SDIWG:Meeting Minutes 20060818

Agenda: Software and Data Integration Working Group (SDIWG)

Top page of SDIWG web site

Friday August 18, 2006: 2:30 -- 3:30 PM Eastern Time

Next SDIWG Friday September 15, 2:30 PM –- 3:30 PM ET: Please contact Peter Lyster for information lysterp@mail.nih.gov

Minutes from the Agust 18, 2006 tcon/meeting.

TCon Agenda

• Roll Call (5 min)

• Minutes from most recent SDIWG tcon June 16, 2006: http://na-mic.org/Wiki/index.php/SDIWG:Meeting_Minutes_20060616 (5 min)

• General Discussion of July 17-19 All Hands Meeting in Bethesda http://www.bisti.nih.gov/ahm2006/ (5 min)

• ACTION ITEM: Need input for 5-pager to Dr. Zerhouni. Can the Working Groups provide a 1 paragraph summarizing: outcome of AHM; pithy anecdotes; any new connections made?; future plans. Due date is this Monday 8/21. We hope to have the final report ready for Dr. Zerhouni by Friday 8/25. Thanks very much, Peter

• Progress in three working groups
  • Yellow Pages and Resourceome (Ivo Dinov, Daniel Rubin, Bill Lorensen, Jonathan Dugan, 15 min)
    • NCBC SW/Tool Complete YellowPage/Resourceome Progress at 2006 NCBC AHM (1 min)
    • Agree on Proposed Resource Descriptions (10 min)
      • Proposed set of Required/Minimal Resource Description Fields (5 min)
      • Optional and Resource-specific description fields (5 min)
    • Is there a need for Graphical Visualization, hierarchical-browsing and traversal of the NCBC SW Tools/algorithms/Resources (e.g., this NCBC Ontology ptototype)? (2 min)
    • Action Items (2 min):
      • Implementation of the required/optional descriptors and store in database (SymBios/Jonathan Dugan).
      • Implementation of OWL export of these descriptors
      • Each NCBC Center to designate one person who will coordinate completion of the resource description for each of that NCBC's tools/resources.
      • Each Center describes their key tools and resources (using these Center-specific prototypes).
      • Begin to think of integration of distributed NCBC Resources (ala XML Resource-Utilization Description, e.g., I/O/Server/Settings/Etc.).
  • 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

• Review of minutes

Athey: Please review online and make direct comments on the Wiki.

• Discussion about 5-pager for Zerhouni/NIH - deadline is Friday Aug 25, 2006

Lyster: Use AHM main topics to organize, particularly the output of the 3 working groups.
Skinner: Views of the highlights of the AHM such as contacts made, accomplishments of the AHM meeting. Goals are to raise awareness and consciousness of the NIH community, that they exist and have applicability to NIH mission.
Kohane: Can send info on science ontologies, but how to get it vetted across all NCBCs quickly?
Skinner: For the working groups, convey either a milestone or a clear sense of where you are headed next.
Athey: Avoid repeating what was said at AHM, but to emphasize the future.
Dugan: Can work with Dinov and Sorensen to get a paragraph for the Resourceome.

• Yellow Pages and Resourceome

Dugan: Mini-milestone of minimal set of information to describe what a resource is. Next step is to finalize this set and then move onto the optional metadata. Symbios is building a prototype implementation of this (just for physics simulation). The assumption is that each NCBC would implement their own resource database using open source available, etc.
Athey: The key is organize other mini-meetings to work these issues outside the main meetings.
Jag: The way to proceed is to send thoughts to any members of the Y&R WG via email. Propose that what is there on the Wiki is in fact the minimal data set: Required/Minimal Fields
Rubin: Need each NCBC to identify one person to review the Y&R datasets.
Skinner: Will there be an underlying resource ontology?
Rubin: The groups at the AHM thought we should avoid the actual ontology (which will be necessary), but should come to consensus on the minimal fields that would contain data from the ontology.
Kohane: Are these telecons to be used to drive these activities?
Athey: We should consider suspending these general tcons until we get those activities done.
Mitigu: Need a responsible person who is responsible for delivering this aspect of cross-NCBC for each of the sites.
Lyster: Not to forget being able to describe the composition of tools.
Jag: Focusing on finding tools problem rather than composition of tools first.

• Scientific Ontologies

Kohane: First work that needs to be done is finishing some annotations of the agreed upon Class I ontologies and releasing documents widely to help newcomers to the area. For ontologies that are not quite right, or ones that are still being built (II - VII), we need to sort out who is interested in helping to complete them or use them.
Lyster: How about comments from outside, such as those from Bill Bug?
Musen: Worried about publication of some form of ontology "rating" to the outside world.
Kohane: Agree, emphasize that these are not ratings, but how these ontologies are relevant to the NCBCs.
Athey: How many NCBCs participate actively in the AHM WG?
Kohane: Most were but imaging NCBCs may have felt that their specific needs were not addressed (but addressable in the future).
Athey: How about linkage of and between ontologies?
Kohane: Looked at UMLS as a candidate, but not much interest in ontologies of ontologies given all the work needed just to get to the first level.
Musen: This is a big area of ongoing ontology research.
Kohane: Cross-ontology stuff is being done in more of an artisanal way right now, not yet in a scientifically rigorous way, so it may need be on the immediate agenda of the SO WG for the moment. We'll move ahead with the WG for the next year with existing invitees as well as new ones.

• Applications of Systems Biology, Modeling, and Analysis

Athey: One question asked of us recently was how well are the NCBCs covering the scope of the work in biomedical sciences? One way to look at this is to look at the scope of of DBPs, which is only a subset of the whole NIH scope. What we wanted to do is put together a group to look at issues across DBP domains of interest across NCBCs. Gates: Need to understand better the output from the other WG so that we don't recreate the wheel. Need good communication across the three WG.
Athey: How can we find a way to synergize WG activities with one another?
Jenkins: Responding to the plethora of phone calls and tasks from NIH to the NCBCs -- it's an important thing to rectify.
Athey: Larger tcons can be somewhat hard, and smaller WG communication may be more effective, and results can be posted up centrally.
Lyster: Have considered this -- how often should the whole SDIWG really "meet"? It's also a way of creating new WG and retiring old ones.
Athey: Consider a quarterly call punctuated by concise e-mail/Wiki requests for other communications/meetings -- this would cut down the verbal time while keeping up communications.
Lyster: Then maybe we should have the SDIWG tcon in 3 months, and let the WG work independently.
Athey: There may be ways to make the Wiki more valuable as well.
Lyster: Yes, have had some comments about this.

• Meeting adjourned

Attendees

• Athey, Lyster, Chueh, Sherman, Gates, Dugan, Mitigu, Rubin, Omenn, Musen, Skinner, Jenkins, Castle, Couch, Cao, Jagadish, Haller, Weymouth, Thalhammer-Reyero
• Note-taker: [Suggested order of note takers for future meetings: Chueh (this one); Sherman; Lorensen; Floratos; Rubin; Jags; Dinov]

Action Items

• Working group leads to send Karen paragraphs for NIH 5-pager
• Next full SDIWG tcon in 3 months
• Working groups to independently move forward