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Getting Serious About A Community Bio Service Catalogue

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Why do we need a catalogue of bio Web Services?
Get the answer from these slides presented by Prof. Carole Goble

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Getting Serious About A Community Bio Service Catalogue

  1. 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. 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. 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. 4. Taverna Workflow Workbench http://taverna.sourceforge.net
  5. 5. <ul><li>3000+ services </li></ul><ul><li>Open domain services and resources. </li></ul><ul><li>Third party. </li></ul><ul><li>Enforce NO common data model. </li></ul><ul><li>No common typing. </li></ul><ul><li>Missing metadata. </li></ul><ul><li>Input0: string </li></ul><ul><li>Output0: string </li></ul><ul><li>. </li></ul>
  6. 6. <ul><li>Body </li></ul><ul><ul><li>Large experiments or large research groups/labs, possibly distributed </li></ul></ul><ul><ul><li>Large service provider institutes. </li></ul></ul><ul><ul><li>Tightly coupled provider-consumer of resources. </li></ul></ul><ul><ul><li>Commonly resource providers. </li></ul></ul><ul><ul><li>Lots of facilities. Some access to sys admin etc </li></ul></ul><ul><ul><li>Not many of them </li></ul></ul><ul><li>Long tail </li></ul><ul><ul><li>Small, isolated, independent, groups/individuals </li></ul></ul><ul><ul><li>Loosely coupled provider-consumer of resources. </li></ul></ul><ul><ul><li>Commonly resource consumers. </li></ul></ul><ul><ul><li>Boutique suppliers. </li></ul></ul><ul><ul><li>Poor access to facilities, instruments, sys admins. </li></ul></ul><ul><ul><li>Many of them – esp. in Life Sciences! </li></ul></ul>
  7. 7. Information Providers Information Consumers Decoupled suppliers and consumers
  8. 8. Shim Services
  9. 9. A Community Bio-Service Catalogue <ul><li>For my Grid. </li></ul><ul><li>For other middleware developers like BioMOBY. </li></ul><ul><li>For application developers in the community. </li></ul><ul><li>For bioinformaticians. </li></ul><ul><li>Semantic annotations for the community’s services. </li></ul><ul><li>Storage and discovery framework. </li></ul><ul><li>We have pieces. We have been investigating. We have been prototyping. Time to get serious! </li></ul><ul><li>SIX things: tech infrastructure, semantic infrastructure, tools, curation, community buy-in, institutional support </li></ul>
  10. 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. 11. Semantic Infrastructure <ul><li>Written in OWL, deployed as RDFS </li></ul><ul><li>The perspective of the scientist </li></ul>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
  12. 12. Tools, Tools, Tools Feta Search tool Pedro Annotation tool
  13. 13. webTaverna GUI - main
  14. 15. Adapt what is out there
  15. 16. Adapt what we have?!? http://biomoby.open-bio.org/
  16. 17. Adapt what we have?!?
  17. 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
  18. 19. Capture and Curation Effort Ontology and Annotation Curation Team Franck Tanoh and Katy Wolstencroft Community Service Providers Community Scientists
  19. 20. Community Buy-In <ul><li>The services are owned and developed by the community. </li></ul><ul><li>Partnership with the European Bioinformatics Institute to improve the metadata for services provided by major suppliers at source , and propagate best practice by example . </li></ul><ul><li>Enthusiasm for a catalogue in the community. </li></ul>
  20. 21. Institutional Support <ul><li>Hosting the registry, curating, resources to develop the infrastructure, partnering with suppliers. </li></ul><ul><li>Sustainability and impact. </li></ul><ul><li>OMII-UK and the EBI </li></ul>
  21. 22. So why is it taking so damn long? <ul><li>The final 9 yards and 80:20 rule. </li></ul><ul><li>All or nothing. </li></ul><ul><li>Dedicated resources and best intentions. </li></ul><ul><li>Content, content, content. </li></ul><ul><li>Being too damn, and unnecessarily, clever. </li></ul><ul><li>Can HCLS SIG help? </li></ul>
  22. 23. Let’s get serious <ul><li>Its time to get serious about building and managing a catalogue. </li></ul><ul><li>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. </li></ul><ul><li>We have the parts and enough of the know-how. And a means to the content. </li></ul><ul><li>So lets. Just. Do. It. </li></ul>
  23. 24. <ul><li>my Grid project http://www.mygrid.org.uk </li></ul><ul><li>BioMOBY project http://biomoby.open-bio.org/ </li></ul><ul><li>ISPIDER project http://www.ispider.man.ac.uk/ </li></ul><ul><li>GRIMOIRES project http://twiki.grimoires.org/bin/view/Grimoires/ </li></ul><ul><li>OMII-UK http://www.omii.ac.uk </li></ul><ul><li>EPSRC </li></ul><ul><li>Genome Canada </li></ul>Acknowledgements

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