Transcript Introductions

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
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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
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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
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Workflow Enactor Engine
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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…
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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