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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…