Biological Information and Biological Databases Dr Tan Tin Wee Director Bioinformatics Centre National University of Singapore

Nature of Life Science Information Descriptive Classification and Nomenclatural Observational and Phenomenological Experimental Deduced/Computed Simulated? Theoretical?

Descriptive

Classify and Give Names Classification and Nomenclature Linnaeus - binomial nomenclature Group into kingdoms, phyla, classes, orders, families, genera, species, subspecies, strains, etc associate descriptions to these classification schema, and classify according to description etc

Observational/Phenomenological Like descriptive, yet more active Observe a lot of biological phenomenon Charles Darwin and the Beagle voyage Gregor Mendel to McClintock Start to do some experiments

Experimental From dissections to complex genetic engineering experiments Reductionist approach Occam's Razor

Fundamental Dogma

Work from the Code of Life

Deduced and Computed Information in the Era of Computational Biology

The Strategic Simulation Initiative (SSI) Revolutionising Science Through Simulation

Complexity of Genome Systems Simulation - Track expression of 100,000 genes as a function of time, conditions and environment - Genes interact in complex non-linear ways - Dynamic systems capable of chaotic behaviour - The next large simulation problem

Examples of the New Biology 1. Full genome-genome comparisons 2. Rapid assessment of polymorphic genetic variations 3. Complete construction of orthologous or paralogous groups of genes 4. Structure determination of large macromolecular assemblies/complexes 5. Dynamically simulation of realistic oligomeric systems 6. Rapid structural/topological clustering of proteins 7. Prediction of unknown molecular structures; Protein folding 8. Computer simulation of membrane structure and dynamic function 9. Simulation of genetic networks and the sensitivity of these pathways to component stiochiometry and kinetics 10. Integration of observations across scales of vastly different dimensions and organization to yield realistic environmental models for basic biology and societal needs

Theoretical? The day will dawn when we will have sufficient information to understand how basic life functions are integrated into a living cell, and how such cells intercommunicate and interoperate to function as a living whole. Then maybe, we can start talking about theoretical biology

Blast Results

Mapping/Pathways From Genetic Maps of genomes To Metabolic Pathways To Signal Transduction circuitry To Immunological regulatory networks

Categories of BioDbs - by domain of information DNA RNA Protein Genomic Mapping Pathways Structure Bibliographic Biochemical/Molecular/Miscellaneous

Other categories By category of species By families or superfamilies of molecules etc Demo http://www.infobiogen.fr/services/dbcat/

Demonstration of BioDatabases Majority of Life Science databases are online, accessible with Web via Internet Catalogs of databases available Need for a Registry to keep track and offer quality control