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EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery
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EDF2014: Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands Open PHACTS: A Data Platform for Drug Discovery

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Invited Talk by Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands at the European Data Forum 2014, 20 March 2014 in Athens, Greece: Open PHACTS: …

Invited Talk by Paul Groth, Department of Computer Science & The Network Institute, VU University Amsterdam, Netherlands at the European Data Forum 2014, 20 March 2014 in Athens, Greece: Open PHACTS: A Data Platform for Drug Discovery.

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  • 10Can go get everythingOPS not a repo of the world, specific sources
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  • MOE: Molecular Operating Environment http://www.chemcomp.com
  • Transcript

    • 1. A Data Platform for Drug Discovery Paul Groth (@pgroth) http://www.few.vu.nl/~pgroth
    • 2. 1. WHY 2. THE PLATFORM 3. APPS 4. THE FUTURE
    • 3. Pre-competitive Informatics: Pharma are all accessing, processing, storing & re-processing external research data Literature PubChem Genbank Patents Databases Downloads Data Integration Data Analysis Firewalled Databases Repeat @ each company x Lowering industry firewalls: pre-competitive informatics in drug discovery Nature Reviews Drug Discovery (2009) 8, 701-708 doi:10.1038/nrd2944
    • 4. Number sum Nr of 1 Question 15 12 9 All oxidoreductase inhibitors active <100nM in both human and mouse 18 14 8 Given compound X, what is its predicted secondary pharmacology? What are the on and off,target safety concerns for a compound? What is the evidence and how reliable is that evidence (journal impact factor, KOL) for findings associated with a compound? 24 13 8 Given a target find me all actives against that target. Find/predict polypharmacology of actives. Determine ADMET profile of actives. 32 13 8 For a given interaction profile, give me compounds similar to it. 37 13 8 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. 38 13 8 Retrieve all experimental and clinical data for a given list of compounds defined by their chemical structure (with options to match stereochemistry or not). 41 13 8 A project is considering Protein Kinase C Alpha (PRKCA) as a target. What are all the compounds known to modulate the target directly? What are the compounds that may modulate the target directly? i.e. return all cmpds active in assays where the resolution is at least at the level of the target family (i.e. PKC) both from structured assay databases and the literature. 44 13 8 Give me all active compounds on a given target with the relevant assay data 46 13 8 Give me the compound(s) which hit most specifically the multiple targets in a given pathway (disease) 59 14 8 Identify all known protein-protein interaction inhibitors Business Question Driven Approach http://www.sciencedirect.com/science/article/pii/S1359644613001542
    • 5. ChEMBL DrugBank Gene Ontology Wikipathways UniProt ChemSpider UMLS ConceptWiki ChEBI TrialTrove GVKBio GeneGo TR Integrity “Find me compounds that inhibit targets in NFkB pathway assayed in only functional assays with a potency <1 μM” “What is the selectivity profile of known p38 inhibitors?” “Let me compare MW, logP and PSA for known oxidoreductase inhibitors”
    • 6. THE OPEN PHACTS DISCOVERY PLATFORM
    • 7. Nanopub Db VoID Data Cache (Virtuoso Triple Store) Semantic Workflow Engine Linked Data API (RDF/XML, TTL, JSON) Domain Specific Services Identity Resolution Service Chemistry Registration Normalisation & Q/C Identifier Management Service Indexing CorePlatform P12374 EC2.43.4 CS4532 “Adenosine receptor 2a” VoID Db Nanopub Db VoID Db VoID Nanopub VoID Public Content Commercial Public Ontologies User Annotations Apps
    • 8. Data Sources Compound Disease (in testing) PathwayTarget ✔ ✔ ✔
    • 9. Play! https://dev.openphacts.org/
    • 10. Secure Cloud Hosted + Virtualized Triple Store - Virtuoso 7 column store - Scale to > 100 billion triples Network - AMX-IS - Extensive memcache - Monitored Hardware (development) - 2 x Intel Xeon E5-2640 
- 384 GB DDR3 1333MHz RAM
- 1.5 TB SSD 
- 3TB 7200rpm
    • 11. Dealing With The Really Tough Parts John Wilbanks http://del-fi.org/ Data Licensing
    • 12. Provenance everywhere
    • 13. Its easy to integrate, difficult to integrate well:
    • 14. PubChemDrugbankChemSpider Imatinib Mesylate What Is Gleevec?
    • 15. Strict Relaxed Analysing Browsing Dynamic Equality LinkSet#1 { chemspider:gleevec hasParent imatinib ... drugbank:gleevec exactMatch imatinib ... } chemspider:gleevec drugbank:gleevec
    • 16. APPS
    • 17. API Hits (April 2013 – March 2014)
    • 18. http://explorer.openphacts.org
    • 19. ChemBioNavigtor 1 March 2013 Open PHACTS Tech Talk @ CSHALS2013 22
    • 20. THE FUTURE
    • 21. App Developers Data Providers Pharma Companies Academic Research Next Gen IT Life Science Companies Connecting Communities
    • 22. Sustaining Impact “Software is free like puppies are free - they both need money for maintenance” …and more resource for future development
    • 23. Pfizer Limited – Coordinator Universität Wien – Managing entity Technical University of Denmark University of Hamburg, Center for Bioinformatics BioSolveIT GmBH Consorci Mar Parc de Salut de Barcelona Leiden University Medical Centre Royal Society of Chemistry Vrije Universiteit Amsterdam Spanish National Cancer Research Centre University of Manchester Maastricht University Aqnowledge University of Santiago de Compostela Rheinische Friedrich-Wilhelms-Universität Bonn AstraZeneca GlaxoSmithKline Esteve Novartis Merck Serono H. Lundbeck A/S Eli Lilly Netherlands Bioinformatics Centre Swiss Institute of Bioinformatics ConnectedDiscovery EMBL-European Bioinformatics Institute Janssen OpenLink pmu@openphacts.org @Open_PHACTS Open PHACTS
    • 24. Backup
    • 25. Present Content
    • 26. hTRPV1  2328 ligands from Open PHACTS HEK293 capsaicin http://www.openphacts.org TRPV1

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