www.pistoiaalliance.org
Ramesh Durvasula, PhDDirector, Molecular Sciences & Candidate Optimization Informatics, Bristol-Myers Squibb
BioITWorld Expo, Boston, April 2011
The Pistoia AllianceStrategy, Progress, Momentum
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Agenda
• Industry Drivers• The Origins of Pistoia• The Mission and Strategy of
Pistoia• The Initiatives of Pistoia
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What is Core to your Business? What is Critical?
Core?
Cri
tical?
YES NO
NO
YES
FocusStaff on
Innovation
Externalize for Cost
Reduction
Externalizefor
Best Practices
ReduceNon-Value
Added Work
1990
2011
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The Mission of the Pistoia Alliance
Lowering the barriers to innovation
by improving the interoperability of R&D business processes
via pre-competitive collaborations
Pistoia MembershipFebruary2011
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Domains of Action
Biology & Translational Medicine
Chemistry
Scientific Collaboratio
n
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The Focus of Each Domain
Big Data, Analytics, Semantics
Supply Chain, Tech
Transfer
Vocabularies, Use
Cases, Best Practices
Biology Chemistry
Scientific Collaboration
2010-2013 2012-2014
2012+
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A Reality Check: Setting Expectations
VS.
VS.
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The Biology Domain
1.Sequence Services
2.SESL3.Biology Domain
Roadmap
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Sequence Services – the Rationale
“It takes all the running you can do, to keep in the same place!” -- Red Queen
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Put Sequence Services in the Cloud
Public Data, Private DataPublic Tools, Private ToolsConfigurable , Secure Access
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Sequence Services: Proofs-of-Concept
1. Cognizant & Eagle2. Constellation & Microsoft3. Infosys4. Thomson Reuters
4 proof-of-concept implementations were built
Sequence Services site
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The Biology Domain
1.Sequence Services
2.SESL3.Biology Domain
Roadmap
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SESL: Try this at your desk….
Which diseases are correlated to TCF7L2?
Gene/Protein Literature – Full TextLiterature - Abstracts
Inherited diseases Gene expression
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Try it again with Pistoia’s SESL….Gene naming/synonymsGene FunctionLiterature statisticsDisease co-occurrencesGene/protein interactions
…all in one report from one search
HOW? A standard ontology, data model, query language, report structure, etc.
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The Standards used within SESL
Category Name Community
Triple Store
RDF W3CSPARQL W3C
Jena, Sesame, Virtuoso Varied
Text Mining
leXML EBI & CALBC
LexEBI/BioLexicon EBI, NaCTeM, U of Pisa
CALCBC EBI & CALBC
URIs
UniProt EBI, PIR, SBI, etcDisease Ontology and
UMLS
ArrayExpress EBINCBI Taxonomy NCBI
RDF Schema
Dublin Core N3 notation W3C
Co-occurrence of gene-disease EBI
PMC doc standard NCBI
SESL-2 Relation ontology OBOURI server W3C
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The Deliverables of SESL
• A Proof-of-Concept to demonstrate feasibility and clarify requirements
• A functional specification for query brokering, result filtering, report generation
• A potential for a new Business Model
SESL website
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The Biology Domain
1.Sequence Services
2.SESL3.Biology Domain
Roadmap
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Breadth of Information Integrated (content)
Breadth of Information Integrated (content)
Com
ple
xity
of S
erv
ice-
En
ab
lem
en
tC
om
ple
xity
of S
erv
ice-
En
ab
lem
en
t
SESL
SequenceServices
Secure integrated multi-domain information
services
…
caBIG
SAGE
EATRIS
ELIXIR
Sequences
Expression
Scientific Literature
Biology Domain Roadmap
Large ScaleAnalytics
Multi-tenant
Security
Hosting &integration of private
data
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Our industry needs a Disruptive Innovation. That Disruption...is Pistoia
IF YOU WANT TO GO FAST, GO ALONEIF YOU WANT TO GO FAR, GO TOGETHER
Click to edit Master title styleThank you
This presentation: http://goo.gl/tVdpywww.pistoiaalliance.org
