A simple overview of Bio Moby Mark Wilkinson
A simple overview of Bio. Moby Mark Wilkinson i. CAPTURE Centre St. Paul’s Hospital Vancouver
St. Paul’s Hospital i. CAPTURE Centre
Harnessing the Power Of communities
A brief history of Bio. Moby • 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!
What does Bio. Moby do?
The Bio. Moby Plan • • • 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
Overview of Bio. Moby Transactions MOBY hosts & services Alignment Sequence Gene names Sequence Align Express. Phylogeny Protein Primers Alleles … MOBY Central
Overview of Bio. Moby Transactions Discovery of services That consume things LIKE sequences! Sequence MOBY Central Align Phylogeny Primers A sequence is a ___ What is a sequence? That has these features __ Object ontology
Pipeline discovery “on the fly” • No explicit coordination between providers • Dynamic discovery of ~appropriate Services • Automated execution of services
Some Bio. Moby statistics
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
Moby: Impact • Mailing list count 200+ members (90 on developers mailing list) • Google Scholar – ‘Bio. MOBY’ 225 – Citations of 2002 Bio. MOBY paper 98
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
Moby Registry Activity Pla. Net implements own MOBY Central
Most recent numbers Calls to the MOBY Central web service brokering API
Moby: Exemplar Users • Pla. Net consortium (7+ sites, 100 -130 services) • EBI – SOAPLAB – my. Grid • Generation Challenge Programme of the CGIAR (18+ sites) • Genome Espania uses MOBY for much of the bioinformatics service provision in the GE Bioinformatics Platform
Moby: Clients • Gbrowse_moby (M Wilkinson) • Browser-style client • Ahab & Ishmael (B Good, M Wilkinson) • “BLAST” & Semantic Web style clients • Pla. Net Locus_View (H Schoof, R Ernst) • Aggregator-style client • Blue-Jay (P Gordon) and RGD prototype (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. )
Taverna Workbench Tom Oinn and Martin Senger my. Grid 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 – ~Complete – not yet deployed… • Mirroring of registries • Mirroring of Services
Future plans for Moby • Enhanced registry usage metadata capture • Ontological markup of Object Ontology Terms • Better support for Web Service tooling if possible – Unfortunately, W 3 C XML Schema is unable to describe MOBY messages… • RDF-based messaging (will come in MOBY II) – Bio. Moby 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! • Two novel Moby clients - Ahab and Ishmael – are starting to have conspicuously Semantic Webby outputs…
The Internet Credit to P. Lord, my. Grid
The World Wide Web Credit to P. Lord, my. Grid
The Semantic Web (low stack) same. As Transcript. Of ISA activates component. Of has. Product address cloned. By Credit to P. Lord, my. Grid
Web Services over databases… no documents to point to! same. As Transcript. Of ISA activates component. Of has. Product address cloned. By
The Ahab Bio. Moby Client
Ahab
Ahab RDF
But Bio. Moby 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 • Bio. Moby can build a massive Entity/Relationship model completely unattended
Okay, so get rid of the GUI… 1. Tell Ahab engine to chose all discovered 2. 3. 4. 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 Bio. Moby client
The Output from Ishmael same. As Transcript. Of ISA activates component. Of has. Product address cloned. By
my. SWeb • 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) O|B|F • Bio. MOBY: A Bioinformatics Platform for Genome Canada • Ahab, Ishmael, i. CAPTURer: Genome BC Better Biomarkers in Transplantation • Cardio. SHARE: Canadian Institutes for Health Research (CIHR) • Taverna: my. Grid • Ben Good: CIHR Bioinformatics Training Programme
It doesn’t always rain in Vancouver It just feels like it does…
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