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Semantic e-(Life)Science @Manchester

Semantic e-(Life)Science @Manchester. Professor Carole Goble carole.goble@manchester.ac.uk. Semantics. Bioinformatics. Computer Science. Biology. BioHealth informatics. Clinical & Public Health. Social Science. Bioinformatics. Computer Science. Biology. BioHealth informatics.

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Semantic e-(Life)Science @Manchester

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  1. Semantic e-(Life)Science @Manchester Professor Carole Goble carole.goble@manchester.ac.uk

  2. Semantics Bioinformatics Computer Science Biology BioHealth informatics Clinical & Public Health Social Science

  3. Bioinformatics Computer Science Biology BioHealth informatics Clinical & Public Health Social Science MIB North West eHealth e-Science North West Centre Manchester Informatics Research Computing Services North West Grid

  4. BioHealth Informatics Group Open Middleware Infrastructure Institute-UK National Centre for Text Mining Manchester Centre for Integrative Systems Biology National Centre e-Social Science North West Institute for BioHealth Informatics eScience@Manchester North West e-Health Information Management Group Manchester Interdisciplinary BioCentre

  5. Computer Science Biology Bioinformatics BioHealth informatics Clinical & Public Health Obesity eLab Social Science CLAHRC Collaboration for Leadership in Applied Health Research and Care Shared genomics e-Lico

  6. Collaboration and Standards • Bio-Standardisation: FUGE, OBI, SBML, SBRML, MIAME, BioPAX, MIBBI • Networks: EMBRACE, CASIMIR, IPlant, BioSapien, Enfin • Systems Biology Centres throughout UK and EU • NBIC: Dutch National Bioinformatics Centre • caBIG: cancer Biomedical Informatics Grid • SysMO: Systems Biology of MicroOrganisms • EMBL-European Bioinformatics Institute

  7. Ontologies Ontology for Psychosis http://www.neuropsygrid.org/ Research Reasoners and expressivity Languages Ontology building, text mining Explanation, modularisation Methodologies Collaborative ontology development Training 1st-2nd April 2009 Building OWL ontologies tutorial @ Manchester Semantics Bioinformatics Computer Science BioHealth informatics Clinical & Public Health Semantics@Manchester

  8. Semantics@Manchester Languages and Standardisation • OWL, SWRL, RDF, SKOS, Probabilistic OWL • SPARQL, SPARQL/OWL, RIF • WDSL, WS-Policy, OWL-S, SWSI Tools • Protégé 4, SWOOP, SKOSed • Reasoners: Fact++, Pellet • OWL API, SKOS API and OPPL • Applications • Semantic Web Services, Risk Assessment, Medical Image Annotation, Semantic Document Hyperlinking, Classifying Entities/Data, Form Generation, Policy analysis, Semantic Grid metadata management http://owl.cs.manchester http://www.co-ode.org/

  9. Data Tools Document Document Enterprise Search Text Mining Visualisation Semantic Technologies

  10. Semantic Grid Browser for the Life Sciences Study of infectious disease, From cells, via tissues to patients - Evidence-based medicine - Patent and Literature mining - Molecular Biology Connecting existing Web to e-science infrastructure Text-mining, ontologies and workflows GoPubMed: Semantic search COHSE: Conceptual Open Hypermedia Service CORESE: COnceptual REsource Search Engine SKOS: Simple Knowledge Organization System http://cohse.cs.manchester.ac.uk/ http://www.biotec.tu-dresden.de/sealife

  11. http://utopia.cs.man.ac.uk/ Interactive tools for analysing protein sequence and structure based on a semantic platform. Visualisation, semantic service annotations, semantic layout, workflows, RDF store. 2000+ registered users + many more anonymous users Papyro Exploring the scientific literature and seamless linking between data, publications and methods. Typographic analysis of PDF documents; mimicked-reading; rich interaction with document content.

  12. Data Tools Document Scientific Workflow Process Process

  13. Data Tools Document Scientific Workflow Process Process

  14. Workflow Application Platform Workflow Enactor Engine Taverna Graphical workbench Drag and drop interface Plug-in architecture Nested Workflows Incorporate new service without coding. Access to local and remote resources and analysis tools Workflow enactor Local and remote enactor Implicit iteration over large data collections Automation of data flow Logging and data provenance tracking long running workflows, data reference handling, data streaming and staging, multiple extensibility points. 2 2 http://www.taverna.org.uk

  15. Access to 3000+ public service operations 57,048 sourceforge downloads 5822 downloads v1.7 1239 downloads v2.0 727+ active users at the moment 328 organisations 17 known commercial Users throughout UK, Europe, North America, SE Asia, Latin America, and Australasia. Netherlands Bioinformatics Centre Genome Canada Bioinformatics Platform BioMOBY US iPlant Consortium US FLOSS social science program RENCI French SIGENAE farm animals project ThaiGrid CARMEN Neuroscience project SPINE consortium EU Enfin, EMBRACE, BioSapian, Casimir EU SysMO Consortium NERC Centre for Ecology and Hydrology Bergen Centre for Computational Biology Max-Planck institute for Plant Breeding Research Genoa Cancer Research Centre AstroGrid 30 USA academic and research institutions

  16. http://www.myexperiment.org 1472 users 129 groups 562 workflows 157 files 44 packs 16000+ unique Visits Taverna, Triana, Trident, GWorkflowDL, WSVLAM, Kepler, BioExtractor, Pipeline Pilot…

  17. Started June 08 • Closed pilot Dec 08 • Pilot release April 09 • BioCatalogue-Friends focus group • Perpetual beta • Three year award http://www.biocatalogue.org

  18. Workflow Enactor Engine

  19. Research Methods Experts Development e-Laboratory Scientific Research Objects Scripts Data sets Services Publications Workflows Application e-Laboratory Delivery Experts Policy makers

  20. Harnessing Local Ownership in a Federationof Service-Development and Research Assets F I R E W A L L ResearchNetworks e-Lab Local NHS Research e-Lab Local NHS Local NHS e-Lab Service development Federation of e-Labs  scalable & sustainable

  21. Schedule 10.00 - 10.10   Introductions 10.10 - 10.30   Presentation by Eli-Lilly 10.30 - 10.50   Manchester: overview (Carole Goble) 10.50 - 11.20   SKOS (Sean Bechhofer) 11.20 - 11.50   Sealife (Simon Jupp) 11.50 - 12.30   Discussion 12.30 - 12.50   Lunch 12.50 - 13.10   e-Labs - (Sean Bechhofer) 13.10 - 13.40   Obesity e-Lab (Shoaib Sufi) 14.40 - 14.10   Discussion 14.10 - 14.40   Taverna and myExperiment (Katy Wolstencroft and Paul Fisher) 14.40 - 15.10   Biocatalogue (Carole Goble, Jiten Bhagat) 15.10 - 15.40   UTOPIA and Papyro (Steve Pettifer ) 15.40 - 16.30   Discussion and identification of other people to speak to. Manchester Informatics Launch registration and dinner

  22. Jiten Bhagat Katy Wolstencroft Simon Jupp Steve Pettifer Franck Tanoh Sean Bechhofer Paul Fisher Paolo Missier Shoaib Sufi John Ainsworth

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