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Semantic e-(Life)Science @Manchester Professor Carole Goble [email protected] Semantics Bioinformatics Biology Computer Science BioHealth informatics Clinical & Public Health Social Science Bioinformatics Biology Computer Science MIB BioHealth informatics Clinical & Public Health Social Science North West eHealth e-Science North West Centre Manchester Informatics Research Computing Services North West Grid eScience@Manchester BioHealth Informatics Group Information Management Group Open Middleware Infrastructure Institute-UK National Centre for Text Mining National Centre e-Social Science Manchester Interdisciplinary BioCentre Manchester Centre for Integrative Systems Biology North West Institute for BioHealth Informatics North West e-Health Biology Bioinformatics Computer Science BioHealth informatics Clinical & Public Health CLAHRC Shared genomics e-Lico Collaboration for Leadership in Applied Health Research and Care Obesity Social eLab Science 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 Semantics@Manchester Ontologies Semantics – Ontology for Psychosis http://www.neuropsygrid.org/ Research Bioinformatics Computer Science BioHealth informatics Clinical & Public Health – – – – – – 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@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/ Enterprise Search Document Text Mining Document Data Visualisation Tools Semantic Technologies 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 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. Scientific Workflow Data Document Process Tools Process Scientific Workflow Data Document Process Tools Process 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. http://www.taverna.org.uk 2 Workflow Enactor Engine 2 Workflow Application Platform • 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 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… • • • • http://www.biocatalogue.org Started June 08 Closed pilot Dec 08 Pilot release April 09 BioCatalogue-Friends focus group • Perpetual beta • Three year award Workflow Enactor Engine Research Methods Experts Development e-Laboratory Scripts Data sets Scientific Research Objects Services Publications Workflows Application e-Laboratory Delivery Experts Policy makers Harnessing Local Ownership in a Federation of Service-Development and Research Assets e-Lab Local NHS e-Lab Local NHS e-Lab Service development Federation of e-Labs scalable & sustainable FIREWALL Local NHS Research Networks Research Schedule 10.00 - 10.10 10.10 - 10.30 10.30 - 10.50 10.50 - 11.20 11.20 - 11.50 11.50 - 12.30 12.30 - 12.50 12.50 - 13.10 13.10 - 13.40 14.40 - 14.10 14.10 - 14.40 Introductions Presentation by Eli-Lilly Manchester: overview (Carole Goble) SKOS (Sean Bechhofer) Sealife (Simon Jupp) Discussion Lunch e-Labs - (Sean Bechhofer) Obesity e-Lab (Shoaib Sufi) Discussion 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 Jiten Bhagat Franck Tanoh Shoaib Sufi Simon Jupp Sean Bechhofer John Ainsworth Steve Pettifer Paul Fisher Katy Wolstencroft Paolo Missier