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Proposed OMG/LSR Effort for Modeling Domain Objects

Proposed OMG/LSR Effort for Modeling Domain Objects. Scott Markel, Ph.D. Principal Software Architect & Co-chair, Life Sciences Research DTF Object Management Group™. OMG & LSR. Object Management Group world’s largest software consortium UML, CORBA, XMI, ... www.omg.org

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Proposed OMG/LSR Effort for Modeling Domain Objects

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  1. Proposed OMG/LSR Effort for Modeling Domain Objects Scott Markel, Ph.D. Principal Software Architect & Co-chair, Life Sciences Research DTF Object Management Group™

  2. OMG & LSR • Object Management Group • world’s largest software consortium • UML, CORBA, XMI, ... • www.omg.org • Life Sciences Research Domain Task Force • Mission: Adopt model and interface specifications to enable interoperable software components in the life sciences research “vertical domain” • lsr.omg.org • lifesciences@omg.org • lsr-chair@omg.org (David Benton, Karl Konnerth, Scott Markel) • LSR specifications • Biomolecular Sequence Analysis, Genomic Maps, Bibliographic Query Service, Macromolecular Structures, Gene Expression, LECIS, Chemical Structures, Lab Workflow

  3. Biomolecular Sequence Analysis Specification • RFP • issued 3 April 1998 • doc.omg.org/lifesci/1998-03-05 • Specification • adopted 1 February 2000 • doc.omg.org/formal/2001-06-08 • Content • Biological objects: biological sequences, regions and annotations on sequences, genetic codes, sequence alignments, similarity searching • Analysis objects: AnalysisService, AnalysisInstance, JobControl, AnalysisState, AnalysisType, InputPropertySpec, OutputPropertySpec, AnalysisEvent and sub-types

  4. Biomolecular Sequence Analysis Entities RFP • RFP • issued 15 December 2000 • doc.omg.org/lifesci/2000-12-16 • Current submission • doc.omg.org/lifesci/2001-03-04 (EBI, LION) • Content • Biomolecular sequence alphabet • Fuzzy locations • Weight matrices, patterns, profiles, and HMMs • Phylogenetic trees • Assembly (including trace and quality data) • Composite (nested) annotations • Gene • GeneticCode extensions (initiators, terminators) • Taxonomy

  5. Open Source Efforts • BioPerl • BioJava • BioCORBA • BioPython • BioRuby • BioSQL • BSML • Agave • GAME • … • All with different domain models

  6. OMG’s Model Driven Architecture™ • Solve the domain problem once (Platform Independent Model) • Add the middleware details as needed (Platform Specific Models) • www.omg.org/mda

  7. Possible New OMG RFP • Given the number of Open Source efforts underway, it doesn’t seem to make sense to continue the BSANE submission • Any interest in a minimal, unified data model? • If yes, please contact Martin Senger (senger@ebi.ac.uk) or me (scott.markel@lionbioscience.com) • If there’s enough community interest, we’ll issue a new OMG RFP to provide a focal point (similar to what happened with gene expression, resulting in MAGE)

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