Bioinformatics Database Resources

Bioinformatics Database Resources

Icxa Khandelwal (Jaypee University of Information Technology, India), Aditi Sharma (Jaypee University of Information Technology, India), Pavan Kumar Agrawal (G. B. Pant Engineering College, India) and Rahul Shrivastava (Jaypee University of Information Technology, India)
DOI: 10.4018/978-1-5225-1871-6.ch004
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Abstract

Various biological databases are available online, which are classified based on various criteria for ease of access and use. All such bioinformatics database resources have been discussed in brief in this book chapter. The major focus is on most commonly used biological/bioinformatics databases. The authors provide an overview of the information provided and analysis done by each database, information retrieval system and formats available, along with utility of the database to its users. Most widely used databases have been covered in detail so as to enhance readers' understanding. This chapter will serve as a guide to those who are new to the field of bioinformatics database resources, or wish to have consolidated information on various bioinformatics databases available.
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Introduction

The National Center for Biotechnology Information (NCBI) defines bioinformatics as: “the field of science in which biology, computer science, and information technology merge into a single discipline”. Bioinformatics can be considered an amalgam of three sub-disciplines:

  • 1.

    Development of new algorithms as well as statistics so that the relationship between the elements of huge datasets can be determined.

  • 2.

    Analysis as well as interpretation of biological data i.e. various types of sequences and structures.

  • 3.

    Development of tools and software to ensure efficient access as well as management of biological data (Toomula, 2011).

The bioinformatics database resources focus primarily on the third sub-discipline of bioinformatics. A database can be defined as a computerized and organized storehouse of related information that provides a standardized way for searching, inserting and updating data. The data stored in these databases is persistent and organized. Database Management System (DBMS) is a software application that deals with the user, other applications, and the database itself in order to perform analysis and capture data in a systematic manner.

Bioinformatics databases or biological databases are storehouses of biological information. They can be defined as libraries containing data collected from scientific experiments, published literature and computational analysis. It provides users an interface to facilitate easy and efficient recording, storing, analyzing and retrieval of biological data through application of computer software. Biological data comes in several different formats like text, sequence data, structure, links, etc. and these needs to be taken into account while creating the databases.

There are various criteria on the basis of which the databases can be classified. On the basis of structure, databases can be classified as a text file, flat file, object-oriented and relational databases. On the basis of information, they can be classified as general and specialized databases. Most commonly, they are classified on the basis of the type of data stored in primary, secondary and composite databases (Kumar, 2005).

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