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Semantics
BiologyComputerScience
Bioinformatics
Clinical & Public Health
Social Science
BioHealth informatics
BiologyComputerScience
Bioinformatics
Clinical & Public Health
Social Science
BioHealth informaticsMIB
North West eHealth
e-Science North West CentreManchester Informatics
Research Computing ServicesNorth West Grid
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
ComputerScienceBioinformatics
Clinical & Public Health
Social Science
BioHealth informatics
CLAHRC
ObesityeLab
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
ComputerScience
Bioinformatics
Clinical & Public Health
BioHealth informatics
Semantics@ManchesterOntologies
– 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@ManchesterLanguages 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
ApplicationsSemantic 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 SearchDocument
Text MiningText Mining Semantic TechnologiesSemantic TechnologiesVisualisationVisualisation
Data Tools
Document
Semantic Grid Browser for the Life SciencesStudy of infectious disease, From cells, via tissues to patients- Evidence-based medicine- Patent and Literature mining- Molecular Biology
Connecting existing Web to e-science infrastructureText-mining, ontologies and workflows
GoPubMed: Semantic searchCOHSE: Conceptual Open Hypermedia ServiceCORESE: COnceptual REsource Search EngineSKOS: Simple Knowledge Organization Systemhttp://cohse.cs.manchester.ac.uk/http://www.biotec.tu-dresden.de/sealife
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.
Scientific WorkflowDocument
ProcessProcess ProcessProcess
Data Tools
Scientific WorkflowDocument
ProcessProcess ProcessProcess
Data Tools
Workflow Enactor Engine
Workflow enactorLocal and remote enactorImplicit iteration over large data collectionsAutomation of data flowLogging and data provenance trackinglong running workflows, data reference handling, data streaming and staging, multiple extensibility points.
Graphical workbenchDrag and drop interfacePlug-in architectureNested WorkflowsIncorporate new service without coding. Access to local and remote resources and analysis tools
Taverna
2
Workflow Application Platform2
http://www.taverna.org.uk
• 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 CentreGenome Canada Bioinformatics PlatformBioMOBYUS iPlant ConsortiumUS FLOSS social science programRENCIFrench SIGENAE farm animals projectThaiGridCARMEN Neuroscience projectSPINE consortiumEU Enfin, EMBRACE, BioSapian, CasimirEU SysMO ConsortiumNERC Centre for Ecology and HydrologyBergen Centre for Computational BiologyMax-Planck institute for Plant Breeding
ResearchGenoa Cancer Research CentreAstroGrid
30 USA academic and research institutions
1472 users129 groups
562 workflows157 files44 packs
16000+ unique Visits
Taverna, Triana, Trident,
GWorkflowDL, WSVLAM, Kepler,
BioExtractor, Pipeline Pilot…
http://www.myexperiment.org
• Started June 08• Closed pilot Dec 08• Pilot release April 09• BioCatalogue-Friends focus
group• Perpetual beta• Three year awardhttp://www.biocatalogue.org
Workflow Enactor Engine
Scientific Research Objects
Scientific Research Objects
Workflows
Data sets
Services
Scripts
Publications
Development e-Laboratory
Application e-Laboratory
ResearchMethodsExperts
Policy makers
Delivery Experts
Harnessing Local Ownership in a Federationof Service-Development and Research Assets
Local NHS
Local NHS
Local NHS
e-Lab
e-Lab
e-Lab
ResearchNetworks
Research
Service development
F I R
E W
A L
L
Federation of e-Labs scalable & sustainableFederation of e-Labs scalable & sustainable
Schedule10.00 - 10.10 Introductions 10.10 - 10.30 Presentation by Eli-Lilly10.30 - 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
Franck Tanoh
Simon JuppJiten Bhagat
Sean Bechhofer
Steve Pettifer
Paul Fisher
Katy Wolstencroft
Paolo Missier
Shoaib Sufi John Ainsworth
