2011-12-02 Open PHACTS at STM Innovation
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Transcript of 2011-12-02 Open PHACTS at STM Innovation
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Literature
Patents
News
Pipeline
SAR
SafetyIn vivo
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data integration
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data integration
data integration
data integration
data integration
data integration
data integration
data integration
data integration
data integration
data integration
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The Innovative Medicines InitiativeEC funded public-private partnership for
pharmaceutical research
Focus on key problemsEfficacy
Safety
Education & Training
Knowledge Management
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Open PHACTS an infrastructure project
Develop / apply a set of robust standards…
Implementing the standards in a semantic integration platform (“Open Pharmacological Space”)…
Delivering services to support on-going drug discovery programs in pharma and public domain
Mix ideal with the pragmatic. Build open that can accommodate non-open components in the real world.
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23 partners
9 pharma
14 academic/SME/society
5 new partners in the process
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Pre-competitive collaboration
Agreement on standards, approaches
Research questions drive development
Clear use cases
Drive and direction
Pharma bring...
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Example research questions
Give all compounds with IC50 < xxx for target Y in species W and Z plus assay data
What substructures are associated with readout X (target, pathway, disease, …)
Give all experimental and clinical data for compound X
Give all targets for compound X or a compound with a similarity > y%
73 questions identified across consortium
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OPS Open - open access to all
OPS Consortia - data sets licensed just to the consortia
OPS Academia - fully open to academia
“My OPS”
Open Source
Open Access Infrastructure. GUI and back-end platform, online
or download both + data for local setup
Open Services: for example, RSC services
Open Data + Private Data: licensing fun for all the family
Commercial providers: abstract service interface to swap in commercial and open source platforms
What does ‘Open’ mean?
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Agile Development: 6 month ‘lash up’• Produce a working ‘lash up’ system • Constrained to technologies in consortium + a few data
sources• Focused on 2 prioritized research questions
• All oxidoreductase inhibitors active <100nM in both human and mouse
• For a given compound [clozapine], give me the interaction profile with [human or mouse] targets
• Minimum requirements: two data sources (one targets, one compounds) and able to produce answers in ‘manual time’.
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‘lash-up’: youtube.com/openphacts
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UTOPIA Documents (U Manchester)
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Sustainability and community
Data in and data out
Consortium (pharma) members
Public and commercial databases
Publishers
Services built on OPS
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Sustainability $
After 3 years?
Pharma customers
Public funders
Services built on top
Publishing data in
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Focus and future
One area - pharmacology“Production Level” softwareSemantic pragmatics: everyday use by
scientists not informaticians
An infrastructure that can be built upon, to provide a stable foundation for further pre-competitive informatics collaboration
Developers(Builders)
End users(Drivers)
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NanopublicationsCapturing scientific information in the Triple Store
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Onwards and UpwardsConnection between developers and usersArchitectureServices: e.g. entity identification and resolution and representing similarity, ORCID, DataCiteModels: RDF / Nanopublication model spec and guidelines
PrototypeMarch 2012: Internal Prototype DeliverySeptember 2012: Release 1st Prototype
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Why should you care?
Will be first real large scale semantic data integration project – a pilot that can be extended
Provides a single delivery format and pipeline to your customers?
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Find out more?
Email me
Apr/May 2012 - a workshop and intro for publishers
also for data providers/vendors
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Time’s Up!
About your speaker:Name: Richard Kidd
Company: RSC
Tel: +44 1223 432344
Email: [email protected]
Social Media: @open_phacts
slideshare.com/open_phacts
Lash-up: youtube.com/openphacts