Biological database

Biological databases are libraries of life sciences

information, collected from scientific experiments,
published literature, high-throughput experiment
technology, and computational analysis.[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 can be broadly classified into Home page of a biological database called STRING which
sequence, structure and functional databases. Nucleic acid [1]
characterises functional links between proteins.
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. Model Organism Databases are functional databases that provide species-specific data.
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. 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 thehistory of life.

Biological knowledge is distributed among 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.

Contents
1 Types of Biological Databases
2 Nucleic Acids Research Database Issue
3 Access
4 Species-specific databases
5 See also
6 References
7 External links
Types of Biological Databases
There are two common concepts of biological databases: Primary Databases and
Secondary Databases. These two differ in their archive structure. Primary databases
often hold only one type of specific data which is stored in their own archive. They
upload new data explored in experiments and update entries to ensure the quality of
the data.

Secondary databases are databases, which use other databases as their source of
Concept of Primary databases
information, thus they get their data by requesting other databases. They often
already process or analyze the data matching the corresponding request to get new
results.

Nucleic Acids Research Database Issue

An important resource for finding biological databases is a special yearly issue of
the journal Nucleic Acids Research (NAR). The Database Issue of NAR is freely
available, and categorizes many of the publicly available on line databases related to
biology and bioinformatics. A companion database to the issue called the Online
Molecular Biology Database Collection lists 1,380 online databases.[5] Other Concept of Secondary databases
collections of databases exist such as MetaBase and the Bioinformatics Links
Collection.[6][7]

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 byPubMed and OMIM.

Sequence data is provided byGenBank, in terms of DNA, andUniProt, in terms of protein.
Protein structures are provided byPDB, SCOP, and CATH.

Species-specific databases
Species-specific databases are available for some species, mainly those that are often used in research (Model Organisms). For
example, EcoCyc is an E. coli database. Other popular Model Organism Databases include Mouse Genome Informatics for the
laboratory mouse, Mus musculus, the Rat Genome Database for Rattus, ZFIN for Danio Rerio (zebrafish), PomBase for the fission
yeast Schizosaccharomyces pombe, FlyBase for Drosophila, WormBase for the nematodes Caenorhabditis elegans and
Caenorhabditis briggsae, and Xenbase for Xenopus tropicalis and Xenopus laevis frogs.

See also
Model Organism Databases
Gene Disease Database
Biobank
Biological data
Chemical database
European Bioinformatics Institute
Integrative bioinformatics
List of biological databases
MetaBase (a database of biological databases)
 NCBI
PubMed (a database of biomedical literature)
Death Domain database

References
1. Szklarczyk D; Franceschini A; Kuhn M; et al. (January 2011)."The STRING database in 2011: functional interaction
networks of proteins, globally integrated and scored"(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013807).
Nucleic Acids Res. 39 (Database issue): D561–8.PMC 3013807 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC301
3807) . PMID 21045058 (https://www.ncbi.nlm.nih.gov/pubmed/21045058). doi:10.1093/nar/gkq973 (https://doi.org/
10.1093%2Fnar%2Fgkq973).
2. Attwood T.K., Gisel A.; Eriksson N-E. & Bongcam-Rudloff E. (2011). "Concepts, Historical Milestones and the Central
Place of Bioinformatics in Modern Biology: A European Perspective"(http://www.intechopen.com/articles/show/title/c
oncepts-historical-milestones-and-the-central-place-of-bioinformatics-in-modern-biology-a-european-)
. Bioinformatics
- Trends and Methodologies. InTech. Retrieved 8 Jan 2012.
3. Altman RB (March 2004)."Building successful biological databases"(http://bib.oxfordjournals.org/cgi/pmidlookup?vie
w=long&pmid=15153301). Brief. Bioinformatics. 5 (1): 4–5. PMID 15153301 (https://www.ncbi.nlm.nih.gov/pubmed/1
5153301). doi:10.1093/bib/5.1.4 (https://doi.org/10.1093%2Fbib%2F5.1.4).
4. Bourne P (August 2005)."Will a biological database be different from a biological journal?" (https://www.ncbi.nlm.nih.
gov/pmc/articles/PMC1193993). PLoS Comput. Biol. 1 (3): 179–81. PMC 1193993 (https://www.ncbi.nlm.nih.gov/pm
c/articles/PMC1193993) . PMID 16158097 (https://www.ncbi.nlm.nih.gov/pubmed/16158097).
doi:10.1371/journal.pcbi.0010034(https://doi.org/10.1371%2Fjournal.pcbi.0010034) .
5. Galperin MY; Fernández-Suárez XM (January 2012)."The 2012 Nucleic Acids Research Database Issue and the
online Molecular Biology Database Collection"(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245068). Nucleic
Acids Res. 40 (Database issue): D1–8.PMC 3245068 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245068) .
PMID 22144685 (https://www.ncbi.nlm.nih.gov/pubmed/22144685). doi:10.1093/nar/gkr1196 (https://doi.org/10.109
3%2Fnar%2Fgkr1196).
6. Bolser DM; Chibon PY; Palopoli N; et al. (January 2012)."MetaBase--the wiki-database of biological databases"(htt
ps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245051). Nucleic Acids Res. 40 (Database issue): D1250–4.
PMC 3245051 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245051) . PMID 22139927 (https://www.ncbi.nlm.ni
h.gov/pubmed/22139927). doi:10.1093/nar/gkr1099 (https://doi.org/10.1093%2Fnar%2Fgkr1099).
7. Brazas MD; Yim DS; Yamada JT; Ouellette BF (July 2011). "The 2011 Bioinformatics Links Directory update: more
resources, tools and databases and features to empower the bioinformatics community"(https://www.ncbi.nlm.nih.go
v/pmc/articles/PMC3125814). Nucleic Acids Res. 39 (Web Server issue): W3–7.PMC 3125814 (https://www.ncbi.nl
m.nih.gov/pmc/articles/PMC3125814) . PMID 21715385 (https://www.ncbi.nlm.nih.gov/pubmed/21715385).
doi:10.1093/nar/gkr514 (https://doi.org/10.1093%2Fnar%2Fgkr514).

External links
Interactive list of biological databases, classified by categories, fromNucleic Acids Research, 2010
DBD: Database of Biological Databases
Lecture notes for Databases in bioinformatics course
Biosharing (a database of biological databases)

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