Web Services Interoperability Through Standardisation The EMBRACE Technology Recommendation.

Web Services Interoperability Through Standardisation

The EMBRACE Technology Recommendation

Why Use Web Services In The First Place?

Interoperability

Interoperability

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Web Services Interoperability organisation was founded to establish more restrictive specifications– Similar services– Outdated tools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 industrySAPOracle IBMMicrosoft

SOA Is A Part Of Society

Applications in Norway:All parts of governmentPoliceMajor hospitalsCompanies

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

<Warning> XML </Warning>

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

<Element> ... </Element>

<Element attribute="..." ></Element>

XML Schema

Schema

<element name=“Person"> <complexType> <sequence> <element name="firstname"

type="string"/> <element name="lastname" type="string"/> <element name="age" type="int"/>

</sequence> </complexType> </element>

Instance

<person> <firstname>John</firstname> <lastname>Doe</lastname> <age>40</age> </person>

Person

First Name

Last NameAge

Class

Person

JohnDoe40

Object

XML Binding

Representing the information in an XML document as an object in computer memory

<person> <firstname>John</firstname> <lastname>Doe</lastname> <age>40</age> </person>

Person

JohnDoe40

Namespaces

• Avoids naming conflicts• We can use prefixes for shorter notation

<ParentElement xmlns:ns1="http://mysite.com/NS1">

<ns1:Element> ... </ns1:Element>

</ParentElement>

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

<Envelope><Header> </Header><Body> </Body>

</Envelope>

Or just:

<Envelope><Body> </Body>

</Envelope>

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

<definitions>

<types> XML Schema definitions of data formats

<message> Definition of messages for input and output of the operations in this service.

<portType> Definition of the operations available at this service.

<binding> The binding of the operations to a set of protocols. SOAP over HTTP is most commonly used

<service> Name and network address of this service

</definitions>

Schema part of a WSDL

.......<xs:element name="getMatrixById"> <xs:complexType> <xs:sequence> <xs:element name="Id" type="xs:string"/> <xs:element ref="Format"/> <xs:element ref="Database"/> </xs:sequence> </xs:complexType></xs:element>.......

Corresponding SOAP message

<soapenv:Envelope xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/" xmlns:jas="http://bccs.uib.no/Jaspar"><soapenv:Header/> <soapenv:Body> <jas:getMatrixById> <jas:Id>MA0003</jas:Id> <jas:Format>PFM</jas:Format> <jas:Database>CORE</jas:Database> </jas:getMatrixById> </soapenv:Body></soapenv:Envelope>

Sample Perl Client

my $wsdl = XML::LibXML->new->parse_file('http://api.bioinfo.no/wsdl/JasparDB.wsdl');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

IRCThe 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 Pettifer UMAN

Inge JonassenPål PuntervollRein Aasland BCCS

Toby Gibson EMBL

Web Services Interoperability Through Standardisation The EMBRACE Technology Recommendation.

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