BigDataEurope - Big Data & Health

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Big Data and the Health domain (vis-a-vis the respective H2020 Societal Challenge) - Opportunities, Challenges and Requirements. As presented and discussed in the public launch of the BigDataEurope project.

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  • Open open open
    And its not just pharma companies
  • 10’
  • Open and free
    Raising standard of resources for ALL researchers
  • integration of heterogeneous data sources
    Mashup
    Open and private
    Need it all
    Get answers in hands of people that need them without waiting for expert to dig it up
  • pharmacology and biomarkers, disease categorisation and data analysis
    CONTEXT AND PROVENANCE
  • It was a big data and semantics experiment AND IT WORKED !!!
    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
  • Fundamental issue:
    There is a *lot* of science outside your walls
    It’s a chaotic space
    Scientists want to find information quickly and easily
    Often they just “cant get there” (or don’t even know where “there” is)
    And you have to manage it all (or not)
  • BigDataEurope - Big Data & Health

    1. 1. BIG DATA & DRUG DISCOVERY Opportunities, Challenges and Requirements27/2/2015
    2. 2. Literature PubChem Genbank Patents Databases Downloads Data Integration Data Analysis Firewalled Databases Repeat @ each companyx Lowering industry firewalls: pre-competitive informatics in drug discovery Nature Reviews Drug Discovery (2009) 8, 701-708 doi:10.1038/nrd2944 Pre-competitive Informatics: Pharma companies are all accessing, processing, storing & re-processing external open research data
    3. 3. • EC funded public-private partnership for pharmaceutical research • Focus on key problems – Efficacy, Safety, Education & Training, Knowledge Management The Innovative Medicines Initiative The Open PHACTS Project • Create a semantic integration hub (“Open Pharmacological Space”)… • Runs 2011-2014, ENSO till 2016 • Deliver services 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 • 10 EFPIA companies, 15 academics, 6 SMEs • Focus on sustainability and long term impact of the Open PHACTS infrastructure
    4. 4. Integrate Multiple Research Biomedical Data Resources Into A Single Open & Free Access Point Open PHACTS Mission
    5. 5. ChEMBL DrugBank Gene Ontology Wikipathways UniProt ChemSpider UMLS ConceptWiki ChEBI TrialTrove GVKBio GeneGo TR Integrity What do research scientists want to know?
    6. 6. 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 Questions’
    7. 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 The Open PHACTS Discovery Platform http://dx.doi.org/10.1016/j.websem.2014.03.003
    8. 8. Sustaining Impact  “Software is free like puppies are free - they both need money for maintenance”  …and more resource for future development
    9. 9. How do we move data about and integrate it?
    10. 10. http://imgs.xkcd.com/comics/standards.png Data Standardisation is vital
    11. 11. P12047 X31045 GB:29384 Yet the bioscience world really struggles to agree on names
    12. 12. info@openphactsfoundation.org @Open_PHACTS Open PHACTS Practical Semantics bryn@openphactsfoundation.org Acknowledgements GlaxoSmithKline – 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 Novartis Merck Serono H. Lundbeck A/S Eli Lilly Netherlands Bioinformatics Centre Swiss Institute of Bioinformatics ConnectedDiscovery EMBL-European Bioinformatics Institute Janssen Esteve Almirall OpenLink Scibite 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 Pfizer

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