Implementing computational analysis

through Web services

Arnaud KerhornouCRG/INBBarcelona

-BioMed Workshop

IRBNovember 2007

Current situation in Bioinformatics

•Discovery

•Service description

•Ontologies

•Data transfert

•Automation

Limits

BioMoby architecture

PublishFind

Bind

Service registry

Service Provider

Service Descriptions

Service Description

Service

WDSL, UDDIWSDL, UDDI

Service Requestor

A web service is an interface that describes a collection of operations that are network accessible through standardized XML messaging

BioMoby

a unifying framework approach

The bioMoby project aims to provide bioinformatics resources through the web. It can be data retrieval resources or analysis resources.

It defines an ontology-based messaging standard The services are registered in a central “yellow pages”

server to facilitate the discovery The services specifications are formalized in a description

language.

It provides:•A Central Registry of services•A set of standards to specify:

•Message formatting,•Error reporting•Asynchronous requests

•An API written in two languages, perl and java •Ontologies to represent

•Types of services,•Data types

The BioMoby framework

Ontology

• Data exchange relies on the use of Ontologies.

• Ontology to represent knowledge in a given domain

• In bioinformatics: – OBO (GO, SO and many many more)

• http://obo.sourceforge.net/cgi-bin/table.cgi

– Biomoby datatypes to classify service input/output– Biomoby service types

Establish Ontologies to formalize the representation of:•Types of services•Types of data

The BioMoby ontologies

Bioinformatics

Sequence

Analysis

MultipleSequence

Alignment

PairwiseSequence

Alignment

Alignment

GeneFinding

is-a

Service

The Service TypeOntology

Object

String

Integer

Virtual

SequenceGeneric

Sequence

DNA

Sequence

AminoAcid

Sequence

text_plain text_formatted GFF

has-a

is-a

is-a

has-a

has-a

The Data TypeOntology

<DNASequence>

<String articleName=”Sequence”>

AAATGTCGCTCGATACGATCAGCTACGA

</String>

<Integer articleName=”Length”>

28

</Integer>

</DNASequence>

Moby DNASequenceObject

BioMobyService specs

• Service name: Free Text

• Service type: Moby service type ontology

• Description: Free text

• One or more inputs: Moby data type ontology

• One or more outputs: Moby data type ontology

• One or more parameters: – name (a string)– value (an ‘primitive’, ie a String or an Integer etc.)

Example

• Service type: GeneFinding

• Description: ab-initio gene finding software

• Input: a DNASequence object

• Output: a GFF object

• Parameters:– Profile (Default is Human)– Strand (Default is both strands)

RunGeneIDGFF service specifications:

Client Side

MobyCentral

ServiceProvider

Internet

ServiceClient

• There are different kind of clients

• Some of them allow the creation of workflows

Programmatic

libraries:

• Java based graphical integrated workbench

• It allows the construction of complex distributed workflows

• It can handle different kind of services (Moby and others)

Client Side: Taverna I

Processors = Webservices

Inputs

Outputs

Client Side: Taverna II

Client Side: Taverna III

Moby Web service Configuration

• All the info accessible at the Moby homepage at:– http://www.biomoby.org/

• Taverna Web site– http://www.inab.org/MOWServ

• Remora Web interface– http://lipm-bioinfo.toulouse.inra.fr/remora/cgi/remora.cgi

• MowServ Web interface– http://www.inab.org/MOWServ/

• Genome Analysis services page– http://genome.imim.es/webservices

BioMoby on the Web