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• http://pistoiaalliance.org Pistoia Alliance April 2011 Eagle Genomics Symposium Nick Lynch
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• http://pistoiaalliance.org
Pistoia Alliance
April 2011
Eagle Genomics SymposiumNick Lynch
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NATURE Reviews | Drug Discovery Volume 9 | March 2010
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NOW
Background—How it all started
In Pistoia, Italy
Meeting of GSK, AZ, Pfizer and Novartis—identified similar challenges and frustrations in discovery informatics
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Learn from Other Industries
Transportation
Geospatial
Automotive
ClinicalRetail
Banking
Healthcare
Lowering the barriers to innovation by improving inter-operability of R&D business processes through pre competitive collaboration
Pistoia MembershipMarch 2011
Energy
Influence
Delivery
Trust
Networked and Externalised Life Science Research
Chemistry Externalization Processes
Image/quote from Abdul-Malik Shakir
Greater Challenge: Unknown Semantic Collisions
Revealing assumptions is an essential component of effective communication.
Crossing the Chasm
Pistoia is the BRIDGE to cross the chasm to a more agile pre-competitive environment
STANDARDIZE SIMPLIFY CENTRALIZEPISTOIA MEMBERS SUPPLIERS
Our Projects….
Sequence ServicesVocabulary StandardsSESLELN Query
SEQUENCE SERVICESWORKING GROUP
Slide 19
Project Rationale - Sequence ServicesProblem / Opportunity Statement
There is no competitive advantage for each bioscience company to maintain the latest version of the many informatics databases and software tools within their company firewall.
To maintain even a core set of sequence databases, as the Red Queen told Alice: “it takes all the running you can do, to keep in the same place”!
Slide 21
Define standards for the provision of secure access to pre-competitive databases and software tools.
Invite external suppliers to provide those services to multiple consumers who would effectively share the cost of the maintenance.
Proposed Solution
Documentation / Deliverables UpdateSequence Services – Phase 1
• Heavy focus on non-functional requirements in Phase 1 (security, performance, scalability, availability, maintenance, and on-going business model)
• 4 Vendor proof of concept projects currently being evaluated. Slide 22
Ethical hack
Example ScreenShot
Slide 23
Why a Vocabulary Standards Initiative (VSI)?
• A key aspect of our work is naming and identifying:– Genes, Sequences, Diseases, Tissues, Anatomy, Cell Lines, Bioprocesses, Species, Phenotypes,
Compounds, Drugs, Mode of Action, People, Places, Adverse Events, Targets, Reagents, etc, etc...– Many other Pistoia initiatives require support in this area
• There are many gaps, organisations, vocabularies and standards (Semantic & Syntatic)– Syntax: OBO, RDF/OWL, ANSI; Content: GO, FMA, SNOMED SO, OBI, NCI Taxonomy, SAO, CL, ChEBI,
PRO, BioLexicon, ICD-10, NCBI Species, HDO, IDO, MedDRA; Organisations: NCBO, OBO, W3C ..etc– Science is continually evolving, and so are vocabularies - constant flux.
• Connecting data across content providers, academic & internal systems often difficult– Significant branching / ab initio vocabulary development within each organization – No common language
• Leaving this to the external environment to fix is not an option (current position), industry needs to be much more proactive
• While we can create ontologies internally, or in public collaboration, what is lacking is central governance, and a service infrastructure
– Manage vocabulary interfaces– Manage change processes– Promote standards – Promote use– Respond to feedback
• Thus VSI...• This is a BIG challenge, and will not be easy to solve
Power Grid 2010
Power Grid 1940
Power Grid 1900 Local/internal power suppliersNo standards (v, amps, sockets)No national gridLittle innovation in electric apps
Central power suppliersStandard accessNational grid – utility powerLots of innovation in electric apps
1000s of power suppliersStandard supply & accessNational gridMass use of electric applications
The Electric Power Grid Analogy (beyond utility computing...)
c.f. “ The Big Switch” Nicholas Carr 2008
Small number of suppliersFew standards (delivery)No information gridLittle innovation in information useSupplier specific interfaces
1000s of suppliersStandards (content)‘Information & model grid’ – semantic webInnovation in information useUser specific interfaces
Info & Model Grid 2015?
Consumers can combine info from any supplier and tailor to need.
Consumers have stand-alone information from few suppliers.
Info & ModelGrid 2011?
c.f. “ The Big Switch” Nicholas Carr 2008
The Electric Power Grid Analogy (beyond utility computing...)
Standardising Drug Target Types
A Pistoia Vocabulary Standard InitiativeLee Harland, Christopher Larminie
With input from the Pistoia VSI group
PUBLIC DOCUMENT
Pistoia Working Group: VSI
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High Level Summary
• Representation of a molecular drug target in structured databases is ad-hoc– Single protein-targets are “OK” (being linked via Entrez gene, but this is not an agreed standard)– Multi-protein targets, complexes, biologicals and many more are poorly described, often simply raw text
• This project will focus on industry & suppliers to describe a specification for reporting drug targets within structured content
– Minimal cost, just FTE time required– This could feed into the IMI Open Pharmacology (OPS) call as an industry-publisher requirement– Output would be a specific set of “rules” regarding the representation of complex molecular targets– Aim would not be to define a list of all known targets, this would be out of scope. As will any text-mining
efforts.– Recommendation to suppliers and industry to adopt specification along with industry-generated mappings
for pre-existing targets– Deliverable – specification & publication
• Could be a start to a future, wider phamacological data standard project – All databases providing pharmacological activity content delivered in a standard way– Could gain a quick-start building on MIABE standard
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Drug Targets
• A ‘simple’ monomer? – HTR1B(or 5ht-1b, 5ht1b, htr1b…etc)
• A ‘stable’ (core) complex – 2(NR1:NR2A)
• A ‘dynamic’ complex – NMDA-MASC
From: A. J. Pocklington, J. D. Armstrong and S. G. N. Grant (2006): Organization of brain complexity — synapse proteome form and function. Briefings in Functional Genomics and Prot 5(1), pp66-73
New Arrivals:
siRNA,
vaccines,
aptamers….
What is the “target” of
insulin?
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Signpost clearly
What can we do? – Call to Arms
Signpost what we already have
Show the value to Life Science workflows
Vocabulary Standards are critical
Pistoia Alliance can foster this new approach
Acknowledgements
Pistoia Working Group Leads and their groupsSimon Thornber, Richard Bolton, Lee Harland, Ian Dix, Wendy Filsell, Ian Harrow & many others
Our Working Group partners
If you want to go fast, go alone. If you want to go far, go together.
www.pistoiaalliance.org
Discussion Questions
• What are the barriers to precompetitive collaborations in research, development, commercial, medical, etc. arenas?
• What are the factors that are stimulating precompetitive collaborations?
• What is the “tipping point” and how far away is it?
• More…
