OMG & LSR:
OMG andamp; 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
Biomolecular Sequence Analysis Specification:
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
Biomolecular Sequence Analysis Entities RFP:
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
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)
www.omg.org/mda
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 (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)