BioCatalogue at EMBL-EBI SME Workshop

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Presentation of BioCatalogue Web Services registry at the EMBL-EBI Small and Medium Size(SME) workshop in Munich in October 2010. Presentation done by Eric Nzuobontane.

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  • (Yes its Boring. But GOOD.)
  • Web services can be used as building block to model business process. So different combinations/permutations of services would lead to different products from the same base services. This is the enabler of service oriented architectures.
  • Machine machine communication over a network. Web services are designed to be consumed by applications.
  • - Cost reduction – Infrastructure needed to run the service needs not be local. Maintenance is done by service provider
    - Provider can reach a wide consumer base with a relatively controlled infrasture
    Workflow engines help visualization of business process, pipelines
    Commercial and open-source workflow engines.
  • Workflow engines may have a connection to a service registry,
  • DDBJ – one of the three institutes that constitutes the DDBJ/EMBL/GenBank international nucleotide sequence database which was established through cooperation with EBI and NCBI
  • - Which order this takes depends on how knowledgeable the user is about the service they are looking for.
  • The WS-Reliability specification defines a method for exchanging SOAP-based messages with a particular level of quality of service, no duplicates, and a particular message order.
  • BioCatalogue at EMBL-EBI SME Workshop

    1. 1. EBI is an Outstation of the European Molecular Biology Laboratory. The Life Science Web Service Registry BioCatalogue 01/29/15 Eric Nzuobontane European Bioinformatics Institute SME Workshop/Munich 2010
    2. 2. E Nzuobontane - SME Workshop 2010 Web Services(1) • Programmatic Interfaces to Services. • Standard interfaces. • HTTP, XML • Two big families: • SOAP and REST. • Three main roles • Provider, Consumer, Registry 2 01/29/15
    3. 3. E Nzuobontane - SME Workshop 2010 3 01/29/15 Web Services(2) (as building blocks) products Software Lego™ that works across the web and underpins enterprise SOA.
    4. 4. E Nzuobontane - SME Workshop 2010 Web Services(3) • Software system designed to support interoperable machine-to-machine interaction over a network 4 01/29/15 Machine-machine communication
    5. 5. E Nzuobontane - SME Workshop 2010 Web Service Orchestration • Accomplish complex business processes • Use multiple services • Reduced cost • Standardized communication interfaces & protocols • Workflow ( service orchestration) engines • Visualize business process composition • Some engines used in life science • Pipeline PilotTM , VIBE® • Taverna, Kepler, Triana, MIGenAS, 5 01/29/15
    6. 6. E Nzuobontane - SME Workshop 2010 Transmembrane and signal peptide prediction using three methods ( services ): EMBOSS tmap with a single sequence: Uses Soaplab tmap. Phobius: Uses EBI's WSPhobius web service. TMHMM and SignalP: Uses the TMHMM and SignalP methods of InterProScan via the EBI's WSInterProScan service. The results of the three methods are converted into GFF format and collated.. 6 01/29/15 http://www.myexperiment.org/workflows/216.html
    7. 7. E Nzuobontane - SME Workshop 2010 Web Services in Life Science • Providers • European Bioinformatics Institute (EBI) • http://www.ebi.ac.uk/Tools/webservices/ • National Centre for Biotechnology Information (NCBI) • http://www.ncbi.nlm.nih.gov/guide/data-software/ • DNA Databank of Japan (DDBJ) • http://www.ddbj.nig.ac.jp/ • Commercial & other providers 7 01/29/15
    8. 8. E Nzuobontane - SME Workshop 2010 Searching for web services • Search engines • Google, bing, yahoo… • Web service search engines • Generic • seekda, xmethods, service finder… • Domain Specific • BioCatalogue, DAS, Biomoby • Providers websites • EMBL-EBI, DDBJ, NCBI • Ask someone! 8 01/29/15
    9. 9. E Nzuobontane - SME Workshop 2010 Publishing web services • Company website • Does that have max exposure? • Search engines • Are keyword search good enough? • Search engines designed for web page, not applications • Journals • Selected audience 01/29/159
