A simple overview of BioMoby

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

2. St. Paul’s HospitaliCAPTURE Centre

3. Harnessing the Power Of communities

4. A brief history of BioMoby • Model Organism Bring Your own Database Interface Conference, Sept, 2001 (MOBY-DIC) • May 21, 2002 – Genome Canada Platform Award • 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) • 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!

5. What does BioMoby do?

6. 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

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

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

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

19. Some BioMoby statistics

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

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

22. Moby: Developer Activity • MOBY-DIC Chapter 7 meeting • Vancouver, May 6-8, 2005 • 23 Developers attending • Asia • USA • Canada • Germany • Spain • France • Mapped-out the route to the final 1.0 version of the API

23. Moby Registry Activity PlaNet implements own MOBY Central

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

25. Moby: Exemplar Users • PlaNet consortium (7+ sites, 100-130 services) • EBI – SOAPLAB – myGrid • Generation Challenge Programme of the CGIAR (18+ sites) • Genome Espania uses MOBY for much of the bioinformatics service provision in the GE Bioinformatics Platform

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

27. Taverna Workbench Tom Oinn and Martin Senger myGrid Project

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

29. Mare Nostrum Barcelona Supercomputing Centre

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

32. Future plans for Moby • Enhanced registry usage metadata capture • Ontological markup of Object Ontology Terms • 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) • BioMoby pre-dates commodity Semantic Web tools like RDF/OWL by a couple of years…

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

34. The Internet Credit to P. Lord, myGrid

35. The World Wide Web Credit to P. Lord, myGrid

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

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

38. The Ahab BioMoby Client

39. Ahab

40. Ahab RDF

41. But BioMoby can run unattended! • Because of syntactic agreement among service providers, 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 • BioMoby can build a massive Entity/Relationship model completely unattended

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

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

44. mySWeb • 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

45. Acknowledgements (Wilkinson) O | B | F • 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

46. It doesn’t always rain in Vancouver It just feels like it does…