getting serious about a community bio service catalogue

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