1. Helping scientists collaborate BioCAD

2. ©2003 All Rights Reserved

3. Researcher “Data” Overload  Exponential growth of Data  Tens of millions of publications  Multi-disciplinary Collaboration  Proteomics, functional genomics, “…ics”  Disease involving multiple pathways Home grown computing tools Investigator Community Hypothetical Pathways Lab Books Public Databases

4. ©2003 All Rights Reserved Informatics Challenge  Is there a better way to explain a complex biological process than using prose?  Can we create fully integrated models that combine knowledge of:  Geneticists  Pathologists  Immunologists  Cell Signaling Researchers  Clinicians, Chemists, Physicists, Mathematicians…  How do we find appropriate experimental evidence and downgrade obsolete evidence?  How can we make sense of thousands of statistically relevant high throughput data points?

5. ©2003 All Rights Reserved The Need To Enable…  Tools/Methods for researchers to create integrated biological models  Multi-disciplinary models with millions of concepts  Represent all possible contexts that a gene, protein or cell system can function under  Computer applications that can understand these concepts

6. ©2003 All Rights Reserved Semantic Networks  Artificial Intelligence concept from the 1960’s  Formalize, Capture and Communicate Meaning  Influenced object-oriented technology and relational databases  Robust, Efficient and Flexible  Basis for many A.I. efforts for last 30 years  Previously Beyond the Power of Hardware / Networks

7. ©2003 All Rights Reserved Female Male Son Mother Male Brother Son Model of a Family All Relationships are Represented in the Network Not In Code or Queries

8. ©2003 All Rights Reserved Sally RobertCharles mother brother Joe GWB ? Smith Family

9. ©2003 All Rights Reserved Ask the network…  How are Robert and Charles Related?  Who is my second cousin third removed?  Which six people connect me to the President of the United States (GWB)?

10. ©2003 All Rights Reserved Ask the network…  How is Protein A related to Protein B?  If this gene is mutated what pathways are affected and how?  Which six drug targets will down-regulate the expression of this Gene?  What dysfunctional pathways model this disease?

11. ©2003 All Rights Reserved Semantic Web  Announced by Tim Berners-Lee (inventor of WWW) Scientific American May 2002 “ A new form of Web content that is meaningful to computers will unleash a revolution of new possibilities ”  Science and The Semantic Web James Hendler Science, Jan 24, 2003 “ The current World Wide Web … is insufficient for the needs of collaboration across scientific disciplines.”

12. ©2003 All Rights Reserved Visual Knowledge  Highly scaleable semantic database platform  12 years of intense/focused R&D  6 years delivering real systems to complex problems  Absorbs knowledge of large multi-disciplinary cultures  Domain expertise driven  Very large scale Adaptive Schema

13. ©2003 All Rights Reserved Visual Knowledge  Servers, each containing millions of Semantic Agents  Each Agent is a proxy for gene, protein, cell, researcher or experiment  Each Agent is “aware” of relationships that it holds with all other agents in the network  Agents organize into complex societies that give rise to adaptive behaviour  Versions of Semantic Agents can be packaged and distributed into other servers

14. ©2003 All Rights Reserved Visual Knowledge Specialty  Systems driven by knowledge of many experts  Integration of Social, Economic and Scientific Models  Cause and Effect  Modeling systems that rapidly evolve and change shape

15. ©2003 All Rights Reserved BioCAD  Semantic Database  Interactive Pathway Editor  2 Tier Server Architecture  Cell System modeling  Experimental Management High Throughput Research Community Private Servers Research Operations Lab Books Curated Knowledge Base

16. ©2003 All Rights Reserved Semantic Models Public Databases Genomic/ Proteomic Experiments InferenceHypothesisDiscovery Pathway Editors

17. ©2003 All Rights Reserved Interactive Pathway Editor  Easy to use drag and drop interface  Gene regulatory, protein signaling and metabolic pathways  Different conceptual levels  Hypothetical cause and effect compared to experimental results

18. ©2003 All Rights Reserved 2 Tier Architecture  Web based  XML interaction  Public Collaboration Server(s)  Hypothetical normal and pathological pathways  Curated and connected to experimental evidence  Peer review and release process Public Knowledge Server Private Research Server Peer Review

19. ©2003 All Rights Reserved 2 Tier Architecture  Private Collaboration Server(s)  Role/Team based security  Semantic Change control (Model Versioning)  Develop proprietary hypothesis and test  Multiple Experimental Protocols  Micro Array, PCR, Western, Mass Spect  Publish results to private or public collaboration network Public Knowledge Server Private Research Server Peer Review

20. ©2003 All Rights Reserved Summary  Life Science Research now involves millions of multi-disciplinary concepts  Large scale Internet Wide Semantic Networks can help us communicate biological processes  Visual Knowledge is a mature powerful technology for Semantic Networks cshankey@visualknowledge.com www.visualknowledge.com

21. ©2003 All Rights Reserved Helping scientists collaborate BioCAD