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Lecture12 - Range of Relational DBMSs Lecture 12...

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Lecture 12: Bioinformatics Databases • Overview of Bioinformatics Databases • Database example: ATHENA Slides created by Dr. Curtis Dyreson 2 Range of Relational DBMSs About 30 major products BerkeleyDB ! Public domain ! Storage only, no query language MySQL (a great free database!) ! Public domain ! Limited SQL implementation, limited functionality ! No management tools (some 3 rd party) ! Others – Interbase, Postgres Oracle ! Commercial ! Full functionality ! Suite of support tools (GUI tools for everything) 3 Major Data Models Flat-file ! Text files ! Programs to manage/query Relational ! Tables ! Relational database management system (RDBMS) ! SQL ! 90% of all traditional databases Object-oriented ! Persistent objects ! OODBMS XML ! Text files in the Extensible Markup Language (XML) ! XQuery 4 Outline Traditional vs. bioinformatics applications Bioinformatics databases ATHENA: Arabidopsis promoter database
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5 Scientific Discovery Data Data is produced in the course of scientific discovery Share with others performs experiment produces data shared (internet) 6 Characteristics of Bioinformatics Data Highly complex ! BLOBs, images ! Lots of “linkage” between data collections In scientific discovery ! Outliers are of interest ! Schemas change rapidly ! Data is shared, public ! Data is append-only ! Lots of readers, few writers ! MITOMAP – 15,000 users each month, 20 additions, no revisions “Small” collections are common, shared and replicated !
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