Teranode Tools and Platform for Pathway Analysis

1. Teranode Tools and Platform for Pathway Analysis Michael Kellen, Solution Manager June 16, 2006

2. Emerging Biopharma Major Research Institutions Top 10 Biopharma Teranode Introduction • A software company providing tools to support research and development in the life sciences • Founded on University of Washington technology in 2002 • Series B venture-backed • Headquarters: Seattle, WA Regional Office: Boston, MA • 40+ Employees

3. Science advances through the informal collaboration within distributed and fluid communities Parkinson’s Research Molecular Biologist Computational Biologist Proteomics Researcher Cell Biologist Clinical Researcher Geneticist Neurologist

4. But each working group develops its own tools and standards for data storage and manipulation Parkinson’s Research Molecular Biologist Computational Biologist Proteomics Researcher Cell Biologist Clinical Researcher Geneticist Neurologist

5. App 2 A P I App 1 A P I App 3 A P I App 4 A P I Data Integration Today:Costly Point-to-Point Integration Custom Integrat. Software Custom Integrat. Software Custom Integrat. Software

6. So Many Applications, So Few Resources!

7. Source software, APIs, and even IT standards become obsolete Changing scientific requirements break pre-defined application schemas Data, and especially the context needed to use it become lost The Data Reuse Challenge: Time

8. Information exchange, especially between domains, ends up being document-driven Parkinson’s Research Molecular Biologist Computational Biologist Proteomics Researcher Cell Biologist Clinical Researcher Geneticist Neurologist

9. R&D Scientist Integrating Data Manually Static, Untagged, Siloed Dolor Sit Amet Consectetuer Lacreet Dolore Euismod Volutpat Lacreet Dolore Magna Volutpat Nibh Euismod Tincidunt Aliguam Erat Dolor Sit Amet Consectetuer Lacreet Dolore Euismod Volutpat Lacreet Dolore Magna Volutpat Nibh Euismod Tincidunt Aliguam Erat LIMS Bioinformatics Cheminformatics Public Data Sources Existing Web provides data access but not data integration

10. Dynamic, Linked, Searchable LIMS Bioinformatics Cheminformatics Public Data Sources The Semantic Web promises automated data integration through flexible, evolvable data models R&D Scientist

11. Key Semantic Web Technologies • URIs like Life Sciences Identifiers (LSIDs) provide standard ways to reference resources • Resource Description Framework (RDF) provides a way to describe new relationships between data sets without changing old schemas • Web Ontology Language (OWL) allows scientists to formally specify how knowledge is structured for a particular domain

12. Life Sciences Identifiers (LSIDs) • A standard way to describe life sciences resources • Identifies a resource through 3-4 properties: • The authority issuing the identifier • A namespace • An object ID • An optional revision ID urn:lsid:teranode.com:pathways:9203901234980 • A resolution service provides LSID resources on the internet: • Is a standard service defined by the OMG • Usable by both computer agents and humans • Provides the resource data • Provides metadata about the resource

13. Teranode's LSIDResolution Service • TMS repositories are described by LSIDs • Any number of TMS repositories • TMS repository = LSID namespace • All TMS documents have an LSID • All TMS documents are accessible

14. The current web allows information to be linked in one way Bob’s Home page Link Alice’s Home page Link Link Pathway X Link Link Proteomics Lab Modeling Study Protein A Protein B Protein C Link Link Link Data Set

15. RDF replaces generic links with typed relationships Bob’s Home page Has Collaborator Alice’s Home page Conducts Studies Is member of Pathway X Contains proteins Proteomics Lab Modeling Study Produces data Protein A Protein B Protein C Uses data Measures expression of Data Set

16. RDF Benefits • Built on URIs to leverage web • Machines can automatically assemble relevant information • New information doesn’t break old relationships • Can be built bottom-up by referencing existing data sources

17. Teranode Object Model • VLX/RDF describes annotated, directed graphs • Typed nodes and edges • Hierarchy • Arrays • Embedded mathematics engine • Nodes and edges are annotated with typed properties

18. OWL for scientific ontologies • Built on RDF, OWL allows further specification of data types and relationships between data types • Can also represent business layers • Legal rights • Versioning • Corporate standards

19. Teranode Type Dictionary • Type Dictionaries can be created through Teranode Kernel API • Create dictionary • Define property, node, edge, graph types • Save dictionary as .owl • Load dictionary from .owl Teranode Pallet created from BioPAX ontology

20. Teranode applications extend a common framework built on Semantic Web standards Biological Modeler Nodes: Chemical Species, Reactions Edges: Biochemical relationships Application Logic: Conversion to ODE-based simulations Protocol Modeler / Player Nodes: Steps in Labortory process Edges: Workflow specification Application Logic: Automated protocol execution and data capture

21. Enterprise Storage Lab TERANODE Model Server Documentum, OpenText Oracle ELN Teranode VLX enables new applications based on Semantic Web standards Teranode VLX and platform technologies enables tools to leverage existing with Semantic Web TERANODE Design Suite LIMS Visualization Tools Analysis Tools VLX Kernel VLX Kernel VLX Kernel Web