Web Services Interoperability Through Standardisation The EMBRACE Technology Recommendation

Why Use Web Services In The First Place? Interoperability

Service Oriented Architecture (SOA) Functionality is most commonly expressed as services. Each service provides one clearly defined basic functionality. Higher level functionality is achieved using service composition.

Web Services Interoperability organisation Initial Web Service specifications were quite flexible –Many different ways to make Web Services –Hard to make tools that could be used for all types of services Web Services Interoperability organisation was founded to establish more restrictive specifications –Similar services –Outdated tools

The Evolution Of Web Services

SOA Is Becoming Boring  Has become part of the software industry SAP Oracle IBM Microsoft

SOA Is A Part Of Society  Applications in Norway: All parts of government Police Major hospitals Companies

The Technology Recommendation: An EMBRACE of WS-I WS-I is ready (ish) to use Many tools and supporting technologies available Competence is available

A closer look at Web Services XML

Client WSDL File Web service Usage scenario

Client WSDL File Web service Client reads the WSDL file

Client WSDL File Web service Client sends request

Client WSDL File Web service Client receives the response

Extensible Markup Language A way of structuring information Use Elements and attributes...

XML Schema Schema Instance John Doe 40 Person First Name Last Name Age Class Person John Doe 40 Object

XML Binding Representing the information in an XML document as an object in computer memory John Doe 40 Person John Doe 40

Namespaces Avoids naming conflicts We can use prefixes for shorter notation...

SOAP –The protocol formerly known as “Simple Object Access Protocol”  The SOAP Envelope for messages  Processing model for how to deal with the messages  Protocol binding framework

SOAP Message Or just:

Web Service Description Language –Provides an abstract definition of a Web Service and a binding which ties it to a concrete endpoint. –Is completely independent of the Web Service it describes.

WSDL file XML Schema definitions of data formats Definition of messages for input and output of the operations in this service. Definition of the operations available at this service. The binding of the operations to a set of protocols. SOAP over HTTP is most commonly used Name and network address of this service

Schema part of a WSDL

Corresponding SOAP message MA0003 PFM CORE

Sample Perl Client my $wsdl = XML::LibXML->new->parse_file(' my $proxy = XML::Compile::WSDL11->new($wsdl); my $getMatrixById = $proxy->compileClient('getMatrixById'); my $answer = $getMatrixById->( Id => $get_by_id, Format => $format, Database => $db ); my $matrix = $answer->{parameters}{Matrix}; _print_matrix($matrix);

eVita Project Norwegian research council eScience program Has funded a 2.3 me project to build a SOA to support systems biology research at BCCS. Built with WS-I Web Services Partners in UK –MyGrid –Manchester Interdisciplinary Biocentre

EuTRACC The European Transcriptome, Regulome & Cellular Commitment Consortium Aims to identify TFs and interacting partners expressed in neuronal and haematopoietic cell types. European NoE Primarily partners with biological competence Lenhard group responsible for analysis

EuTRACC tasks Integrative analysis of proteomics, gene expression, chip-chip and chip-seq data Determine the principal regulatory network components Build supporting infrastructure –Performed by the eVita project

IRC The International Regulome Consortium –The discovery of how gene function is regulated in mammalian cells during development –Collaborates closely with EuTRACC –Will use same/simmilar infrastructure

Jaspar Database Database of profiles of transcription factor binding sites Prediction of over-represented TFBS i sets of genes Statistical analysis

Steps forward in EMBRACE Define common data types Links to ontologies

Acknowledgements Vincent Breton Jean Salzemann CNRS /Clermont-Ferrand All other members of the Technology Recommendation and Watch WP Steve PettiferUMAN Inge Jonassen Pål Puntervoll Rein AaslandBCCS Toby GibsonEMBL