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A pilot KB of biological pathways important in Alzheimer’s Disease

This pilot project aims to create a web-deployed knowledge base of biological pathways important in Alzheimer's Disease. The KB will be curated by domain experts, utilize semantic web technology, and promote active discussion and collaboration within the scientific community.

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A pilot KB of biological pathways important in Alzheimer’s Disease

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  1. A pilot KB of biological pathways important in Alzheimer’s Disease Tim Clark twclark@partners.org MassGeneral Institute for Neurodegenerative Disease June Kinoshita junekino@alzforum.org Alzheimer Research Forum October 27, 2004

  2. A pilot KB of biological pathways important in Alzheimer’s Disease • Core goals • Collaborators • Technology • Target: core pathways • Curation and deployment • Computability & KB concept model • Truth maintenance approach • Community involvement • Summary

  3. Core goals • KB of biological signaling pathways in AD • Web-deployed via the AlzForum website • Curation by true domain experts • Computability & linkability of all statements • Keep database current with the science • Promote and incorporate active discussion

  4. Collaborators • Alzheimer Research Forum • www.alzforum.org • MassGeneral Institute for Neurodegenerative Disease • www.mghmind.org • Industrial partners • Alzheimer Disease researchers • at Harvard-affiliated hospitals & clinical centers

  5. Technology • Semantic Web (SW) technology is highly appropriate for this application • This application is also an excellent demonstration platform for SW technology

  6. Target: core pathways in AD • Zero in on pathways of central relevance • Proposed initial focus • genetics relevance (presenilin pathway) • therapeutics relevance (cholesterol pathway) • Expansion of focus • multiple-disease relevance (protein misfolding) • Others as proposed by advisors

  7. Curation by true domain experts • We want real, leading researchers to curate • Experts must not become fulltime curators • Implies limitation of scope for each curator • The toys in the cereal box (motivation) • Credit for ideas • Private whiteboard space in KB • Active collaboration space • Ability to disagree & challenge statements • Part of the KB design

  8. Web-deployed via AlzForum • AlzForum is a global platform on AD • 70,000+ sessions per month • 32,000 visitors view 150,000 pages per month • Referenced by 7,700+ web sites • 2,000+ registered members • 3,000+ subscribers to newsletter • The very top scientists in AD research serve each year on the AlzForum Editorial Board • There is an active participant community • Online scientific dialogues and discussions

  9. Computability: beyond the “dead” graphical model…

  10. …to a formal “computable” modelKB concept model -example-

  11. AlzForum public view of KB Drs. Sane, Doe & Roe see these statements (public KB): “Dr. Sane believes (100%) that A inactivates B” “Dr. Schmo believes (90%) that A inactivates B”

  12. Individual private view of KB Dr. Sane also sees these “private” statements in addition to the public view: “Dr. Sane believes (65%) that B complexes with D and E (private finding)” “Dr. Schmo believes (60%) that A activates B (personal communication)”

  13. Truth maintenance: Absolute or relative? • Truth maintenance is typically conceived to be about eliminating contradiction in the KB • Okay on “boutique” scientific KBs • Does not scale as a process due to limitations of expertise • Successful large KBs studiously avoid truth maintenance • Medline: correct bibliographic info = correct entry • Disregard truth or falsity of the science • “Let community process deal with it”, outside the KB • Our approach: consciously import contradiction into the KB • “Relativization” (reification) of all statements • Private “idea incubation” sections of KB (the Personal Whiteboard) • Explicit statement publication to wide or narrow audience

  14. Promote and incorporate active discussion as part of the KB • Scientists currently play an active role in AlzForum • We plan to leverage the investment that developed this community, into participation in the KB-building effort • We will support commentaries upon (and criticisms of) KB statements as part of the KB itself • We will feed back the KB contents and software via the AlzForum website to registered members

  15. Why we think it will work • Right time for this KB • Right technology for this KB • Right KB for this technology • Right technology and science community

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