SDIWG:Meeting Minutes 20060421

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Agenda: Software and Data Integration Working Group (SDIWG)

Top page of SDIWG web site

Friday April 21, 2006: 2:30 -- 3:30 PM Eastern Time

Next SDIWG Friday May 19, 2:30 PM –- 3:30 PM ET: Pls contact Peter Lyster for information

Preliminary Agenda

(Sherm is guest host today -- Peter is on vacation.)

  • Review minutes and action items from the last SDIWG tcon
    • Leaders of the 3 working groups please describe the charters of your groups and invite participation
    • Yellow pages (Ivo, Daniel, Bill):
      • Have looked at Kennedy's IATR; describes approx 450 tools. Nice software interface, with tool metdata. Peter had idea to have something similar for NCBC's. We want to include libraries so can describe exact syntax of API mode. SIMBIOS has worked on an intitial prototype as well. Want to automatically populate XML database, add ratings, discussions, blogs, etc. Also want to create ontology of tools and Web services. Need flexible XML descriptions of each of the tools.
    • Ontologies (Zak and Suzi)
      • Idea is to poll people about what ontologies they are using and share those among Centers. Status: just got started, will be posting email to establish who needs to be involved. Will be receiving email survey soon. Difference from BioMoby--a service registry (where can look up where different services are available). Task is to look for opportunities to consolidate use of ontologies for describing data results.
    • Aystems biology (Aris from Columbia):
      • Charter not yet determined.
  • Progress on Yellow Pages effort, e.g., draft charter statement, progress at individual Centres,...
    • Simbios center will describe new Ruby on Rails implementation for the Simbiome resource inventory (see, and hopefully a demo on the breeze.
    • Other demos?
  • Plan for progress leading up to July 17-19 (Mon-Wed) NCBC All Hands Meeting (AHM). Check out working groups at Top page of SDIWG web site
  • ** Action plan for providing framework to join efforts of DBP's: Can we envision a protocol to tie together tools of different NCBC's? Want to shoot for demo at July AH meeting.
  • ** There is time on agenda for July meeting where WGs will meet concurrently. Waiting for responses from all the centers.
  • Other...
  • ** Action items: each group should try to determine membership of each group before July meeting. The ontology and systems biology WGs should have a mission statement.
  • ** Ivo would like us to develop a scenario to automate a pipeline connecting NCBC tools. This is similar to issues being taken by caBIG. Implementation should follow standards. Do all these services really need to interact? Isn't there value simply in getting the community to be aware of these tools? This is a goal of the Yellow Pages ("level 1") vs. longer-term goals.
  • ** Need use cases to define scope of our activities. Two possible goals:
      • 1. Use Yellow Pages to describe all NCBC software to make the biomedical community aware of NCBC tools and resources
      • 2. Use software ontology to create pipelines that link tools across NCBCs to solve complex biomedical probolems.

Source Documents:

The Internet Analysis Tools Registry, A Public Resource for Image Analysis, an article by David N. Kennedy and Christian Haselgrove to appear in Neuroscience.


Attendees: Michael Sherman, Jon Dugan, Bill Katz (Simbios), Bill Lorensen, Aris (Columbia), Suzi Lewis, Karen Skinner (NIH), David States;

Note taker: Daniel Rubin

[Suggested order of note takers for future meetings: Daniel Rubin; (this one); Jags; Dinov; Chueh; Sherman; Lorensen; Floratos]


Action Items