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Object-oriented knowledge bases for the analysis of prokaryotic and eukaryotic genomes
G Perrière1, F Dorkeld, F Rechenmann
1Laboratoire BGBP, Univ. Claude Bernard Lyon I, Villeurbanne, France.
Proceedings. International Conference on Intelligent Systems for Molecular Biology
|January 1, 1993
Summary
New models, ColiGene and MultiMap, formalize complex biological knowledge and relationships between data types. These tools aid in analyzing gene expressivity and genome mapping across species, enhancing molecular evolution research.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Increasing biological sequence data and knowledge complexity necessitate advanced modeling.
- Existing models struggle to capture intricate relationships between diverse biological data types.
Purpose of the Study:
- To introduce ColiGene and MultiMap, novel computational models for formalizing biological knowledge.
- To demonstrate applications in molecular evolution, gene expressivity analysis, and cross-species genome mapping.
Main Methods:
- Development of ColiGene for E. coli genetics, linking genomic sequences and gene expressivity.
- Implementation of MultiMap for a "maps of maps" formalization of genome maps across species.
- Utilization of an object-oriented knowledge base (SHIRKA) and genomic database (ACNUC).
Main Results:
- ColiGene enables analysis of relationships between genomic sequences and gene expressivity.
- MultiMap facilitates manipulation of genome maps and cross-species data inference.
- Models provide graphical interfaces mimicking biological representations for user-friendliness.
Conclusions:
- ColiGene and MultiMap offer powerful tools for molecular evolution and genome analysis.
- MultiMap's cross-species inference capabilities are crucial for diverse mapping projects (human, mouse, pig).
- These models enhance biological data management and knowledge discovery.