Teranode Tools and Platform for Pathway AnalysisMichael 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 BiopharmaEmerging BiopharmaMajor Research InstitutionsMajor Research InstitutionsTop 10 BiopharmaTop 10 Biopharma

Parkinson’s Research

Science advances through the informal collaboration within distributed and fluid communities

ComputationalBiologist

ProteomicsResearcher

Clinical Researcher

NeurologistGeneticist

MolecularBiologist

Cell Biologist

Parkinson’s Research

But each working group develops its own tools and standards for data storage and manipulation

ComputationalBiologist

ProteomicsResearcher

Clinical Researcher

NeurologistGeneticist

MolecularBiologist

Cell Biologist

Data Integration Today:Costly Point-to-Point Integration

App 1API

CustomIntegrat.Software

App 2API

App 3API

App 4API

CustomIntegrat.Software

CustomIntegrat.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

ComputationalBiologist

ProteomicsResearcher

Clinical Researcher

NeurologistGeneticist

MolecularBiologist

Cell Biologist

Static,Untagged,

Siloed

Existing Web provides data access but not data integration

R&D ScientistIntegrating

Data Manually

LIMS Bioinformatics Cheminformatics Public Data Sources

Dolor Sit Amet ConsectetuerLacreet Dolore Euismod VolutpatLacreet Dolore Magna Volutpat

Nibh Euismod Tincidunt Aliguam Erat

Dolor Sit Amet ConsectetuerLacreet Dolore Euismod VolutpatLacreet Dolore Magna Volutpat

Nibh Euismod Tincidunt Aliguam Erat

The Semantic Web promises automated data integration through flexible, evolvable data models

R&D Scientist

Bioinformatics CheminformaticsLIMS Public 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: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

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

The current web allows information to be linked in one way

Alice’s Home page

Proteomics Lab

Link

Data Set

Link

Bob’s Home pageLink

Link

Modeling Study

Link

Pathway X

Link

Link

Protein A Protein B Protein C Link

RDF replaces generic links with typed relationships

Alice’s Home page

Proteomics Lab

Studies

Data Set

Produces data

Bob’s Home pageHas Collaborator

Conducts

Modeling Study

Measures expression of

Pathway X

Contains proteins

Is member of

Protein A Protein B Protein 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 ModelerNodes: Chemical Species, ReactionsEdges: Biochemical relationshipsApplication Logic: Conversion to ODE-based simulations

Protocol Modeler / PlayerNodes: Steps in Labortory processEdges: Workflow specificationApplication Logic: Automated protocol execution and data capture

Web

Teranode VLX and platform technologies enables tools to leverage existing with Semantic Web

TERANODEDesignSuite

LIMSVisualization

ToolsAnalysis

Tools

TERANODEModelServer

Lab

Documentum,OpenText

Enterprise Storage

Oracle ELN

VLX Kernel VLX Kernel VLX Kernel

Teranode VLX enables new applications based on Semantic Web standards