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BIOLOGICAL DATABASES Biological databases are libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics. Information contained in biological databases includes gene function, structure, localization clinical effects of mutations as well as similarities of biological sequences and structures. Biological databases can be broadly classified into sequence, structure and functional databases. Nucleic acid and protein sequences are stored in sequence databases and structure databases store solved structures of RNA and proteins. Functional databases provide information on the physiological role of gene products, for example enzyme activities, mutant phenotypes, or biological pathways. Types of Biological Databases There are two common concepts of biological databases, Primary Databases and Secondary Databases these two differ in their archive structure. I. Primary database 1. It is also known as archival database. 2. Database consisting of data derived experimentally such as nucleotide sequences and three dimensional structures are known as primary databases. 3. Experimental results are directly submitted into database by researchers across the globe. 4. Example: Gen Bank,DDBJ,SWISS-PROT II. Secondary databases 1. It is also known as curated database. 2. Databases consisting of data derived from the analysis of primary data such as sequences, secondary structures etc. 3. It contains results of analysis of primary databases and significant data in the form of conserved sequences, signature sequences, active site residue of proteins etc. 4. Example: PROSITE, BLOCKS, PRINTS, OMIM. Database Management System for Biological Data Biological databases typically consist of a mixture of raw data, metadata, sequences, annotations, and related data obtained from various sources. Current database technology lacks several functionalities that are needed by biological databases. Bdbms is an extensible prototype database management system for supporting biological data. Bdbms extends the functionalities of current DBMSs to include: (1) Annotation and provenance management (2) Local dependency tracking (3) Update authorization (4) Non-traditional and novel access methods. INTRODUCTION TO SQL SQL, often referred to as Structured/Sequence Query Language, is a database computer language designed for managing data in relational database management systems (RDBMS), and originally based upon relational algebra. SQL was initially developed at IBM by Donald D. Chamberlin and Raymond F. Boyce in the early 1970s.This version, initially called SEQUEL was designed to manipulate and retrieve data stored in IBM's original relational database management system. SQL commands are divided into several different types: i. ii. iii. iv. Data manipulation language (DML) Data definition language (DDL) Data control language (DCL) Transaction control language (TCL) Language elements The SQL language is subdivided into several language elements, including: Clauses Expressions Predicates Queries Statements