the pistoia alliance: strategy, progress, momentum

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

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This presentation: http://goo.gl/tVdpywww.pistoiaalliance.org