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.
1. EBI is an Outstation of the European Molecular Biology Laboratory.
The Life Science Web Service Registry
BioCatalogue
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Eric Nzuobontane
European Bioinformatics Institute
SME Workshop/Munich 2010
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Web Services(1) • Programmatic Interfaces to
Services.
• Standard interfaces.
• HTTP, XML
• Two big families:
• SOAP and REST.
• Three main roles
• Provider, Consumer, Registry
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Web Services(2) (as building blocks)
products
Software Lego™ that works across the
web and underpins enterprise SOA.
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Web Services(3)
• Software system designed to support interoperable
machine-to-machine interaction over a network
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Machine-machine communication
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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,
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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..
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http://www.myexperiment.org/workflows/216.html
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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
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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!
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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
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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
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Service Properties
• Different classes of consumers
• Systemic, non-systemic
• Varying importance( for different users)
• Availability
• Reliability
• Consistency
• Updates
• Latest updates
• Specific revisions
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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?
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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
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BioCatalogue’s Mission
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http://www.biocatalogue.org
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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
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Service Search(2)
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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
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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
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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
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Setup Private instance(1)
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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
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Questions?
Sign up to BioCatalogue
http://www.biocatalogue.org
Contact us
contact@bioCatalogue.org
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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
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.