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

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

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

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

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

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. Semantics Computer Science Bioinformatics Clinical & Public Health BioHealth informatics Semantics@Manchester Ontologies –Ontology for Psychosis http://www.neuropsygrid.org/ 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

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.manchesterhttp://owl.cs.manchester http://www.co-ode.org/

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

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. Papyro 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 http://utopia.cs.man.ac.uk/ 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. Scientific Workflow Document Process Data Tools

13. Scientific Workflow Document Process Data Tools

14. Workflow Enactor Engine 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. 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 Taverna 2 Workflow Application Platform 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

17. 1472 users 129 groups 562 workflows 157 files 44 packs 16000+ unique Visits Taverna, Triana, Trident, GWorkflowDL, WSVLAM, Kepler, BioExtractor, Pipeline Pilot… http://www.myexperiment.org

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

19. Workflow Enactor Engine

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

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

22. 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

23. Franck Tanoh Simon Jupp Jiten Bhagat Sean Bechhofer Steve Pettifer Paul Fisher Katy Wolstencroft Paolo Missier Shoaib SufiJohn Ainsworth

24. Basic and Applied Research User Engagement & Support System Integration & Collaboration Development & Deployment Science Knowledge Transfer Technology Transfer Platform for Applied Research Driver for Basic Research Exploitation & Innovation Software Engineers Bioinformaticians Computer Scientists Adoption Relevance Theory Practice