The Open PHACTS Discovery Platform

1. The Open PHACTS Discovery Platform Open PHACTS for Academia

2. Generic Competition Patent Expiry Improve R&D Productivity Cost Containment http://www.rsc.org/chemistryworld/Issues/2009/January/PharmaRefocusesOnThePatentCliff.asp PwC - Pharma 2020 – Which Path will you take

3. Public Domain Drug Discovery Data:Pharma are accessing, processing, storing & re-processing

4. GSK Pfizer AstraZeneca Roche Novartis Merck-Serono We are all doing this many times……

5. Over the last decade • Data has become more open • Data has become better represented (Standards) • Major providers are becoming more organised (NCBI, EBI, FDA) BUT Integration across sources, and across providers is still a gap

6. Pre-competitive Informatics: Pharma are all accessing, processing, storing & re-processing external research data 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

7. The Innovative MedicinesInitiative • The Open PHACTS Project • Createa semantic integration hub (“Open Pharmacological Space”)… • Runs 2011-2014, ENSO till 2016 • Deliverservices to support on-going drug discovery programs in pharma and public domain • Leading academics in semantics, pharmacology and informatics, driven by solid industry business requirements • 31 academic partners, 9 pharmaceutical companies, 3 software SMEs • Work split into clusters: • Technical Build • Scientific Drive • Community & Sustainability • EC funded public-private partnership for pharmaceutical research • Focus on key problems • Efficacy, Safety, Education & Training, Knowledge Management

8. Open PHACTS Mission: Integrate Multiple Research Biomedical Data Resources Into A Single Open & FreeAccess Point

9. The Real Mission Starting from a relatively blank canvas, build a pharmacology-centric integration system that’s as good as, or better than, that which pharma already have after decades of working in this space…. …with a distributed set of people who have never met and many of which have not worked on drug-discovery previously… …using an emerging, actively evolving technology… …with an architecture that fulfils the need of both public and private users… …in just over a couple of years… …whilst doing some research at the same time

10. “Let me compare MW, logP and PSA for known oxidoreductase inhibitors” “What is the selectivity profile of known p38 inhibitors?” “Find me compounds that inhibit targets in NFkB pathway assayed in only functional assays with a potency <1 μM” ChEMBL DrugBank Gene Ontology Wikipathways GeneGo ChEBI UniProt UMLS GVKBio ConceptWiki ChemSpider TrialTrove TR Integrity

11. Business Question Driven Approach

12. The open phactsDISCOVERY platform

13. The Open PHACTS Discovery Platform • Cloud-Based “Production” Level System. Secure & Private • Guided By Business Questions • Uses Semantic Web Technology But provides a simple REST-ful API for everyone else http://dx.doi.org/10.1016/j.drudis.2013.05.008 http://dx.doi.org/10.1016/j.websem.2014.03.003

14. http://imgs.xkcd.com/comics/standards.png • Basic Semantic web standards • SPARQL 1.1, RDF(S), SKOS • Dataset descriptions • Vocabulary of InterlinkedDatasets (VoID) • VoIDlinkset descriptions • QUDT Quantities, Units, Dimensions and Types • Provenance • W3C PROV, PAV, Nanopublications • BioPortal, ConceptWiki, ChEMBL, identifiers.org, Uniprot, ChemSpider

15. Are These Two Molecules The Same(*) Yeah No way! *Really: Is it sensible to combine data associated with these two molecules?

16. Data Licensing Solution Chose John Wilbanks as consultant A framework built around STANDARD well-understood Creative Commons licences – and how they interoperate Deal with the problems by: • Interoperable licences • Appropriate terms • Declare expectations to users and data publishers • One size won‘t fit all requirements

18. Kick-Starting Sustainability Apps Open PHACTS Industry Grants Collaboration API Users API

19. Open PHACTS Associate Partner Community

20. Associated partners Development partnerships Influence on API developments Opportunities to demo ideas & use cases to core team Need MoU and annexe Associated partners Organisations, most will join here Support, information Exchange of ideas, data, technology Opportunities to demo at community webinars Need MoU Leveraging Our Community MoU Development partnerships +Annexe Consortium Consortium 31 current members

21. Open PHACTS Mission: Integrate Multiple Research Biomedical Data Resources Into A Single Open & FreeAccess Point

22. Sustaining Impact • “Software is free like puppies are free - they both need money for maintenance” • …and more resource for future development

25. bryn@connecteddiscovery.co.uk Acknowledgements Open PHACTS PracticalSemantics Pfizer Limited – Coordinator Universität Wien – Managing entity Technical University of Denmark University of Hamburg, Center for Bioinformatics BioSolveITGmBH Consorci Mar Parc de Salut de Barcelona Leiden University Medical Centre Royal Society of Chemistry VrijeUniversiteit Amsterdam Novartis Merck Serono H. Lundbeck A/S Eli Lilly Netherlands Bioinformatics Centre Swiss Institute of Bioinformatics ConnectedDiscovery EMBL-European Bioinformatics Institute Janssen EsteveAlmirall OpenLinkScibite The Open PHACTS Foundation Spanish National Cancer Research Centre University of Manchester Maastricht University Aqnowledge University of Santiago de Compostela Rheinische Friedrich-Wilhelms-Universität Bonn AstraZeneca GlaxoSmithKline pmu@openphactsfoundation.org@Open_PHACTS