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

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 Emerging Biopharma Major Research Institutions Top 10 Biopharma

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

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

Data Integration Today: Costly Point-to-Point Integration App 1 APIAPI Custom Integrat. Software App 2 APIAPI App 3 APIAPI App 4 APIAPI Custom Integrat. Software Custom Integrat. Software

So Many Applications, So Few Resources!

The Data Reuse Challenge: Time 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

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

Static, Untagged, Siloed Existing Web provides data access but not data integration R&D Scientist Integrating Data Manually LIMS Bioinformatics CheminformaticsPublic Data Sources 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

The Semantic Web promises automated data integration through flexible, evolvable data models R&D Scientist BioinformaticsCheminformaticsLIMSPublic Data Sources Dynamic, Linked, Searchable

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

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:  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

Teranode's LSID Resolution 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

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

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

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

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

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

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

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

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