teranode tools and platform for pathway analysis michael kellen, solution manager june 16, 2006
TRANSCRIPT
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Teranode Tools and Platform for Pathway AnalysisMichael 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
Emerging BiopharmaEmerging BiopharmaMajor Research InstitutionsMajor Research InstitutionsTop 10 BiopharmaTop 10 Biopharma
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Parkinson’s Research
Science advances through the informal collaboration within distributed and fluid communities
ComputationalBiologist
ProteomicsResearcher
Clinical Researcher
NeurologistGeneticist
MolecularBiologist
Cell Biologist
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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
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Data Integration Today:Costly Point-to-Point Integration
App 1API
CustomIntegrat.Software
App 2API
App 3API
App 4API
CustomIntegrat.Software
CustomIntegrat.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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Parkinson’s Research
Information exchange, especially between domains, ends up being document-driven
ComputationalBiologist
ProteomicsResearcher
Clinical Researcher
NeurologistGeneticist
MolecularBiologist
Cell Biologist
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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
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The Semantic Web promises automated data integration through flexible, evolvable data models
R&D Scientist
Bioinformatics CheminformaticsLIMS Public Data Sources
Dynamic,Linked,
Searchable
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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
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
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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
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
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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
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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
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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 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
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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