A simple overview of BioMoby Mark Wilkinson iCAPTURE Centre St. Paul’s Hospital Vancouver

St. Paul’s Hospital iCAPTURE Centre

Harnessing the Power Of communities

A brief history of BioMoby Model Organism Bring Your own Database Interface Conference, Sept, 2001 (MOBY-DIC) Model Organism Bring Your own Database Interface Conference, Sept, 2001 (MOBY-DIC) May 21, 2002 – Genome Canada Platform Award May 21, 2002 – Genome Canada Platform Award May 25, 2002 – API Version 0.1 deployed, including object ontology serialization into XML May 25, 2002 – API Version 0.1 deployed, including object ontology serialization into XML July 18, 2002 – first Moby Client released (now gbrowse_moby, part of gbrowse from GMOD) July 18, 2002 – first Moby Client released (now gbrowse_moby, part of gbrowse from GMOD) June 9, 2003 – API Version 0.5 deployed June 9, 2003 – API Version 0.5 deployed Currently, the API is at version 0.86; version 1.0 API in preparation for release SOON! Currently, the API is at version 0.86; version 1.0 API in preparation for release SOON!

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 Plan

Gene names MOBY Central MOBY hosts & services Sequence Alignment Sequence Express. Protein Alleles … Align Phylogeny Primers Overview of BioMoby Transactions

MOBY Central Sequence Align Phylogeny Primers Overview of BioMoby Transactions Object ontology What is a sequence? A sequence is a ___ That has these features __ Discovery of services That consume things LIKE sequences!

Pipeline discovery “on the fly” No explicit coordination between providers No explicit coordination between providers Dynamic discovery of ~appropriate Services Dynamic discovery of ~appropriate Services Automated execution of services Automated execution of services

Some BioMoby statistics

Moby: Breadth Namespaces (semantic datatypes): 281 Namespaces (semantic datatypes): 281 Objects (data syntaxes): >300 Objects (data syntaxes): >300 Service Types (analytical categories): 36 Service Types (analytical categories): 36 Authorities: 56 active Authorities: 56 active Service Instances: >630 Service Instances: >630 –In main server and in “boutique” Moby registries serving specialized communities worldwide

Moby: Impact Mailing list count 200+ members (90 on developers mailing list) Mailing list count 200+ members (90 on developers mailing list) Google Scholar Google Scholar –‘BioMOBY’ 225 –Citations of 2002 BioMOBY paper 98

Moby: Developer Activity MOBY-DIC Chapter 7 meeting MOBY-DIC Chapter 7 meeting –Vancouver, May 6-8, Developers attending 23 Developers attending –Asia –USA –Canada –Germany –Spain –France Mapped-out the route to the final 1.0 version of the API Mapped-out the route to the final 1.0 version of the API

Moby Registry Activity PlaNet implements own MOBY Central

Most recent numbers Calls to the MOBY Central web service brokering API

Moby: Exemplar Users PlaNet consortium (7+ sites, services) PlaNet consortium (7+ sites, services) EBI – SOAPLAB – myGrid EBI – SOAPLAB – myGrid Generation Challenge Programme of the CGIAR (18+ sites) Generation Challenge Programme of the CGIAR (18+ sites) Genome Espania uses MOBY for much of the bioinformatics service provision in the GE Bioinformatics Platform Genome Espania uses MOBY for much of the bioinformatics service provision in the GE Bioinformatics Platform

Moby: Clients Gbrowse_moby (M Wilkinson) Gbrowse_moby (M Wilkinson) Browser-style client Browser-style client Ahab & Ishmael (B Good, M Wilkinson) Ahab & Ishmael (B Good, M Wilkinson) “BLAST” & Semantic Web style clients “BLAST” & Semantic Web style clients PlaNet Locus_View (H Schoof, R Ernst) PlaNet Locus_View (H Schoof, R Ernst) Aggregator-style client Aggregator-style client Blue-Jay (P Gordon) and RGD prototype (S Twigger) Blue-Jay (P Gordon) and RGD prototype (S Twigger) Menu-style clients Menu-style clients MOBY Graphs (M Senger) MOBY Graphs (M Senger) Auto-workflow discovery tool Auto-workflow discovery tool Taverna (T Oinn, M Senger, E Kawas), and MOWserv (INB, Spain) Taverna (T Oinn, M Senger, E Kawas), and MOWserv (INB, Spain) Workflow builder/publisher/execution client Workflow builder/publisher/execution client Enhanced support for MOBY currently being built Enhanced support for MOBY currently being built Remora (S Carrere, J Gouzy, INRA) Remora (S Carrere, J Gouzy, INRA) MOBYLE (B Néron, P Tufféry, C Letondal, Pasteur Inst.) MOBYLE (B Néron, P Tufféry, C Letondal, Pasteur Inst.)

Taverna Workbench Tom Oinn and Martin Senger myGrid Project

MOWServ Web interface to the Spanish Instituto Nacional de Bioinformatica MOBY Central installation

Mare Nostrum Barcelona Supercomputing Centre

Future plans for Moby “Decentralization” and enrichment of the registry through distributed RDF-based service instance annotations + LSID resolution “Decentralization” and enrichment of the registry through distributed RDF-based service instance annotations + LSID resolution –~Complete – not yet deployed… Mirroring of registries Mirroring of registries Mirroring of Services Mirroring of Services

Future plans for Moby Enhanced registry usage metadata capture Enhanced registry usage metadata capture Ontological markup of Object Ontology Terms Ontological markup of Object Ontology Terms Better support for Web Service tooling if possible Better support for Web Service tooling if possible –Unfortunately, W3C XML Schema is unable to 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 tools like RDF/OWL by a couple of years…

How do we make Web Services look like the Semantic Web? Moby can help! Moby can help! Two novel Moby clients - Ahab and Ishmael – are starting to have conspicuously Semantic Webby outputs… Two novel Moby clients - Ahab and Ishmael – are starting to have conspicuously Semantic Webby outputs…

The Internet Credit to P. Lord, myGrid

The World Wide Web Credit to P. Lord, myGrid

The Semantic Web (low stack) sameAs activates TranscriptOf hasProduct ISA clonedBy address componentOf Credit to P. Lord, myGrid

Web Services over databases… no documents to point to! sameAs activates TranscriptOf hasProduct ISA clonedBy address componentOf

The Ahab BioMoby Client

Ahab

Ahab RDF

But BioMoby can run unattended! Because of syntactic agreement among service providers, and Because of syntactic agreement among service providers, and Because a client can automatically disassemble complex objects, and Because a client can automatically disassemble complex objects, and Because discovery and execution of services that act on those objects can be fully automated Because discovery and execution of services that act on those objects can be fully automated BioMoby can build a massive Entity/Relationship model completely unattended BioMoby can build a massive Entity/Relationship model completely unattended

Okay, so get rid of the GUI… 1. Tell Ahab engine to chose all discovered services for a piece of data 2. Execute every service 3. Take each output, and go to (1) 4. Go home for an early weekend… This is Ishmael - a prototype BioMoby client

The Output from Ishmael sameAs activates TranscriptOf hasProduct ISA clonedBy address componentOf

my SWeb The output of Ishmael is “My Semantic Web” The output of Ishmael is “My Semantic Web” –Personalized Semantic Web RDF graph –Centered around your data of interest –Cachable/explorable by e.g. IBM’s Haystack –Because each node is a Moby-like URI with a namespace & id, it auto-detects “re-discovery” of data elements and merges the nodes

Acknowledgements (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

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