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Biological Databases

Biological Databases. By: Komal Arora. Introduction. Biological databases are libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. Introduction.

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Biological Databases

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  1. Biological Databases By: Komal Arora

  2. Introduction • Biological databases are libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis.

  3. Introduction • Information contained in biological databases includes • gene function, structure, (both cellular and chromosomal), effects of mutations as well as similarities of biological sequences and structures.

  4. Classification • Biological databases can be broadly classified into sequence and structure databases. • Nucleic acid and protein sequences are stored in sequence databases and structure database only store proteins.

  5. Sequence DB • In the field of bioinformatics, a sequence database is a type of biological database that is composed of a large collection of computerized ("digital") nucleic acid sequences, protein sequences, or other polymer sequences stored on a computer. • The UniProt database is an example of a protein sequence database.

  6. Structure databases • structure database is a database that is modeled around the various experimentally determined protein structures. • The aim of most protein structure databases is to organize the protein structures, providing the biological community access to the experimental data in a useful way.

  7. Importance • These databases are important tools in assisting scientists to analyze and explain a host of biological phenomena from the structure of biomolecules and their interaction, to the whole metabolism of organisms and to understanding the evolution of species.

  8. Importance • This knowledge helps facilitate the fight against diseases, assists in the development of medications, • predicting certain genetic diseases and in discovering basic relationships among species in the history of life.

  9. Relation with RDBMS • Relational database concepts of computer science and Information retrieval concepts of digital libraries are important for understanding biological databases.

  10. How to access • Most biological databases are available through web sites that organise data such that users can browse through the data online. • In addition the underlying data is usually available for download in a variety of formats. • Biological data comes in many formats. These formats include text, sequence data, protein structure and links.

  11. Example • STRING uses a relational database system (PostgreSQL) to store primary data and precomputed predictions. • For convenience, STRING provide selected data-items as flatfiles .

  12. END

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