the pistoia alliance biology domain strategy april 2011

http://pistoiaalliance.org

Michael Braxenthaler, PhDExternal Liaison Officer, The Pistoia AllianceStrategic Alliances, Pharma Research & Early Development Informatics, Roche

Pistoia Alliance ConferenceBoston, MA – April 12th 2011

The Pistoia AllianceBiology Domain Strategy

Agenda

Recap: Pistoia Mission and Domains

Hands-On Example: Sequence Services

Expanding the Concept

Many Partners – How Do They Fit?

Roadmap: Where next?

Recap: Pistoia Mission & Vision

Lowering the barriers to innovation

by improving inter-operability of R&D business processes

through pre competitive collaboration

Pistoia Activity Domains

Biology/Translational

Research“Understanding Disease”

Chemistry Live

“Linking Structure with Outcome”

Scientific Collaboration

Agenda






Sequence Services Phase 1 (2010)

7

Sequence Services in the Cloud

“Bring analysis to the data”

e.g. 1,000 Genomes

Sequence Services Phase 2 (2011)

Management and Analysis of Next Generation Sequencing Data

Sequence Services – Key Features

• Establishes cloud-based secure services

• Provides public data and tools

• Allows private data and tools

• Allows commercial third party data and tools

• Provides scientifically aware collaboration space

9

Agenda






Co

mp

lexity of Service

-En

ablem

ent

Co

mp

lexity of Service

-En

ablem

ent

SequenceServices


Large ScaleAnalytics

Multi-tenant

Security

Hosting &integration of private data

11

Breadth of Information Integrated (content)Breadth of Information Integrated (content)

Co

mp

lexity of Service

-En

ablem

ent

Co

mp

lexity of Service

-En

ablem

ent

SequenceServices

Secure integrated multi-domain information

services

Sequences Expression ScientificLiterature



Multi-tenant

Security


12BiologicalNetworks


Co

mp

lexity of Service

-En

ablem

ent

Co

mp

lexity of Service

-En

ablem

ent

SequenceServices


services

…

caBIG

SAGE

EATRIS

ELIXIR




Multi-tenant

Security



Pistoia Ambition

Foster the evolution of a global collaborative information

ecosystem of

secure

integrated

interoperable

internal/external information services

Agenda






Many Partners – How Do They Fit

Life Sciences Information Ecosystem

The scenario:

All industry data services are delivered in an interoperable form so that I can • buy target data from commercial providers mined from literature, • connect to public services from EBI and NCBI, • and use open source, commercial, and proprietary analysis tools • in a trusted hosted environment.


The scenario:

All industry data services are delivered in an interoperable form so that I can • buy target data from commercial providers mined from literature, • connect to public services from EBI and NCBI, • and use open source, commercial, and proprietary analysis tools • in a trusted hosted environment.

The cast:

Life Science IT

Life ScienceScientist

SoftwareVendor

Service Provider

PublicContent Provider

CommercialContent Provider


Life Science IT

Life ScienceScientist

SoftwareVendor

Service Provider

PublicContent Provider

CommercialContent Provider

Hosted solutions are fit for purpose and easy to use. I

can find everything I need.

Pistoia compliant services lower cost and decrease time to deliver customer

solutions.

Pistoia compliant services lower cost and decrease time to deliver customer

solutions.

Decreases costs and increases the value of the software by

reducing number of interfaces that need

to be supported.

Increases value of products as data is more

easily consumed. Eliminates middleman who reformats, sells

data repacked as more consumable.

Increases utilization of a public good and

provides commercial advocacy for

government investment

Life Sciences Information Services

• Business Services– Data marketplace– Solution marketplace– Hosting environment

• Collaboration Services/Solutions

• Scientific Services/Solutions– Biology Services/Solutions– Chemistry Services/Solutions

Agenda







Co

mp

lexity of Service

-En

ablem

ent

Co

mp

lexity of Service

-En

ablem

ent

SequenceServices


services

…

caBIG

SAGE

EATRIS

ELIXIR


Biology Domain Roadmap


Multi-tenant

Security



Biological samples

Anonymized samples

Sample metadata

NGS

Candidate list

Public canonical pathways

Internal bionetwork information

Scientific literature text mining

DNA seq,RNA-seq

Biological insight:“understanding

disease”

clinical information

Generic NGS relateduse case

Biological samples

Anonymized samples

Sample metadata

NGS

Candidate list




DNA seq,RNA-seq


disease”


SequenceServices

Pistoia Activities

Biological samples

Anonymized samples

Sample metadata

NGS

Candidate list




DNA seq,RNA-seq


disease”


SequenceServices

SESL

Pistoia Activities

26

Assertion & Meta Data MgmtTransform / TranslateIntegrator

Service Layer

Corpus 1

‘Consumer’Firewall

SupplierFirewall

Common Service Broker

MultipleConsumers

SESL (Semantic Enrichment of Scientific Literature)

Db 2

Db 3

Db 4

Corpus 5

Std PublicVocabularies

KnowledgeApplications

ContentProviders

BusinessRules

OpenStds

Disease Dossier

SESL (Semantic Enrichment of Scientific Literature)

• Phase 1 completed– Demonstrated that knowledge brokering is technically feasible– A unique consortium from three cultures: industry, publishers and

academia sharing costs and risks– Raised awareness of biomedical community need and business

opportunity

• Currently waiting for alignment with IMI OPS project

Biological samples

Anonymized samples

Sample metadata

NGS

Candidate list




DNA seq,RNA-seq


disease”


SequenceServices

BiologicalNetworks

SESL

Pistoia Activities

Biological Networks

• The external landscape covering pathways/biological networks is fairly complex

• Fits directly with Pistoia’s ambition to signpost existing work

Proposal– Establish a working group to map this landscape

and develop a proposal how Pistoia should proceed in this area (3 months).

Biological samples

Anonymized samples

Sample metadata

NGS

Candidate list




DNA seq,RNA-seq


disease”


SequenceServices

BiologicalNetworks

Vocabulary

Services

SESL

Pistoia Activities

Dictionaries & Dollars. Why core biomedical vocabularies matter to life-science industryLee Harland, Chris Larminie, Susanna-Assunta Sansone, Mark Burfoot, Jasmin Saric, Michael Braxenthaler, Enoch Huang, Michael Cantor, Wendy Filsell, John Wise and Ian Dix

Abstract

The life science industries are in the midst of developing new business models based around “networked research and development” such as open innovation, pre-competitive alliances, public-private consortia and academic partnerships. While these offer much in transforming the way applied science is done, they bring with it major information management challenges in environments. Here we look at the role of basic biological and chemical vocabularies in this process, and propose that increased efforts in this space are essential to commercial success. We identify the gaps in current industry infrastructure and describe the business, technology and logistical hurdles that must be addressed to support a diverse set of use cases including biomarker discovery, translational medicine and contract research organisation interactions. Our review concludes with a series of suggested next steps that prepare the way for a more proactive engagement in this area.

Vocabulary Paper

Vocabulary Services

• Many commercial and non-commercial providers and consumers of vocabularies, taxonomies, ontologies

• No service environment to provide and maintain a consistent and consistently used set of core terminologies

ProposalEngage consulting firm to clarify the existence of a solid business case

Biology Domain Roadmap

ProjectSequence ServicesSESLVocabulary Services PubBiological Networks

2010 2011 2012Phase 1 Phase 2 Phase 3

BizCase Phase 1Landscape Phase 1

Phase 1 Phase 2

Thank You!

the pistoia alliance biology domain strategy april 2011

Technology