Semantic Professor Carole Goble

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

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

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

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

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 Computer Science Bioinformatics Clinical & Public Health BioHealth informatics Ontologies –Ontology for Psychosis Research –Reasoners and expressivity –Languages –Ontology building, text mining –Explanation, modularisation –Methodologies –Collaborative ontology development Training –1st-2nd April 2009 Building OWL ontologies 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

Enterprise Search Document Text Mining Semantic Technologies Visualisation Data Tools Document

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

Papyro Interactive tools for analysing protein sequence and structure based on a semantic platform. Visualisation, semantic service annotations, semantic layout, workflows, RDF store registered users + many more anonymous users 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 Document Process Data Tools

Scientific Workflow Document Process Data Tools

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

Access to public service operations 57,048 sourceforge downloads 5822 downloads v downloads v 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

1472 users 129 groups 562 workflows 157 files 44 packs unique Visits Taverna, Triana, Trident, GWorkflowDL, WSVLAM, Kepler, BioExtractor, Pipeline Pilot…

Started June 08 Closed pilot Dec 08 Pilot release April 09 BioCatalogue-Friends focus group Perpetual beta Three year award

Workflow Enactor Engine

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

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

Schedule 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) Biocatalogue (Carole Goble, Jiten Bhagat) UTOPIA and Papyro (Steve Pettifer ) Discussion and identification of other people to speak to. Manchester Informatics Launch registration and dinner

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

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