    10. 10. E Nzuobontane - SME Workshop 2010 Understanding/Using web services • What the service really does(?) • Interface show syntax (wsdl) • Function + operational info needed • Sample clients • Any available for immediate use • Constraints • Conditions of use of service 01/29/1510
    11. 11. E Nzuobontane - SME Workshop 2010 Service Properties • Different classes of consumers • Systemic, non-systemic • Varying importance( for different users) • Availability • Reliability • Consistency • Updates • Latest updates • Specific revisions 01/29/1511
    12. 12. E Nzuobontane - SME Workshop 2010 Four Major Problems • Web Services are hard to find • Where and how do I find them? • My web services are not visible • Where do I publish my web services to achieve maximum visibility? • Web services can be volatile (life cycle) • What is the status of the services I am interested in? • Web Services can be poorly describe • Is there sufficient information available to allow proper use of service? 12 01/29/15
    13. 13. E Nzuobontane - SME Workshop 2010 BioCatalogue The Life Science Web Service Registry http://www.biocatalogue.org An Open, Public, Curated Catalogue of Web Services in Life Sciences Launched – June 2009 Publication Nucl Acids Res, June 2010, Web Servers issue doi: 10.1093/nar/gkq394 01/29/1513
    14. 14. E Nzuobontane - SME Workshop 2010 BioCatalogue’s Mission 01/29/1514
    15. 15. E Nzuobontane - SME Workshop 2010 15 01/29/15 http://www.biocatalogue.org
    16. 16. E Nzuobontane - SME Workshop 2010 Service Search(1) • Keyword search • Google style simple keyword search • Browse by tags • Community and ontology tags • Navigate by service categories • Categorization of services by providers/curators/users • Navigate by service providers • Service grouped by their institutes/organization 01/29/1516
    17. 17. E Nzuobontane - SME Workshop 2010 Service Search(2) 01/29/1517
    18. 18. E Nzuobontane - SME Workshop 2010 Service Registration (Publish) • Simple registration process • Only a URL is required • Register different types of Services • SOAP, REST • Register batch of services • Soaplab • Instant availability 18 01/29/15
    19. 19. E Nzuobontane - SME Workshop 2010 Service Annotation • Provider & Community annotation • Providers as ‘authority’ on services • Community in addition to providers • Improve search results • Users can easily find service • Improved understandability • Documentation for your service • Information on constraints • Fair use policy 01/29/1519
    20. 20. E Nzuobontane - SME Workshop 2010 01/29/1520
    21. 21. E Nzuobontane - SME Workshop 2010 Programmatic access(1) • REST API available http://www.biocatalogue.org/wiki/public • Integrate in your tool • Taverna, NCRI • http://www.ncri-onix.org.uk/portal/#S103a • Query programmatically • Eg service status 21 01/29/15
    22. 22. E Nzuobontane - SME Workshop 2010 Setup Private instance(1) 22 01/29/15
    23. 23. E Nzuobontane - SME Workshop 2010 Setup Private instance(2) • Source code available for free • http://rubyforge.org/projects/biocatalogue/ • Documentation on installation • http://www.biocatalogue.org/wiki/doku.php?id=development:installation • http://www.biocatalogue.org/wiki/doku.php?id=public:help • Help from developers on setting up • Join the BioCatalogue friends • Updates announced and made available for free 01/29/1523
    24. 24. E Nzuobontane - SME Workshop 2010 Questions? Sign up to BioCatalogue http://www.biocatalogue.org Contact us contact@bioCatalogue.org 01/29/1524
    25. 25. E Nzuobontane - SME Workshop 2010 Resources Franck Tanoh Curator Jiten Bhagat Eric Nzuobontane Mannie Tagarira Developers Investigators Rodrigo Lopez Steve Pettifer 25 Carole Goble Robert Stevens Paolo Missier Researchers Hamish McWilliams Thomas Laurent Jerzy Orlowski Sergejs Aleksejevs Katy Wolstencroft
    26. 26. E Nzuobontane - SME Workshop 2010 References • http://www.biocatalogue.org • http://www.biocatalogue.org/wiki/public • http://www.ebi.ac.uk • http://www.myexperiment.org • http://www.w3.org/TR/soap/ • http://energybenchmarking.lbl.gov/aob.html 26 01/29/15
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