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Paul Groth few.vu.nl /~ pgroth / @ pgroth VU University Amsterdam

Paul Groth http:// www.few.vu.nl /~ pgroth / @ pgroth VU University Amsterdam Convergence Meeting: Semantic Interoperability for Clinical Research & Patient Safety in Europe. The Problem. We are all doing this many times……. Pfizer. AZ. GSK. Merck. n. Open PHACTS objective. Platform.

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Paul Groth few.vu.nl /~ pgroth / @ pgroth VU University Amsterdam

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  1. Paul Groth http://www.few.vu.nl/~pgroth/ @pgroth VU University Amsterdam Convergence Meeting: Semantic Interoperability for Clinical Research & Patient Safety in Europe Convergence Meeting: Semantic Interoperability for Clinical Research & Patient Safety in Europe

  2. The Problem We are all doing this many times…… Pfizer AZ GSK Merck n

  3. Open PHACTS objective Platform Apps Standards API Convergence Meeting: Semantic Interoperability for Clinical Research & Patient Safety in Europe

  4. Partners Convergence Meeting: Semantic Interoperability for Clinical Research & Patient Safety in Europe

  5. Associate Partners Sequenomics Convergence Meeting: Semantic Interoperability for Clinical Research & Patient Safety in Europe

  6. “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” DrugBank Wikipathways GeneGo ChEMBL Gene Ontology ChEBI UniProt UMLS GVKBio ConceptWiki ChemSpider TrialTrove TR Integrity Convergence Meeting: Semantic Interoperability for Clinical Research & Patient Safety in Europe

  7. Open PHACTS Explorer Convergence Meeting: Semantic Interoperability for Clinical Research & Patient Safety in Europe

  8. PharmaTrek

  9. ChemBioNavigtor Convergence Meeting: Semantic Interoperability for Clinical Research & Patient Safety in Europe

  10. Utopia Documents Convergence Meeting: Semantic Interoperability for Clinical Research & Patient Safety in Europe

  11. Semantic interoperability approach Principles • Respect data providers • Make it easy for application developers Convergence Meeting: Semantic Interoperability for Clinical Research & Patient Safety in Europe

  12. Semantic interoperability approach Convergence Meeting: Semantic Interoperability for Clinical Research & Patient Safety in Europe

  13. Semantic Resources – Data sets • 814,535,923 triples Convergence Meeting: Semantic Interoperability for Clinical Research & Patient Safety in Europe

  14. Semantic Resources - Mappings 18 Million Mappings Convergence Meeting: Semantic Interoperability for Clinical Research & Patient Safety in Europe

  15. Semantic resources - Summary • Types of semantic resources • RDF Datasets • Mappings • Terminologies • Mesh, UMLS, NCIM • Hierarchies are essential • E.G. Target Ontology, Gene Ontology, Enzyme classification • Class reasoning is essential Convergence Meeting: Semantic Interoperability for Clinical Research & Patient Safety in Europe

  16. Methodology for semantic integration • Define use cases • Data Providers – create RDF with VoID headers • Create mappings • between dataset and known datasets (instance level) • index for text to url conversion • Ingest RDF into data cache (i.e. triple store) • Define access paths to core concepts in data • Extend or create sparql queries for API calls • Publish api calls Convergence Meeting: Semantic Interoperability for Clinical Research & Patient Safety in Europe

  17. Its easy to integrate, but difficult to integrate well

  18. Adoption of standards • Basic Semweb 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 Convergence Meeting: Semantic Interoperability for Clinical Research & Patient Safety in Europe

  19. Tooling • Infrastructure • Linked Data API • Bridge DB - identifier to identifier mapping • Concept Wiki - text to identifier mapping and curation • Chemspider: chemistry registration and services • Triple Store: Virtuoso Professional addition • Data • VoID descriptions and http and ftp sites • Github for data conversion scripts • Recommend turtle as RDF syntax • friendly for scripting Convergence Meeting: Semantic Interoperability for Clinical Research & Patient Safety in Europe

  20. Quality assurance of the semantic resources • Provenance Everywhere • Validation • ChemSpider Validation and Standardization Platform (CVSP) for flagging chemical representation issues • Curation • High quality chemical names and synonyms. • Curation interfaces for terminologies (concept wiki) • Report data quality issues to data providers Convergence Meeting: Semantic Interoperability for Clinical Research & Patient Safety in Europe

  21. Semantic interoperability issues • Do not underestimate infrastructure • APIs are important • Allows for tuning of sparql queries • Makes it easy for developers • Ontologies- Requirements vs. Recommendation • Modeling is hard Convergence Meeting: Semantic Interoperability for Clinical Research & Patient Safety in Europe

  22. Open PHACTS Information • http://www.openphacts.org • pmu@openphacts.org • @Open_PHACTS • Publications • Overview paper: Williams, A.J., Harland, L., Groth, P., Pettifer, S., Chichester, C., Willighagen, E.L., Evelo, C.T., Blomberg, N., Ecker, G., Goble, C., Mons, B.: Open PHACTS: Semantic interoperability for drug discovery. Drug Discovery Today. 17, 1188–1198 (2012). • Technical approach: Gray, A.J.G., Groth, P., Loizou, A., et al.: Applying linked data approaches to pharmacology: Architectural decisions and implementation. Semantic Web. (2012). Convergence Meeting: Semantic Interoperability for Clinical Research & Patient Safety in Europe

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