Biological database

As of 2004, there are around 500 public and commercial biological databases. These databases usually contain genomics and proteomics data, but databases are also used in taxonomy. The data are nucleotide sequences of genes or amino acid sequences of proteins. Furthermore information about function, structure, localisation on chromosome, clinical effects of mutations as well as similarities of biological sequences can be found.

Contents

1 Overview 2 Most important public databases for molecular biology 2.1 Primary sequence databases 2.2 Meta-databases 2.3 Specialized databases 2.4 Protein database 2.5 Microarray-databases 2.6 Protein-Protein Interactions

Overview

Biological databases have become 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 medical drugs and in discovering basic relationships amongst species in the history of life

The biological knowledge of databases is usually (locally) distributed amongst many different specialized databases. This makes it difficult to ensure the consistency of information, which sometimes leads to low data quality.

By far the most important resource for biological databases is a special (yearly) issue of the journal "Nucleic Acids Research" (NAR). The Database Issue is freely available, and categorizes all the publically available online databases related to computational biology (or bioinformatics).

The Database Issue of NAR (http://www3.oup.co.uk/nar/database/c/)

See also: NCBI, PubMed

Most important public databases for molecular biology

(from www.kokocinski.net (http://www.kokocinski.net/bioinformatics/databases.php))

Primary sequence databases

1. DDBJ  (http://www.ddbj.nig.ac.jp/Welcome-e.html) (DNA DataBase of Japan)
2. EMBL Nucleotide DB (http://www.ebi.ac.uk/embl/index.html) (European Molecular Biology Laboratory )
3. GenBank [1] (http://www.ncbi.nlm.nih.gov/Genbank/index.html) (National Center for Biotechnology Information)

These databanks represent the current knowledge about the sequences of all organisms. They interchange the stored information and are the source for many other databases.

Meta-databases

1. Entrez (http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi) {Nat.Center for Biotechn.Inf.}
2. euGenes (http://iubio.bio.indiana.edu:8089) (Univ. of Indiana)
3. GeneCards (http://www.dkfz-heidelberg.de/GeneCards) (Weizmann Inst.)
4. SOURCE (http://genome-www4.stanford.edu/cgi-bin/SMD/source/sourceSearch) (Univ. of Stanford)

Strictly speaking a meta-database can be considered a database of databases, rather than any one integration project or technology. It collects information from different other sources and usually makes them available in new and more convinient form.

Specialized databases

1. CGAP Cancer Genes (http://cgap.nci.nih.gov/Genes/GeneFinder) (National Cancer Institute)
2. Clone Registry Clone Collections (http://www.ncbi.nlm.nih.gov/genome/clone) (National Center for Biotechnology Information)
3. DBGET H.sapiens (http://www.genome.ad.jp/dbget-bin/www_bfind?h.sapiens) (Univ. of Kyoto)
4. Ensembl Genome BrowserAnnotated Genomes (http://www.ensembl.org) (EMBL-EBI and Sanger Inst.)
5. GDB Hum. Genome Db (http://www.gdb.org/gdb) (Human Genome Organization)
6. I.M.A.G.E Clone Collections (http://image.llnl.gov/image/IQ/bin/buildIQ?categoryChoice=clone%7EClone) (Image Consortium)
7. KEGG Functional Db (http://www.genome.ad.jp/kegg) (Univ. of Kyoto)
8. MGI Mouse Genome (http://www.informatics.jax.org) (Jackson Lab.)
9. NCBI-UniGene (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene) (National Center for Biotechnology Information)
10. OMIM Inherited Diseases (http://www.ncbi.nlm.nih.gov/Omim) (National Center for Biotechnology Information)
11. Off. Hum. Genome Db (http://www.gene.ucl.ac.uk/nomenclature) (HUGO Gene Nomenclature Committee)
12. List with SNP-Databases (http://hgvbase.cgb.ki.se/databases.htm)

Protein database

1. Protein Data Bank (PDB) (http://www.rcsb.org/pdb/) (Research Collaboratory for Structural Bioinformatics (RCSB))
2. Protein Information Resource (PIR) (http://www-nbrf.georgetown.edu/pir/searchdb.html) (Georgetown University Medical Center (GUMC))
3. SWISS-PROT Protein Db (http://www.expasy.org/sprot/) (Swiss Institute of Bioinformatics)
4. CATH (http://www.cathdb.info/latest/index.html)
5. SCOP (http://scop.mrc-lmb.cam.ac.uk/scop/)
6. SWISS-MODEL (http://swissmodel.expasy.org//SWISS-MODEL.html)
7. PEDANT Protein Db (http://pedant.gsf.de) (Forschungszentrum f. Umwelt & Gesundheit)
8. PROSITE (http://kr.expasy.org/prosite/)
9. Database of Interacting Proteins (http://dip.doe-mbi.ucla.edu) (Univ. of California)
10. SignalP (http://www.cbs.dtu.dk/services/SignalP/)

Microarray-databases

1. ArrayExpress (http://www.ebi.ac.uk/arrayexpress) (European Bioinformatic Institute)
2. Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo) (National Center for Biotechnology Information)
3. maxd (http://www.bioinf.man.ac.uk/microarray/maxd/index.html) (Univ. of Manchester)
4. SMD (http://genome-www5.stanford.edu/MicroArray/SMD) (Univ. of Stanford)
5. GPX (http://www.gti.ed.ac.uk/GPX)(Scottish Centre for Genomic Technology and Informatics)

Protein-Protein Interactions

1. The General Repository for Interaction Datasets (The GRID) (http://biodata.mshri.on.ca/grid) (Samuel Lunenfeld Research Institute)