BOSC Markel

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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 andamp; Co-chair, Life Sciences Research DTF Object Management Group™


OMG andamp; LSR Object Management Group world’s largest software consortium UML, CORBA, XMI, ... Life Sciences Research Domain Task Force Mission: Adopt model and interface specifications to enable interoperable software components in the life sciences research 'vertical domain' (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

Biomolecular Sequence Analysis Specification: 

Biomolecular Sequence Analysis Specification RFP issued 3 April 1998 Specification adopted 1 February 2000 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

Biomolecular Sequence Analysis Entities RFP: 

Biomolecular Sequence Analysis Entities RFP RFP issued 15 December 2000 Current submission (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

Open Source Efforts: 

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

OMG’s Model Driven Architecture™: 

OMG’s Model Driven Architecture™ Solve the domain problem once (Platform Independent Model) Add the middleware details as needed (Platform Specific Models)

Possible New OMG RFP: 

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 ( or me ( 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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