Semantic eLifeScience Manchester Professor Carole Goble carole goblemanchester

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

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

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

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

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

Collaboration and Standards • Bio-Standardisation: FUGE, OBI, SBML, SBRML, MIAME, Bio. PAX, MIBBI • Networks: EMBRACE, CASIMIR, IPlant, Bio. Sapien, Enfin • Systems Biology Centres throughout UK and EU • • NBIC: Dutch National Bioinformatics Centre ca. BIG: cancer Biomedical Informatics Grid Sys. MO: Systems Biology of Micro. Organisms EMBL-European Bioinformatics Institute

Semantics@Manchester Ontologies Semantics – Ontology for Psychosis http: //www. neuropsygrid. org/ Research Bioinformatics Computer Science Bio. Health informatics Clinical & Public Health – – – Reasoners and expressivity Languages Ontology building, text mining Explanation, modularisation Methodologies Collaborative ontology development Training – 1 st-2 nd 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 Go. Pub. Med: 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

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

• Access to 3000+ public service operations • 57, 048 sourceforge downloads • 5822 downloads v 1. 7 • 1239 downloads v 2. 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 Bio. MOBY US i. Plant Consortium US FLOSS social science program RENCI French SIGENAE farm animals project Thai. Grid CARMEN Neuroscience project SPINE consortium EU Enfin, EMBRACE, Bio. Sapian, Casimir EU Sys. MO Consortium NERC Centre for Ecology and Hydrology Bergen Centre for Computational Biology Max-Planck institute for Plant Breeding Research Genoa Cancer Research Centre Astro. Grid 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, GWorkflow. DL, WSVLAM, Kepler, Bio. Extractor, Pipeline Pilot…

• • http: //www. biocatalogue. org Started June 08 Closed pilot Dec 08 Pilot release April 09 Bio. Catalogue-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 Service development Federation of e-Labs scalable & sustainable FIREWALL Local NHS Research Networks Research

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 my. Experiment (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