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Tissue Knowledge Management Workshop: Discovering and Managing Public Drug Discovery Data

Learn how to access, process, store, and manage public drug discovery data for tissue knowledge management at the Tissue Knowledge Management Workshop in Brussels.

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Tissue Knowledge Management Workshop: Discovering and Managing Public Drug Discovery Data

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  1. How does it work? How can it work for tissue knowledge management? Christine Chichester @isb-sib.ch IMI Tissue Knowledge Management Workshop, Brussels

  2. Public Drug Discovery Data:Pharma are accessing, processing, storing, and re-processing public data repeatedly The Challenge

  3. Overview • The Open PHACTS project has many non-technical benefits • The Open PHACTS discovery platform has many technical benefits • Outline • Ecosystem and technical overview • Data sources, integration, and delivery • Dynamic equality via scientific lenses • Community engagement

  4. Components of Open PHACTS Platform SSchurer@med.miami.edu SSchurer@med.miami.edu API Standards Apps

  5. Platform Overview Applications Linked Data API (RDF/XML, TTL, JSON) Identity Resolution Service Domain Specific Services “Adenosine receptor 2a” Semantic Workflow Engine Identifier Management Service P12374 EC2.43.4 Core Platform CS4532 Data Cache (Virtuoso Triple Store) Chemistry Registration Normalisation& Q/C indexing VoID VoID VoID VoID VoID RDF RDF Nanopub Nanopub Nanopub RDF RDF RDF Public Ontologies Db Db Db Db User Annotations Public Content Commercial

  6. Data sources and direct mappings HMDB ChEMBL CAS DrugBank KEGG cmpds PubChemcmpd ChemSpider ChEBI Wikipedia RGD ENZYME MeSH neXtProt WormBase ChEMBL Target Class FlyBase UniProt Ensembl UniGene SGD ConceptWiki ZFIN Gene Ontology MEROPS DisGeNet MGI EntrezGene FDA adverse events Wikipathways PathwayOnto PDB RefSeq Clinical trials.org InterPro

  7. Accessing the platform: Uses URI’s Linked Data API (RDF/XML, TTL, JSON)

  8. API Interaction for data delivery • Resolve User Input • 1. User enters textual string • 2. Resolve to URI for a concept • Request Data about URI (other API calls) • Expand URI for equivalences in each dataset • Run SPARQL query with URIs • Can include filters and restrictions on data returned • Download data in TSV format, import into Excel

  9. Data for ddmore use case • Map compound textual name to URI • Search for compound pharmacology and filter for specific targets • Search for expressiondata for targets • Expression data still in test environment

  10. Flexible mappings Strict Relaxed Analysing Browsing Gives different views on data depending on granularity requirements Scientific Lens Identity Resolution Service “Adenosine receptor 2a” • Tuneable (same data, different questions) • Domain specific • User driven • Traceable Identifier Management Service P12374 EC2.43.4 CS4532

  11. Different views on data

  12. Dynamic equality : Strict

  13. Dynamic equality : Relaxed

  14. Scientific lens for tissue knowledge Flexible mappings Lens #1 Lens #2 Lens #3? Tissues Gross Anatomy Cell Types Genotype-Phenotype Expression Sign, Symptoms, Radiological findings Molecular Pathways UBERON Cell Ontology Foundational Model of Anatomy

  15. Community: Associated Partners

  16. Community building • Open Development: Open Source • Open API: no restrictions • Reuse standards • Respect data providers: provenance, feedback

  17. Acknowledgements Open PHACTS Project Partners Spanish National Cancer Research Centre University of Manchester Maastricht University Aqnowledge University of Santiago de Compostela RheinischeFriedrich-Wilhelms-UniversitätBonn AstraZeneca GlaxoSmithKline Esteve www.openphacts.org Novartis Merck H. Lundbeck A/S Eli Lilly Netherlands Bioinformatics Centre Swiss Institute of Bioinformatics ConnectedDiscovery EMBL-European Bioinformatics Institute Janssen OpenLink Pfizer Limited – Coordinator UniversitätWien – Managing entity Technical University of Denmark University of Hamburg, Center for Bioinformatics BioSolveITGmBH ConsorciMar Parc de Salut de Barcelona Leiden University Medical Centre Royal Society of Chemistry VrijeUniversiteit Amsterdam

  18. Assertion Provenance - nanopublication • Highly curated database • Give credit to the curators • Provenance at the record level • Extends existing RDF based infrastructure • Progressively add these features as needed Provenance Publication Information PTM Nanopublication

  19. Explorer

  20. Workflows

  21. PharmaTrek

  22. Utopia

  23. ChemBioNavigator

  24. iPharm

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