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Getting Serious about a Community Bio-Service Catalogue Carole Goble and Katy Wolstencroft OMII-UK http://www.omii.ac.uk my Grid Project http://www.mygrid.org.uk The University of Manchester, UK http://img.cs.man.ac.uk
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
[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
Taverna Workflow Workbench http://taverna.sourceforge.net
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Information Providers Information Consumers Decoupled suppliers and consumers
Shim Services
A Community Bio-Service Catalogue  ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Importers Importers Ontology Editor Ontologists Domain Service  Registry Shim Service  Registry Workflow  repository Registry Manager Repository Manager Service Providers Public Annotation Tool Shim Service  Registry Domain  Services Domain  Services Shim Services Shim Services Extraction Importers Expert Annotation Tool Expert Annotator Chameleon   change  handler Feta Discovery Tool Feta GUI Text Discovery Scientists Ontology Exporter Publication Services Discovery Services Registry Services Ontology Services BioBay Browsing GUI MatchMaker Auto Annotation Khalid Belhajjame et al Automatic Annotation of Web Services based on Workflow Definitions , ISWC2006
Semantic Infrastructure ,[object Object],[object Object],OPERATION name description task method resource PARAMETER name description namespace objectType SERVICE name description dc: format ORGANISATION name description dc: publisher hasInput hasOutput hasOperation hasOperation my Grid Service Ontology my Grid   Domain Ontology
Tools, Tools, Tools Feta Search tool Pedro Annotation tool
webTaverna GUI  - main
 
Adapt what is out there
Adapt what we have?!? http://biomoby.open-bio.org/
Adapt what we have?!?
Curation Ontology curation team OWL RDFS Service curation team Annotate Services for user discovery Annotate Services for shim discovery Service + Domain Ontology Shim Ontology and Mismatch Ontology Ontology curation team Community taggers Annotate Services for user discovery Scientists Service discovery Service + Domain Ontology OWL Workflow Composition Workflow matchmaker
Capture and Curation Effort Ontology and Annotation Curation Team Franck Tanoh and Katy Wolstencroft Community Service Providers Community Scientists
Community Buy-In ,[object Object],[object Object],[object Object]
Institutional Support ,[object Object],[object Object],[object Object]
So why is it taking so damn long? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Let’s get serious ,[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Acknowledgements

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Getting Serious About A Community Bio Service Catalogue

  • 1. Getting Serious about a Community Bio-Service Catalogue Carole Goble and Katy Wolstencroft OMII-UK http://www.omii.ac.uk my Grid Project http://www.mygrid.org.uk The University of Manchester, UK http://img.cs.man.ac.uk
  • 2. 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
  • 3. [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
  • 4. Taverna Workflow Workbench http://taverna.sourceforge.net
  • 5.
  • 6.
  • 7. Information Providers Information Consumers Decoupled suppliers and consumers
  • 9.
  • 10. Importers Importers Ontology Editor Ontologists Domain Service Registry Shim Service Registry Workflow repository Registry Manager Repository Manager Service Providers Public Annotation Tool Shim Service Registry Domain Services Domain Services Shim Services Shim Services Extraction Importers Expert Annotation Tool Expert Annotator Chameleon change handler Feta Discovery Tool Feta GUI Text Discovery Scientists Ontology Exporter Publication Services Discovery Services Registry Services Ontology Services BioBay Browsing GUI MatchMaker Auto Annotation Khalid Belhajjame et al Automatic Annotation of Web Services based on Workflow Definitions , ISWC2006
  • 11.
  • 12. Tools, Tools, Tools Feta Search tool Pedro Annotation tool
  • 13. webTaverna GUI - main
  • 14.  
  • 15. Adapt what is out there
  • 16. Adapt what we have?!? http://biomoby.open-bio.org/
  • 17. Adapt what we have?!?
  • 18. Curation Ontology curation team OWL RDFS Service curation team Annotate Services for user discovery Annotate Services for shim discovery Service + Domain Ontology Shim Ontology and Mismatch Ontology Ontology curation team Community taggers Annotate Services for user discovery Scientists Service discovery Service + Domain Ontology OWL Workflow Composition Workflow matchmaker
  • 19. Capture and Curation Effort Ontology and Annotation Curation Team Franck Tanoh and Katy Wolstencroft Community Service Providers Community Scientists
  • 20.
  • 21.
  • 22.
  • 23.
  • 24.

Editor's Notes

  1. ; currently 850 databases are publicly web-accessible [1]. To get the most value out of these resources, however, they need to be able to integrate, interrogate and mine heterogeneous data and associated knowledge from distributed sources.
  2. The service providers, decoupled from their consumers, have no obligation to supply such information and no great incentive either.
  3. The automatic reconstruction of genome-scale yeast metabolic pathways from distributed data in the life sciences. Taverna extended to create and manipulate Systems Biology Markup Models.
  4. Technical Infrastructure But its still not all joined up!! Feta keeps coming and going. Grid service descriptions are produced by annotating services with terms from the myGrid ontology, stored in a central registry, GRIMOIRES. Services are found using the Feta discovery service [5]. We have piloted expert manual annotation tools augmented by automated tools using information extraction techniques.
  5. Semantic Infrastructure the controlled vocabulary for our annotations is an suite of ontologies written in OWL, and deployed as RDFS, that describe the bioinformatics research domain and the dimensions with which a service can be characterised from the perspective of the scientist , not the software developer [6].
  6. Tools: Feta uses a “query and respond” registry interface, deployed chiefly as a plug-in to the Taverna workbench. However, for many users an Amazon-style web based browser is preferable, so scientists can “go shopping” for web services; we have piloted BioBay that adapts shopping metaphors to science service discovery [7]. Going further, our myExperiment activity is designing and building a “MySpace-like” collaboration environment, in partnership with an international focus group of users, for light-touch hosting of the registry and a user-controlled workflow and data exchange platform [8].
  7. Would be preceded by Feta Screenshot
  8. We did all sorts of fancy repository ideas and data sharing ideas. But actually something simple is what they needed. Would be preceeded by old MIR screenshot.
  9. BioMOBY Dashboard GO tools for annotation and discovery Flickr style tagging tool!
  10. BioMOBY Dashboard GO tools for annotation and discovery Flickr style tagging tool!
  11. Capture and Curation effort: For the semantic discovery framework to be effective, a critical-mass of service descriptions have to be present. We have employed a full-time curator for the provision and maintenance of these annotations and to design annotation tools for future service providers, and begun to develop the Chameleon infrastructure to help cope with the impact of changes to the services and ontologies on the annotations [9].
  12. Not just annotation, but checking the services still there and mirroring them.
  13. How many services do we need to annotate to make it useful or make a difference? Don’t know. Key services everyone uses? Services that are “tipping points” in workflows? Services that are rare? What about mirroring the services? How reliable are they? How transient are they? Will they still be there tomorrow? If I can’t rely on them I won’t include them in a workflow. What about local services? They are exchange-blockers.