A simple overview of BioMoby

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A simple overview of BioMoby

• Mark Wilkinson
• iCAPTURE Centre
• St. Pauls Hospital
• Vancouver

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St. Pauls HospitaliCAPTURE Centre
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Harnessing the Power Of communities
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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!

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What does BioMoby do?
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• 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
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Overview of BioMoby Transactions
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Overview of BioMoby Transactions
Discovery of services That consume things LIKE
sequences!
Object ontology
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Pipeline discovery on the fly

• No explicit coordination between providers
• Dynamic discovery of appropriate Services
• Automated execution of services

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Some BioMoby statistics
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Moby Breadth

• Namespaces (semantic datatypes) 281
• Objects (data syntaxes) gt300
• Service Types (analytical categories) 36
• Authorities 56 active
• Service Instances gt630
• In main server and in boutique Moby registries
  serving specialized communities worldwide

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Moby Impact

• Mailing list count 200 members (90 on developers
  mailing list)
• Google Scholar
• BioMOBY 225
• Citations of 2002 BioMOBY paper 98

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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

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Moby Registry Activity
PlaNet implements own MOBY Central
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Most recent numbers
Calls to the MOBY Central web service brokering
API
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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

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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 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.)

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Taverna Workbench Tom Oinn and Martin
Senger myGrid Project
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MOWServ Web interface to the Spanish Instituto
Nacional de Bioinformatica MOBY Central
installation
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Mare Nostrum Barcelona Supercomputing Centre
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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

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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

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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

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The Internet
Credit to P. Lord, myGrid
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The World Wide Web
Credit to P. Lord, myGrid
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The Semantic Web (low stack)
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Credit to P. Lord, myGrid
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Web Services over databases no documents to
point to!
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The Ahab BioMoby Client
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Ahab
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Ahab RDF
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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

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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

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The Output from Ishmael
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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. IBMs 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

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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

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It doesnt always rain in Vancouver

• It just feels like it does