SDIWG:Meeting Minutes 20070921

Agenda: NCBC Joint Working Group Meeting

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Notes

Friday, September 21, 2007: 2:30 -- 3:30 PM EST
Please contact Peter Lyster for information Peter Lyster
SDIWG Meetings Page

TCon Agenda

• Roll Call/Note-taker (Jags) (5 min)

• Minutes from most recent SDIWG tcon May 18, 2007 (5 min)

• Progress in three working groups
  • Biositemaps Resourceome (Ivo Dinov, Daniel Rubin, Will Schroeder, Jonathan Dugan, 15 min)
    • NCBC Ontology of Resources (validated in relation to NTRIC; need to improve the node descriptions of the current Resourceome Ontology (http://bioontology.org/projects/ontologies/SoftwareOntology/); Who entered “Atomic” and how to revise its description? Final agreement date Oct. 01, 2007?)
    • State of the NCBC iTools (http://www.loni.ucla.edu/iToolssvc/ncbc_iTools.html)
      • BioSiteMaps.XML/CompBiome.XML – a new framework for de-centralized communication and utilization of the NCBC Resources (http://www.loni.ucla.edu/twiki/bin/view/CCB/NCBC_ToolIntegration_XMLtology_Meeting_103106_ResourceDef).
      • iTools plug-ins: Dedicated crawler vs. Google search
    • White Paper(s) (BioSiteMaps/iTools)
    • NCBC Resourceome WG Liaisons (Please update these, if appropriate!)
  • Scientific Ontologies (Zak Kohane, Mark Musen, and Suzi Lewis, 15 min)
    • enter draft agenda items here
  • NCBC Driving Biological Projects Interactions and Impact (Aris Floratos, Brian Athey, Russ Altman, 15 min)
    • enter draft agenda items here

Minutes

Note taker: (H.V.Jagadish)

• Review of May 18, 2007 Minutes

1. Attending: Karin Remmington, Jane Ye, Aris Floratos, Daniel Rubin, Mark Musen, Dave Kennedy, German Cavalier, Karen Skinner, Mike Sherman, Shawn Murphy, Walter Meixner, Zohara Cohen, Ivo Dinov, Beth Kirschner, H.V. Jagadish, Jim Cavalcoli, David States, Brian Athey, Gil Omenn, Jennie Larkin, Peter Lyster
2. Biositemaps, Resourceome, and iTools (Ivo Dinov et al.)
   • Ivo Dinov summarized the activities of the resourcome working group over the past 18 months, and gave a live demonstration of the software ontology as it currently exists in iTools, including its links to Protégé, its “hyperbolic tree” representation, its cross-linking and querying capability, and biositemaps. He made an appeal to the NCBCs to contribute to the description and classification of resources.
   • The biositemaps site (www.ncbcs.org/biositemaps/) presents a very nice distributed architecture for organizing the intellectual creations of the NCBCs. It became clear that the tool lists and some of the categorization from many of the centers needs some tweaking. Each center needs to review its content and to review and confirm the point-people for each center.
3. Scientific Ontologies (Zak Kohane, et al.)
   • The group is working to formalize the “Ontology” paper with a manuscript to be released soon for review and comments.
   • The group discussed a mapping between the Tools and Ontology working groups. Once categories of software become machine readable and navigable the Tools and Ontologies WG will overlap.
   • What is the expected outcome of our study of software categories? A common well understood software ontology that is widely used across NCBCs and disseminated and used across the broader community.
   • The issue of NIH-forge (as in Source-forge) was mentioned but was not discussed.
4. DBP Interactions (Gil Omenn et al.)
   • National meeting was held between Andrea Califano (MAGNet) and NCIBI to compare common DBP efforts and tools. MAGNet has a DBP for B-cell Lymphoma and NCIBI has DBP in Prostate Cancers. Each group presented their work and results with clear interest in the tools that each group has been developing (Oncomine and MIMI for NCIBI, and ARACNE for MAGnet). The B-cell dataset was shared with NCIBI so that they could analyze using Molecular Concepts Maps and other tools.
   • AMIA translational bioinformatics meeting in March. There will be a panel for NCBC’s to showcase translational research

Attendees

• Note-taker: [Suggested order of note takers for future meetings: Jags (this one); Dinov; Chueh; Sherman; Schroeder; Floratos; Rubin]