SDIWG:Meeting Minutes 20070216

Agenda: NCBC Joint Working Group Meeting

Top page of SDIWG web site

Notes

Friday, February 16, 2007: 2:30 -- 3:30 PM EST
Please contact Peter Lyster for information Peter Lyster
SDIWG Meetings Page

TCon Agenda

• Roll Call/Note-taker (Floratos) (5 min)

• Minutes from most recent SDIWG tcon Nov. 17, 2006 (5 min)

• Progress in three working groups
  • Scientific Ontologies (Zak Kohane, Mark Musen, and Suzi Lewis, 15 min)
    • TBD
  • Yellow Pages and Resourceome (Ivo Dinov, Daniel Rubin, Bill Lorensen, Jonathan Dugan, 15 min)
    • Past Progress
      • Other Attempts to provide archives of SW and tool resources
      • Proposed set of Required/Minimal Resource Description Fields
      • Optional and Resource-specific description fields
      • Current Ontological Description of the NCBC Tool Yellow-Pages
      • Types of CompBio Resources?
      • Center described 3-5 resources?
    • Status of NCBC iTools
      • V1 (v 0.1, 10/12/06)
      • V4 (v 0.4, 02/13/07)
    • Sugested Action Items for the YPR WG:
      • Each Center should ensure that they have 6-12 SW Resources described according to these templates
      • Test, comment and revise iTools. How does it compare with other similar efforts?
  • Applications of Systems Biology, Modeling, and Analysis (Aris Floratos, Brian Athey, Russ Altman, 15 min)
    • TBD

Minutes

Note taker: (Aris Floratos)

• Review of 11/17/06 minutes
  • Yellow Pages and Resourceome
  • Scientific Ontologies
  • Applications of Systems Biology, Modeling, and Analysis

Zak Kohane outlined the process via which the Scientific Ontologies SIG reviewed a select set of ontologies and vocabularies. A summary list along with the a broad assessment of overall "quality" has been compiled by Suzie Lewis and is available at www.berkeleybop.org/sowg/table.cgi. In addition to being an inventory for the vocabularies and ontologies that tbe NCBCs use intenally, the SIG hopes that this list will be a useful starting point to non-experts seeking to identify ontologies/terminologies appropriate for use in their work. Zak recognized that there is a gap in the set of vocabularies reviewed, namely in the area of imaging and neuroscience and he solicited help in identifying the main players in these domains. Daniel Rubin offered to help in this direction.

In response to questions/suggestions from Gil Ommenn and Brian Athey, it was agreed that the Scientific Ontologies SIG will also produce representative use cases, outlining how ontologies/terminologies are used in practice.

Ivo Dinov reviewed the process that led to the definition of the minimum resource descriptors and Dan Rubin's software classification ontology and proceeded to discuss the iTools framework (www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_iTools) and demonstrate the Java prototype front end. The demo outlined several supported search modes as well as the ability of the tool to "scrape" updates to tool description information from Web pages that follow the format of the Resource descriptions on the SDIWG wiki.

Suzie Lewis observed that the scraping approach useb by the iTools could be used to also process the listing of terminologies produced by the Ontologies SIG and allow then to be presented/searched via the iTools application.

A discussion followed about what is the proper manner to release and start using the iTools framework. Suggestions were made taht NIH should centrally host the database and portal, so as to offer the approrpiate branding and central entry point for the general public to access the NCBC resources. One idea was to develop a NCBC-specific web site (e.g., ncbc.org; or nih.ncbc.org) for that purpose. Peter Lyster said that there have been internal discussion in NIH about this topic and some ideas (such as having a central entry point to the NCBC resource listing from NCBI or some other institute) have been vetted.

Brian Athey and Aris Floratos commented on the upcoming March telecon of the Systems Biology SIG and the idea of developing a suite of software tools comprising resources from mulitple NCBCs which will be leveraged in the context of various DBPs. The question came up of how we achieve a good balance between tool development and tool adoption and how we advertise and promote the various tools, in particular since the adoption of these tools by the community will, to a large extent, determine the impact and usefulness of the NCBC program as whole and its potential for renewed funding. Peter Lyster commented that there is no concerted effort at the time wihtin NIH to promote the NCBC tools, rather there are a number of ongoing initiatives like caBIG, BIRN, etc that are procedding in parallel. One course of action might be to start with having the iTools hosted at CCB and then move gradually towards bringing the repository within NIH as an updated NCBC page on the BISTI site (or elsewhere) is created. Peter also said that he will ask John Whitmarsh to get back to the PIs regarding the current plans for the program evaluation.

Attendees

• Sherman, Lyster, Dinov (CCB/UCLA), Lorensen, Michael Montegut (NCBO project mgr), Weymouth, Floratos, Jennie Larkin (NHLBI), Zak & Susanne, Jenkins (NLM), Vivien Bonai, Athey, Kennedy, Mike Mendis, Karen Skinner/NIDA, Musen, Chris Mungall (NCBO), German Cavelier (NIMH), Suzanna Lewis
• Note-taker: [Suggested order of note takers for future meetings: Floratos (this one); Rubin; Jags; Dinov; Chueh; Sherman; Schroeder]

Action Items

• Dan Rubin to point our for the Scientific Ontologies SIG the key imaging/neuroscience ontologies.
• Ontologies SIG to produce use cases describing practical uses of ontologies/vocabularies.
• Peter Lyster (or/and others?) to bring up as an agenda item to the NCBC project team meeting the issue of hosting the Yellow Pages database centrally within NIH.
• Peter Lyster to ask John Whitmarsh to communicate to the PIs the status of plans for the NCBC evaluation program.