Breaking Barriers:getting biologists involved in everyday data

integration using Moby

Paul GordonGenome Canada Bioinformatics

PlatformUniversity of Calgary, Canada

Outline

• concept, usage, future

• Getting Biologists Involved: Seahawk &

DNASequence

NCBI_gi

Sequence_Alignment

Core Moby Service Providers in Europe

Founding partner

SADI In A Nutshell

As OWL Axioms

HomologousMutantImage is owl:equivalentTo {

Gene Q hasImage image P

Gene Q hasSequence Sequence Q

Gene R hasSequence Sequence R

Sequence Q similarTo Sequence R

Gene R = “my gene of interest” }

Mobify the World.

Paul’s Maxims

• You cannot get rid of work• You can:

– Distribute work amongst parties with vested interests & required capabilities

– Avoid redoing the same work repeatedly

Agenda

• Motivation• Audience• Mechanism

Larry Wall’s “Virtues of a Programmer”

HUBRIS

LAZINESSIMPATIENCE

Audience

GodAmoeba

Tave

rna

self-

star

ters

Willin

g to

take

traini

ng

Capab

le b

ut n

o hu

bris

Self-perception of computer skills

Man’s Prayer

• I’m a man…• But I can change…• If I have to…• I guess…

Bioinformatician

Take the output of the U of C service and send itto iHOP, then send its output to DDBJ’s service…

myGRID RDF

Semantic Annotations for WSDL

bioxml.info

MOB Rule Syntax

>gi|12434353 glycerol kinasecgatcagcatcgactagcatcgactatttgctatcatcagctacgatcagctacgactac…

Shared Responsibility

Tu deviens responsable pour toujours de ce que tu as apprivoisé.

• Service Providers• Proxy Provider• Third Party Developers• Biologists

SAWSDL Required Infrastructure

Calgary (Sun v240)

Calgary

Anywhere

Anywhere

Compute CloudCompute Cloud(e.g. Calgary or Google App Engine)(e.g. Calgary or Google App Engine)

To Do

• Formal user studies

• HTML Form wrapping

• Enactment portal

• Biocatalogue?

If you can not measure it, you can not improve it. – Lord Kelvin

Acknowledgements