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Getting Serious about a Community Bio-Service
Catalogue
Carole Goble and Katy WolstencroftOMII-UK http://www.omii.ac.uk
myGrid Project http://www.mygrid.org.uk
The University of Manchester, UK http://img.cs.man.ac.uk
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12181 acatttctac caacagtgga tgaggttgtt ggtctatgtt ctcaccaaat ttggtgttgt 12241 cagtctttta aattttaacc tttagagaag agtcatacag tcaatagcct tttttagctt 12301 gaccatccta atagatacac agtggtgtct cactgtgatt ttaatttgca ttttcctgct 12361 gactaattat gttgagcttg ttaccattta gacaacttca ttagagaagt gtctaatatt 12421 taggtgactt gcctgttttt ttttaattgg gatcttaatt tttttaaatt attgatttgt 12481 aggagctatt tatatattct ggatacaagt tctttatcag atacacagtt tgtgactatt 12541 ttcttataag tctgtggttt ttatattaat gtttttattg atgactgttt tttacaattg 12601 tggttaagta tacatgacat aaaacggatt atcttaacca ttttaaaatg taaaattcga 12661 tggcattaag tacatccaca atattgtgca actatcacca ctatcatact ccaaaagggc 12721 atccaatacc cattaagctg tcactcccca atctcccatt ttcccacccc tgacaatcaa 12781 taacccattt tctgtctcta tggatttgcc tgttctggat attcatatta atagaatcaa
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[Mark Wilkinson, 2006 BioMOBY]
12181 acatttctac caacagtgga tgaggttgtt ggtctatgtt ctcaccaaat ttggtgttgt 12241 cagtctttta aattttaacc tttagagaag agtcatacag tcaatagcct tttttagctt 12301 gaccatccta atagatacac agtggtgtct cactgtgatt ttaatttgca ttttcctgct 12361 gactaattat gttgagcttg ttaccattta gacaacttca ttagagaagt gtctaatatt 12421 taggtgactt gcctgttttt ttttaattgg
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Taverna Workflow Workbenchhttp://taverna.sourceforge.net
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3000+ services Open domain services and
resources. Third party. Enforce NO common data model. No common typing. Missing metadata. Input0: string Output0: string.
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Body Large experiments or large
research groups/labs, possibly distributed
Large service provider institutes.
Tightly coupled provider-consumer of resources.
Commonly resource providers.
Lots of facilities. Some access to sys admin etc
Not many of them
Long tail Small, isolated,
independent, groups/individuals
Loosely coupled provider-consumer of resources.
Commonly resource consumers.
Boutique suppliers. Poor access to facilities,
instruments, sys admins. Many of them – esp. in
Life Sciences!
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Information Providers
Information ConsumersDecoupled
suppliers and consumers
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Shim Services
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A Community Bio-Service Catalogue For myGrid. For other middleware developers like BioMOBY. For application developers in the community. For bioinformaticians.
Semantic annotations for the community’s services. Storage and discovery framework. We have pieces. We have been investigating. We
have been prototyping. Time to get serious! SIX things: tech infrastructure, semantic infrastructure,
tools, curation, community buy-in, institutional support
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ImportersImporters
OntologyEditor
Ontologists
DomainService Registry
ShimService Registry
Workflow repository
RegistryManager
RepositoryManager
Service Providers
PublicAnnotation
Tool
ShimService Registry
Domain ServicesDomain
Services
ShimServicesShim
Services
ExtractionImporters
ExpertAnnotation
Tool
Expert Annotator
Chameleon change handler
FetaDiscovery
Tool
Feta GUI
TextDiscovery
Scientists
OntologyExporter
Publication S
ervicesDiscovery S
ervices
Registry Services
OntologyServices
BioBayBrowsing
GUI
MatchMakerAuto
Annotation
Khalid Belhajjame et alAutomatic Annotation of Web Services based on Workflow Definitions, ISWC2006
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OPERATION
namedescriptiontaskmethodresource
PARAMETER
namedescriptionnamespaceobjectType
SERVICE
namedescriptiondc: format
ORGANISATION
namedescriptiondc: publisher
hasInput hasOutput
hasOperation
hasOperation
myGrid Service OntologymyGrid Domain Ontology
Semantic Infrastructure
Written in OWL, deployed as RDFS The perspective of the scientist
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Tools, Tools, Tools
Feta Search tool
Pedro Annotation tool
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webTaverna GUI - main
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Adapt what is out there
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Adapt what we have?!?
http://biomoby.open-bio.org/
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Adapt what we have?!?
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Ontology curation team
OWL RDFS
Servicecuration team
Annotate Servicesfor user discovery
Annotate Servicesfor shim discovery
Service + Domain Ontology
Shim Ontologyand Mismatch Ontology
Ontology curation team
Community taggers
Annotate Servicesfor user discovery
Scientists
Service discovery
Service + Domain Ontology
OWL
WorkflowComposition
Workflow matchmaker
Curation
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Capture and Curation Effort
Ontology and Annotation Curation Team
Franck Tanoh and Katy Wolstencroft
Community Service Providers
Community Scientists
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Community Buy-In
The services are owned and developed by the community.
Partnership with the European Bioinformatics Institute to improve the metadata for services provided by major suppliers at source, and propagate best practice by example.
Enthusiasm for a catalogue in the community.
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Institutional Support Hosting the registry, curating, resources to
develop the infrastructure, partnering with suppliers.
Sustainability and impact. OMII-UK and the EBI
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So why is it taking so damn long?
The final 9 yards and 80:20 rule. All or nothing. Dedicated resources and best intentions. Content, content, content. Being too damn, and unnecessarily, clever. Can HCLS SIG help?
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Let’s get serious
Its time to get serious about building and managing a catalogue.
The outcome would be a living and useful resource, not just for bioinformaticians but also for those working in the Semantic Web for Life Sciences, or just the Semantic Web.
We have the parts and enough of the know-how. And a means to the content.
So lets. Just. Do. It.
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myGrid project http://www.mygrid.org.uk
BioMOBY project http://biomoby.open-bio.org/
ISPIDER project http://www.ispider.man.ac.uk/
GRIMOIRES project http://twiki.grimoires.org/bin/view/Grimoires/
OMII-UK http://www.omii.ac.uk
EPSRC Genome Canada
Acknowledgements