SDIWG:Meeting Minutes 20061117

Agenda: NCBC Joint Working Group Meeting

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Friday November 17, 2006: 2:30 -- 3:30 PM EST

Please contact Peter Lyster for information Peter Lyster

TCon Agenda

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

• Minutes from most recent SDIWG tcon Aug 18, 2006 (5 min)

• Progress in three working groups
  • Yellow Pages and Resourceome (Ivo Dinov, Daniel Rubin, Bill Lorensen, Jonathan Dugan, 15 min)
    • Yellow-pages (10 min)
    • Proposed set of Required/Minimal Resource Description Fields (5 min)
    • Optional and Resource-specific description fields (5 min)
    • Current Ontological Description of the NCBC Tool Yellow-Pages
    • What are the NCBC Resources? (Downloadable locally-executable SW tools, Web-services (including DBs))?
    • Has each center described 3-5 resources? (2 min)
    • Begin to think of integration of distributed NCBC Resources (ala XML Resource-Utilization Description, e.g., I/O/Server/Settings/Etc.).
    • NCBC iTools (Resourceome Prototype, v 0.1, 10/12/06)
    • Other Attempts to provide archives of SW and tool resources
    • Sugested Action Items for the YPR WG:
      • Each Center should ensure their SW repositories/archives on this page are correct
      • 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?
  • Scientific Ontologies (Zak Kohane, Mark Musen, and Suzi Lewis, 15 min)
  • Applications of Systems Biology, Modeling, and Analysis (Aris Floratos, Brian Athey, Russ Altman, 15 min)

• Action Items: Can leads let us know if/when there are tcons in the next month.

Minutes

Note taker: Michael Sherman (Sherm)

• Review of 060818 minutes

Ivo has control of screen
Peter: went through previous minutes; main result was to meet quarterly

• Yellow Pages and Resourceome

Ivo (UCLA):
Jon Dugan helped delineate what is an NCBC resource.
Ivo went through the above agenda:
Went through "bare bones" resource description fields (no serious objections -- now considered stable). NCBO ontology (DAG using Protege) [1]
Categories: SW resources (tools), data resources (downloadable), services Magnet center did a great job. Ivo advocated thinking about automated integration of tools.
Demo of iTools prototype (Java applet) combining NCBC resources from Wiki and IATR resources from David Kennedy.
Will provide XML template in next week that will allow automated incorporation of tools into iTools.
Showed GAMS tool (gams.nist.gov).
Sherm asked about relationship between iTools & Simbiome Ruby on Rails template. Ivo said he hadn't seen it; Peter said he hadn't distributed it yet. At some point these could be merged & integrated -- goals are very similar.

Action items covered (see above) plus XML schema.

Questions, suggestions, critiques:
Terry: use SOAP interface.
Aris: Q regarding "typed list"; what is relation to ontology? Suggestion: replace with ontology tree.
Aris: why not have multiplicity > 1 for type of resource?

Control returned to Peter.

Peter discussed the (expected) existence of multiple resourcesome efforts. Future action: how to reconcile.
Brian: Zak & I could have used this at the diabetes conference last week. Can we use this now? What is the timeline?
Peter: no timeline yet. He, Karen & Ivo discussed last week.
Ivo: not going to release any prototype until it has at least a dozen tools from each center and tool is robust. Also, need proper URL at NIH. Then it will go on autopilot.
Peter: how will this expand beyond NCBC?
Ivo: iTools will allow addition of plugins to incorporate external resources (must write "adaptor").
Karen: is implementation parse the same as a mediator?
Zak points out that we will be out of time so Peter cut off questions to move on to Zak.

• Scientific Ontologies

Zak: went over 3 ontology classes from AHM. Will ask PIs to endorse (soon), as a simple message from NCBCs: "this is our perspective".
Bill: good news, FMA (foundational model of anatomy) is now open source.

Moved on to next working group (Brian Athey).

• Applications of Systems Biology, Modeling, and Analysis

Athey: not a lot of formal action; much pairwise interaction. Still trying to find our way. Shying away from Systems Biology.

Timely since centers have to swap out DBPs. Collaborative R01 hasn't panned out. How do we scale out NCBCs to broader community?

Asked for comments/thoughts.
None offered, so Peter opened the floor.

Aris: how was the AHM perceived at NIH?
Peter: factoid: Don Lindberg said he was "extremely pleased". Final report (available online: [2]) is very impressive (tangible & intangible results).
Peter mentioned the Compendium of Government Programs, Inititiaves, and Communities with signficant effort in biomedical informatics and computational biology.
Next year's AHM hasn't been scheduled yet.
Discussion regarding how the final report should be circulated.
Peter requested to be kept up to date on WG progress.
Peter closed meeting.

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: Sherman (this one); Lorensen; Floratos; Rubin; Jags; Dinov, Chueh]

Action Items

• See above.