challenge or open source development activity in the future
  • There are gaps, but there are also actionable
  • Q: Is there a way of adjusting the page width of the wiki? A: Can remove the index which would make it wider.
  • Can use to throw bookmark and can configure the pages (change width and font) and print it out to PDF or paper. Another option for viewing is Instapaper.
  • Tables may be forcing the width of the wiki page; we could move tables to a separate page
  • If canonical source is going to be the wiki we should think about how we can better format the wiki document
  • Next meeting will probably be in a couple of weeks once the white paper revisions are completed.

Action Items

  1. Stuart Turner - Follow up with Amnon Shabo for his presentation, then send the presentation by Amnon to Riki and/or the VCDE Workspace Listserv
  2. Stuart Turner - Need to re-work the white paper (in the next week)
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