Biological Databases

Biological databases are libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analyses.[2] They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics.[3] Information contained in biological databases includes gene function, structure, localization (both cellular and chromosomal), clinical effects of mutations as well as similarities of biological sequences and structures.

Biological databases are an important tool in assisting scientists to understand 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. This knowledge helps facilitate the fight against diseases, assists in the development of medications and in discovering basic relationships amongst species in the history of life.

Biological knowledge is distributed amongst many different general and specialized databases. This sometimes makes it difficult to ensure the consistency of information. Integrative bioinformatics is one field attempting to tackle this problem by providing unified access. One solution is how biological databases cross-reference to other databases with accession numbers to link their related knowledge together.

Relational database concepts of computer science and Information retrieval concepts of digital libraries are important for understanding biological databases. Biological database design, development, and long-term management is a core area of the discipline of bioinformatics.[4] Data contents include gene sequences, textual descriptions, attributes and ontology classifications, citations, and tabular data. These are often described as semi-structured data, and can be represented as tables, key delimited records, and XML structures.

Nucleic Acids Research Database Issue

An important resource for finding biological databases is a special yearly issue of the journal

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. Each of these can be found from certain sources, for example:

  • Text formats are provided by PubMed and OMIM.
  • Sequence data is provided by GenBank, in terms of DNA, and UniProt, in terms of protein.
  • Protein structures are provided by PDB, SCOP, and CATH.

Species-specific databases

Species-specific databases are available for some species, mainly those that are often used in research. For example, Colibase (Caenorhabditis briggsae.

See also

References

External links

  • Wiki of biological databases
  • Nucleic Acids Research, 2010
  • DBD: Database of Biological Databases
  • Lecture notes for Databases in bioinformatics course

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