Teranode Tools and Platform for Pathway Analysis

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Teranode Tools and Platform for Pathway Analysis

• Michael Kellen, Solution Manager
• June 16, 2006

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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

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Science advances through the informal
collaboration within distributed and fluid
communities
Parkinsons Research
Molecular Biologist
Computational Biologist
Proteomics Researcher
Cell Biologist
Clinical Researcher
Geneticist
Neurologist
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But each working group develops its own tools and
standards for data storage and manipulation
Parkinsons Research
Molecular Biologist
Computational Biologist
Proteomics Researcher
Cell Biologist
Clinical Researcher
Geneticist
Neurologist
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Data Integration TodayCostly Point-to-Point
Integration
Custom Integrat. Software
Custom Integrat. Software
Custom Integrat. Software
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So Many Applications, So Few Resources!
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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

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Information exchange, especially between domains,
ends up being document-driven
Parkinsons Research
Molecular Biologist
Computational Biologist
Proteomics Researcher
Cell Biologist
Clinical Researcher
Geneticist
Neurologist
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Existing Web provides data access but not data
integration
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The Semantic Web promises automated data
integration through flexible, evolvable data
models
RD Scientist
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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

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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
• urnlsidteranode.compathways9203901234980
• 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

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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

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The current web allows information to be linked
in one way
Bobs Home page
Link
Alices Home page
Link
Link
Pathway X
Link
Link
Proteomics Lab
Modeling Study
Protein A
Protein B
Protein C
Link
Link
Link
Data Set
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RDF replaces generic links with typed
relationships
Bobs Home page
Has Collaborator
Alices 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
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RDF Benefits

• Built on URIs to leverage web
• Machines can automatically assemble relevant
  information
• New information doesnt break old relationships
• Can be built bottom-up by referencing existing
  data sources

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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

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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

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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
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Teranode applications extend a common framework
built on Semantic Web standards
Biological Modeler Nodes Chemical Species,
Reactions Edges Biochemical relationships Applica
tion 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
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Teranode VLX and platform technologies enables
tools to leverage existing with Semantic Web
Teranode VLX enables new applications based on
Semantic Web standards
TERANODE Design Suite
LIMS
Visualization Tools
Analysis Tools
VLX Kernel
VLX Kernel
VLX Kernel
Web