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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