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Adressing Research Questions by Integration of Open PHACTS with Pipeline Pilot
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Adressing Research Questions by Integration of Open PHACTS with Pipeline Pilot


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Accelrys Seminar, Mainz, 14th May 2013

Accelrys Seminar, Mainz, 14th May 2013

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  • 10’
  • Public-private partnership funded by the EU Integrated Medical Initiative28 Partners9 Pharmaceutical companies6 SMEs1 Commercial software company15 academic
  • Thriving communityAround 40 associated partners and risingEarly adoptersPreferential accessHelp drive project direction
  • Driven by real-world use cases40 prioritized business questions by pharma- Top priority business question – 5 people 6 hours
  • Make it easy for application developersRespecting Data ProvidersEasy to expose data to openphactsUse RDF with dataset descriptionssyntactic interoperability firstRecommendations over mandates (we recommend certain ontologies but do not require them)AdaptabilityMappings are crucialMappings between terminologies and data and between data
  • Transcript

    • 1. Adressing Research Questions by Integration of Open PHACTS with Pipeline Pilot Accelrys Seminar, Mainz, 14th May 2013 Christian Herhaus, Global Computational Chemistry
    • 2. Innovative Medicines Initiative • • 2 EC funded public-private partnership for pharmaceutical research Focus on key problems – Efficacy, Safety, – Education & Training, – Knowledge Management The Open PHACTS Project • Runs 2011-2014 • Create a semantic integration hub (“Open Pharmacological Space”) • Deliver services to support ongoing drug discovery programs in pharma and public domain • Leading academics in semantics, pharmacology and informatics, • Driven by solid industry business requirements
    • 3. Open PHACTS Partners 3
    • 4. Associate Partners 4 4
    • 5. Focused on Answering Business Questions “What is the selectivity profile of known p38 inhibitors?” “Find compounds which hit most specifically the multiple targets in a given pathway” 5 “Let me compare MW, logP and PSA for known oxidoreductase inhibitors” “Find me compounds that inhibit targets in NFkB pathway assayed in only functional assays with a potency <1 μM” “For a given interaction profile, give me compounds similar to it.”
    • 6. Datasets and Links 815 millions of Data triples, 18 millions of Mapping triples 6
    • 7. Platform Architecture 7
    • 8. The Open PHACTS Linked Data API 8
    • 9. Pipeline Pilot Hackathon Cambridge, 20th Feb 2013 • Demonstrate that the integration of the Open PHACTS API and Pipeline Pilot (PP) is possible • Create a library of PP components for the Open PHACTS API • Enable: Easy querying of the Open PHACTS API “Drag and drop” creation of useful PP workflows Customisation of PP components PP component transparency 9
    • 10. Connecting to Open PHACTS with PPilot Example URL: https://$(ops_server)/structure/similarity?app_id=$(app_id)&app_key=$(app_key) &searchOptions.Molecule=c1ccccn1&searchOptions.SimilarityType=0 &searchOptions.Threshold=0.7&_format=json 10
    • 11. Answering Questions: Hackathon Example "The current Factor Xa lead series is characterised by substructure X. Retrieve all bioactivity data in serine protease assays for molecules that contain substructure X". Substructure SMILES ChemSpider URI ConceptWiki URI Enzyme class members 11 + Pharmacology information Pharmacology information for desired assay of molecules with substructure
    • 12. By Chris Chau (GSK) Pathway information Entrez ID Example Results: 12 Biomart web service Uniprot IDs Conceptwiki mapping Target URIs Target by pharmacology Results Filter by EC50
    • 13. From Tailored Prototyping to a Toolbox Modularisation of partial solutions along Open PHACTS API calls OUTPUT ISIS/Draw Sketcher Molecule from SMILES Similarity search INPUT 13 Viewer
    • 14. Mapping API Calls to Components 14
    • 15. Open PHACTS Hierarchical Data Structure A Challenge for Pipeline Pilot Data Tree Functionality 15
    • 16. Unfolding the Open PHACTS Data Hierarchy 16
    • 17. Thank you! Slides: • Lee Harland (Connected Discovery Ltd.) • Jack Gibb (Royal Society of Chemistry) • Chris Chau (GlaxoSmithKline) • … and many other authors from EFPIA and Open PHACTS Administration: • Stefan Senger (GlaxoSmithKline) • Noj Malcolm (Accelrys) Merck Serono: • Thomas Grombacher • Oliver Karch • Friedrich Rippmann 17