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MOBY

MOBY. Lincoln Stein Cold Spring Harbor Laboratory. Getting Biological Data. What is out there?. Where do I find it?. How do I get it?. G O O G L E. keyword search. URLs. engage via HTTP. What Happens Now. URLs. engage via HTTP. Issues with Current System.

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MOBY

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  1. MOBY Lincoln Stein Cold Spring Harbor Laboratory

  2. Getting Biological Data What is out there? Where do I find it? How do I get it?

  3. GOOGLE keyword search URLs engage via HTTP What Happens Now

  4. URLs engage via HTTP Issues with Current System Keyword searching is a blunt tool. HTTP/HTML not suitable for automation. Services change without notice GOOGLE keyword search

  5. What we’d Like to Do BioGOOGLE Questions Answers

  6. What’s Been Done So Far • Interoperability on well-defined problem domains • Exchangable flat files • (Genome) DAS • Gene DAS • Protein DAS • Data Warehouses • BioMART • caBIO

  7. The bioMOBY Project • 2001 MOBY-DIC meeting (Model Organism Bring Your Own Database Interconnectivity Conference) • Two proposed architectures: • MOBY Services – PI Mark Wilkinson • Semantic MOBY – Pis Lincoln Stein & Damian Gessler

  8. Accession # Gene name MOBY Services MOBY Central I’ve got a yeast Gbk accession number and want GO terms for the corresponding protein. What services operate on accession #’s? What services operate on gene names? GO Terms

  9. MOBY-S Technology • XML ISA/HASA ontology of biological data types • Services register their call signature with MOBY Central using WSDL • Clients invoke services using SOAP • Perl API • In use by several projects • PlaNET • PlantsP

  10. type type hasMapping mapsTo operatesOn goTermURL type type type type type comment type type Gene Ontology Annotation goTerm URL Provider Graph GOSearch Subject GeneSymbol Object Bag MyGOSearch bnode2 bnode3 bnode1 bnode5 Semantic MOBY HTTP GET “MOBY- Google”

  11. type type hasMapping mapsTo operatesOn goTermURL type type type type type comment type type Gene Ontology Annotation URL goTerm Graph Provider GOSearch Subject GeneSymbol Object Bag MyGOSearch bnode2 bnode3 bnode1 bnode5 Querying S-MOBY HTTP POST “MOBY-Google” URL1 URL2 URL3

  12. ACT1 http://... GO:12345 Engaging a service HTTP POST Subject Object Provider Graph type type type type hasMapping mapsTo operatesOn goTermURL MyGOSearch bnode5 bnode2 bnode3 bnode 1 type type type type type comment Bag goTerm URL GOSearch GeneSymbol Gene Ontology Annotation

  13. S-MOBY & Semantic Web • Graphs written using OWL DL • OWL (Web Ontology Language) is W3C standard for semantic web. • OWL DL (OWL Description Logic) adds constraints that enforce completeness and decidability on OWL. • Based on RDF (Resource Description Framework)

  14. RDF • Objects specified by unique URI • Predicates specified by unique URI • Relationships among objects via Statements (Subject, Predicate, Object) • Blank nodes represent information to be filled in by client or provider application

  15. RDF Example

  16. bnode1 bnode2 bnode3 Provider URL moby:Graph moby:Object moby:Subject moby:Provider Canonical Graph rdf: type rdf: type rdf: type rdf: type moby: hasMapping moby: operatesOn moby: mapsTo

  17. Where We Are • MOBY-Google up and running • Uses IBM’s JENA library for graph reasoning • Java API for creating graphs and engaging with clients. • Perl API pending • Snazzy user interface pending

  18. Genotyping panel SNP Set Genotypes Real Life Example – hapmap.org

  19. cshl: get-individuals cshlterms: CSHLProvider moby: Provider moby: Object rdf: Bag moby: Graph moby: Subject cshlterms: Individual cshlterms: Panel Graph for Panel Query rdf:type rdf:type rdf:type rdf:type rdf:type bnode 2 bnode 4 bnode 1 bnode 5 rdf:_1 rdf:type moby: hasMapping moby: operatesOn moby: mapsTo rdf:type rdf:type cshlterms: indivName rdf:type cshlterms: panelName bnode 6 bnode 3

  20. Searching the Repository

  21. Engaging the Service

  22. The Result

  23. MOBY Software • MOBY (both versions) are open source and available from the CVS repository at www.biomoby.org.

  24. Credits CSHL Lincoln Stein Ardavan Kanani Shuly Avraham Fiona Cunningham NCGR Damian Gessler Gary Schiltz Andrew Farmer University of BC Mark Wilkinson

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