Bioinformatics Databases

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Bioinformatics Databases

  1. 1. BIOINFORMATICS DATABASES: MANAGING THE COMPLEXITY OF LIFE Christopher Schlosberg CS 411 Graduate Project
  2. 2. Motivation of Databases for Bioinformatics <ul><li>Post-Genomic Era </li></ul><ul><li>Systems Biology </li></ul><ul><ul><li>Gene Expression Data </li></ul></ul><ul><ul><li>Proteomic Data </li></ul></ul><ul><ul><li>Metabolomic Data </li></ul></ul><ul><ul><li>Sequence Data </li></ul></ul>[12]
  3. 3. Protein Sequence Search [12]
  4. 4. Standardized Identifiers & Data Formats <ul><li>Identifiers </li></ul><ul><ul><li>Locus name </li></ul></ul><ul><ul><li>Accession numbers </li></ul></ul><ul><ul><li>GenInfo IDs </li></ul></ul><ul><ul><li>Pubmed IDs </li></ul></ul><ul><li>Data Formats </li></ul>
  5. 5. General Bio-DB Development Considerations [11] [2]
  6. 6. Relational Databases: Ontology Implementation <ul><li>Vectors(SpecieID, SpeciesName, SpeciesPopulation, SpeciesInfectionRate) </li></ul><ul><li>VectorsRefuge(SpeciesID, RefugeIR, RefugeName, SamplePopulation) </li></ul><ul><li>SeasonalSpecies(SeasonID, SpeciesID, SeasonName, SpeciesPopulation) </li></ul><ul><li>LocalStat(LocalityID, Latitude, Longitude, SpeciesID, LocalityName, PopSampleSpecies) </li></ul>
  7. 7. Cross-Referencing Multiple Databases <ul><li>Use Data Warehousing </li></ul><ul><li>Create Schema for centralized warehouse </li></ul>[9]
  8. 8. SQL Implementation for Feeder DBs [9]
  9. 9. Functional Querying <ul><li>Basic </li></ul><ul><li>Statistical </li></ul><ul><li>Neighborhood </li></ul><ul><li>Path-finding </li></ul>[10]
  10. 10. Future Outlooks <ul><li>Machine Learning </li></ul><ul><li>Data Mining </li></ul><ul><li>Global Framework & Standardization </li></ul>
  11. 11. References <ul><li>[1] STEWART, H. 2005. Biomolecular Interaction Network Database. Bioinformatics 6, 194-198. </li></ul><ul><li>[2] BORNBERG-BAUER, E., AND PATON, N.W. 2002. Conceptual Data Modelling for Bioinformatics. Bioinformatics 3, 166-180. </li></ul><ul><li>[3] WONG, L. 2002. Technologies for Integrating Biological Data. Bioinformatics 6, 389-404. </li></ul><ul><li>[4] BIRNEY, E., AND CLAMP, M. 2004. Biological Database Design and Implementation. Bioinformatics 5, 31-38. </li></ul><ul><li>[5] SCHONBACH, C., KOWALSKI-SAUNDERS, P., AND BRUSIC, V. 2000. Data Warehousing in Molecular Biology. Bioinformatics. 1, 190-198. </li></ul><ul><li>[6] NG, A., BURSTEINAS, B., GAO, Q., MOLLISON, E., AND ZVELEBIL, M. 2006. Resources for Integrative Systems: From Data Through Databases to Networks and Dynamic System Models. Bioinformatics 7, 318-330. </li></ul><ul><li>[7] CLARK, T., MARTIN, S., AND LIEFELD, T. 2004. Globally Distributed Object Identification for Biological Knowledgebases. Bioinformatics 5, 59-70. </li></ul><ul><li>[8] RAGAN, M. 2005. Research Data in Bioscience and Bioinformatics. In Australian Partnership for Advanced Computing/Australian Partnership for Sustainable Repositories Data Collections Workshop, Canberra, AUS, October 2005. </li></ul><ul><li>[9] LEE, T. ET. AL. 2006. BioWarehouse: a Bioinformatics Database Warehouse Toolkit. BMC Bioinformatics 7, 170. </li></ul><ul><li>[10] KRISHNAMURTHY, L. ET. AL. 2003. Pathways database system: an integrated system for biological pathways. Bioinformatics. 19, 930-937. </li></ul><ul><li>[11] BERGERON, B. 2002. Bioinformatics Computing . 80-101. </li></ul><ul><li>[12] GAUTHAM, N. 2006. Bioinformatics: Databases and Algorithms . 26-53. </li></ul><ul><li>[13] KOUM, G. ET. AL. 2005. Design and implementation of a mosquito database through an entomological ontology. Bioinformatics 21, 2797-2802. </li></ul>

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