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Michael Braxenthaler (Roche and external liaison officer for Pistoia) describes the Pistoia Alliance biology domain strategy at the first Pistoia Alliance Conference in April 2011.
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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
Pistoia Activity Domains
Biology/Translational
Research“Understanding Disease”
Chemistry Live
“Linking Structure with Outcome”
Scientific Collaboration
Agenda
Recap: Pistoia Mission and Domains
Hands-On Example: Sequence Services
Expanding the Concept
Many Partners – How Do They Fit?
Roadmap: Where next?
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
Recap: Pistoia Mission and Domains
Hands-On Example: Sequence Services
Expanding the Concept
Many Partners – How Do They Fit?
Roadmap: Where next?
Co
mp
lexity of Service
-En
ablem
ent
Co
mp
lexity of Service
-En
ablem
ent
SequenceServices
Expanding the Concept
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
Expanding the Concept
Large ScaleAnalytics
Multi-tenant
Security
Hosting &integration of private data
12BiologicalNetworks
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
…
caBIG
SAGE
EATRIS
ELIXIR
Sequences Expression ScientificLiterature
Expanding the Concept
Large ScaleAnalytics
Multi-tenant
Security
Hosting &integration of private data
13BiologicalNetworks
Pistoia Ambition
Foster the evolution of a global collaborative information
ecosystem of
secure
integrated
interoperable
internal/external information services
Agenda
Recap: Pistoia Mission and Domains
Hands-On Example: Sequence Services
Expanding the Concept
Many Partners – How Do They Fit?
Roadmap: Where next?
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.
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 cast:
Life Science IT
Life ScienceScientist
SoftwareVendor
Service Provider
PublicContent Provider
CommercialContent Provider
Life Sciences Information Ecosystem
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
Recap: Pistoia Mission and Domains
Hands-On Example: Sequence Services
Expanding the Concept
Many Partners – How Do They Fit?
Roadmap: Where next?
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
…
caBIG
SAGE
EATRIS
ELIXIR
Sequences Expression ScientificLiterature
Biology Domain Roadmap
Large ScaleAnalytics
Multi-tenant
Security
Hosting &integration of private data
22BiologicalNetworks
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
Public canonical pathways
Internal bionetwork information
Scientific literature text mining
DNA seq,RNA-seq
Biological insight:“understanding
disease”
clinical information
SequenceServices
Pistoia Activities
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
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
Public canonical pathways
Internal bionetwork information
Scientific literature text mining
DNA seq,RNA-seq
Biological insight:“understanding
disease”
clinical information
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
Public canonical pathways
Internal bionetwork information
Scientific literature text mining
DNA seq,RNA-seq
Biological insight:“understanding
disease”
clinical information
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!