A simple overview of BioMoby

A simple overview of BioMoby

Mark WilkinsoniCAPTURE CentreSt. Paul’s Hospital

Vancouver

St. Paul’s HospitalSt. Paul’s HospitaliCAPTURE Centre iCAPTURE Centre

Harnessing the Power Of communities

A brief history of BioMobyA brief history of BioMoby• Model Organism Bring Your own Database Interface Model Organism Bring Your own Database Interface

Conference, Sept, 2001 (MOBY-DIC)Conference, Sept, 2001 (MOBY-DIC)

• May 21, 2002 – Genome Canada Platform AwardMay 21, 2002 – Genome Canada Platform Award

• May 25, 2002 – API Version 0.1 deployed, including May 25, 2002 – API Version 0.1 deployed, including object ontology serialization into XMLobject ontology serialization into XML

• July 18, 2002 – first Moby Client released (now July 18, 2002 – first Moby Client released (now gbrowse_moby, part of gbrowse from GMOD)gbrowse_moby, part of gbrowse from GMOD)

• June 9, 2003 – API Version 0.5 deployedJune 9, 2003 – API Version 0.5 deployed

• Currently, the API is at version 0.86; version 1.0 API in Currently, the API is at version 0.86; version 1.0 API in preparation for release SOON!preparation for release SOON!

What does BioMoby do?What does BioMoby do?

• Create an ontology of bioinformatics data-types• Define a serialization of this ontology (data syntax)• Create an open API over this ontology• Define Web Service inputs and outputs v.v. Ontology• Register Services in an ontology-aware Registry

• Machines can find an appropriate service• Machines can execute that service unattended• Ontology is community-extensible

The BioMoby PlanThe BioMoby Plan

Gene names

MOBYCentral

MOBY hosts & services

SequenceAlignment SequenceExpress. Protein Alleles…

AlignPhylogenyPrimers

Overview of BioMoby Overview of BioMoby TransactionsTransactions

Overview of BioMoby Overview of BioMoby TransactionsTransactions

MOBYCentral

SequenceAlignPhylogenyPrimers

Overview of BioMoby Overview of BioMoby TransactionsTransactions

Overview of BioMoby Overview of BioMoby TransactionsTransactions

Objectontology

What is a sequence?A sequence is a ___That has these features __

Discovery of servicesThat consume things LIKE sequences!

Pipeline discovery “on the fly”Pipeline discovery “on the fly”

• No explicit coordination between No explicit coordination between providersproviders

• Dynamic discovery of ~appropriate Dynamic discovery of ~appropriate ServicesServices

• Automated execution of servicesAutomated execution of services

Some BioMoby statisticsSome BioMoby statistics

Moby: BreadthMoby: Breadth

• Namespaces (semantic datatypes): 281Namespaces (semantic datatypes): 281• Objects (data syntaxes): >300Objects (data syntaxes): >300• Service Types (analytical categories): 36Service Types (analytical categories): 36• Authorities: 56 activeAuthorities: 56 active

• Service Instances: >630Service Instances: >630– In main server and in “boutique” Moby registries In main server and in “boutique” Moby registries

serving specialized communities worldwideserving specialized communities worldwide

Moby: ImpactMoby: Impact

• Mailing list count 200+ members Mailing list count 200+ members (90 on developers mailing list)(90 on developers mailing list)

• Google Scholar Google Scholar – ‘‘BioMOBY’ 225BioMOBY’ 225– Citations of 2002 BioMOBY paper Citations of 2002 BioMOBY paper

9898

Moby: Developer ActivityMoby: Developer Activity

• MOBY-DIC Chapter 7 meetingMOBY-DIC Chapter 7 meeting– Vancouver, May 6-8, 2005Vancouver, May 6-8, 2005

• 23 Developers attending23 Developers attending– AsiaAsia– USAUSA– CanadaCanada– GermanyGermany– SpainSpain– FranceFrance

• Mapped-out the route to the final 1.0 Mapped-out the route to the final 1.0 version of the APIversion of the API

Moby Registry ActivityMoby Registry Activity

Hits on Moby Central API

050000

100000150000200000250000300000350000400000

MONTH

PlaNet implementsown MOBY Central

Most recent numbersMost recent numbers

0

50000

100000

150000

200000

250000

300000

350000

400000

450000

Sep-05

Oct-05

Nov-05

Dec-05

Jan-06

Feb-06

Mar-06

Apr-06

Hits

Log. (Hits)

Calls to the MOBY Central web service brokering API

Moby: Exemplar UsersMoby: Exemplar Users

• PlaNet consortium (7+ sites, 100-130 services)PlaNet consortium (7+ sites, 100-130 services)

• EBI – SOAPLAB – myGridEBI – SOAPLAB – myGrid

• Generation Challenge Programme of the CGIAR Generation Challenge Programme of the CGIAR (18+ sites)(18+ sites)

• Genome Espania uses MOBY for much of the Genome Espania uses MOBY for much of the bioinformatics service provision in the GE bioinformatics service provision in the GE Bioinformatics PlatformBioinformatics Platform

Moby: ClientsMoby: Clients• Gbrowse_mobyGbrowse_moby (M Wilkinson) (M Wilkinson)

• Browser-style clientBrowser-style client

• Ahab & IshmaelAhab & Ishmael (B Good, M Wilkinson)(B Good, M Wilkinson)• ““BLAST” & Semantic Web style clientsBLAST” & Semantic Web style clients

• PlaNet Locus_ViewPlaNet Locus_View (H Schoof, R Ernst) (H Schoof, R Ernst)• Aggregator-style clientAggregator-style client

• Blue-Jay Blue-Jay (P Gordon)(P Gordon) andand RGD RGD prototypeprototype (S Twigger) (S Twigger)• Menu-style clientsMenu-style clients

• MOBY GraphsMOBY Graphs (M Senger) (M Senger)• Auto-workflow discovery toolAuto-workflow discovery tool

• TavernaTaverna (T Oinn, M Senger, E Kawas), and (T Oinn, M Senger, E Kawas), and MOWservMOWserv (INB, (INB, Spain)Spain)

• Workflow builder/publisher/execution clientWorkflow builder/publisher/execution client• Enhanced support for MOBY currently being builtEnhanced support for MOBY currently being built

• RemoraRemora (S Carrere, J Gouzy, INRA) (S Carrere, J Gouzy, INRA)• MOBYLEMOBYLE (B Néron, P Tufféry, C Letondal, Pasteur Inst.) (B Néron, P Tufféry, C Letondal, Pasteur Inst.)

Taverna WorkbenchTom Oinn and Martin SengermyGrid Project

MOWServMOWServWeb interface to the Web interface to the

Spanish Instituto Nacional de BioinformaticaSpanish Instituto Nacional de BioinformaticaMOBY Central installationMOBY Central installation

Mare NostrumBarcelona Supercomputing Centre

Future plans for MobyFuture plans for Moby

• ““Decentralization” and enrichment of Decentralization” and enrichment of the registry through distributed RDF-the registry through distributed RDF-based service instance annotations + based service instance annotations + LSID resolutionLSID resolution– ~Complete – not yet deployed…~Complete – not yet deployed…

• Mirroring of registriesMirroring of registries

• Mirroring of ServicesMirroring of Services

Future plans for MobyFuture plans for Moby

• Enhanced registry usage metadata captureEnhanced registry usage metadata capture

• Ontological markup of Object Ontology TermsOntological markup of Object Ontology Terms

• Better support for Web Service tooling if Better support for Web Service tooling if possiblepossible– Unfortunately, W3C XML Schema is unable to Unfortunately, W3C XML Schema is unable to

describe MOBY messages…describe MOBY messages…

• RDF-based messaging (will come in MOBY II)RDF-based messaging (will come in MOBY II)– BioMoby pre-dates commodity Semantic Web BioMoby pre-dates commodity Semantic Web

tools like RDF/OWL by a couple of years…tools like RDF/OWL by a couple of years…

How do we make Web Services How do we make Web Services look like the Semantic Web?look like the Semantic Web?

• Moby can help!Moby can help!

• Two novel Moby clients - Two novel Moby clients - Ahab and Ahab and IshmaelIshmael – are starting to have – are starting to have conspicuously Semantic Webby conspicuously Semantic Webby outputs…outputs…

The InternetThe Internet

Credit to P. Lord, myGrid

The World Wide WebThe World Wide Web

Credit to P. Lord, myGrid

The Semantic Web (low The Semantic Web (low stack)stack)

sameAs

activates

TranscriptOf

hasProduct

ISA

clonedBy

address

componentOf

Credit to P. Lord, myGrid

Web Services over databases… Web Services over databases… no documents to point to!no documents to point to!

sameAs

activates

TranscriptOf

hasProduct

ISA

clonedBy

address

componentOf

The Ahab BioMoby ClientThe Ahab BioMoby Client

AhabAhab

Ahab RDFAhab RDF

But BioMoby can run But BioMoby can run unattended!unattended!• Because of syntactic agreement among service Because of syntactic agreement among service

providers, and providers, and

• Because a client can automatically disassemble Because a client can automatically disassemble complex objects, andcomplex objects, and

• Because discovery and execution of services Because discovery and execution of services that act on those objects can be fully automatedthat act on those objects can be fully automated

• BioMoby can build a massive Entity/Relationship BioMoby can build a massive Entity/Relationship model completely unattendedmodel completely unattended

Okay, so get rid of the GUI…Okay, so get rid of the GUI…

1.1. Tell Ahab engine to chose Tell Ahab engine to chose allall discovered discovered services for a piece of dataservices for a piece of data

2.2. Execute Execute everyevery service service

3.3. Take each output, and go to (1)Take each output, and go to (1)

4.4. Go home for an early weekend…Go home for an early weekend…

This is This is IshmaelIshmael - a prototype BioMoby client - a prototype BioMoby client

The Output from IshmaelThe Output from Ishmael

sameAs

activates

TranscriptOf

hasProduct

ISA

clonedBy

address

componentOf

mymySWebSWeb

• The output of Ishmael is “My Semantic The output of Ishmael is “My Semantic Web”Web”

– PersonalizedPersonalized Semantic Web RDF graph Semantic Web RDF graph– Centered around your data of interestCentered around your data of interest– Cachable/explorable by e.g. IBM’s HaystackCachable/explorable by e.g. IBM’s Haystack– Because each node is a Moby-like URI with a Because each node is a Moby-like URI with a

namespace & id, it auto-detects “re-discovery” namespace & id, it auto-detects “re-discovery” of data elements and merges the nodesof data elements and merges the nodes

Acknowledgements Acknowledgements (Wilkinson)(Wilkinson)

• BioMOBY: A Bioinformatics Platform for Genome Canada• Ahab, Ishmael, iCAPTURer: Genome BC Better Biomarkers in Transplantation• CardioSHARE: Canadian Institutes for Health Research (CIHR)• Taverna: myGrid• Ben Good: CIHR Bioinformatics Training Programme

O | B | F

It doesn’t always rain It doesn’t always rain in Vancouverin Vancouver

It just feels like it does…It just feels like it does…