As of 2006, there are over 1,000 public and commercial biological databases. These biological 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. 2006 is a common year starting on Sunday of the Gregorian calendar. ... Biology (from Greek Βìο meaning life and Λoγος meaning the study of, see below) is the study of life. ... The term database originated within the computer industry. ... Genomics is the study of an organisms entire genome. ... ECAN Genesis 2000 robot preparing Ciphergen SELDI-TOF protein chips for proteomic pattern analysis. ... Look up taxonomy in Wiktionary, the free dictionary. ... A nucleotide is a chemical compound that consists of a heterocyclic base, a sugar, and one or more phosphate groups. ... This stylistic schematic diagram shows a gene in relation to the double helix structure of DNA and to a chromosome (right). ... Phenylalanine is one of the standard amino acids. ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... Figure 1: A representation of a condensed eukaryotic chromosome, as seen during cell division. ... In biology, mutations are changes to the genetic material (either DNA or RNA). ... A protein primary structure is a chain of amino acids. ...

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 medications and in discovering basic relationships amongst species in the history of life. A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... Overview of the citric acid cycle The citric acid cycle, one of the central metabolic pathways in aerobic organisms. ... This article is about evolution in biology. ... In biology, a species is one of the basic units of biodiversity. ... Oral medication A medication is a licenced drug taken to cure or reduce symptoms of an illness or medical condition. ... This timeline outlines the major events in the development of life on planet Earth. ...

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.== 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 medications and in discovering basic relationships amongst species in the history of life. A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... Overview of the citric acid cycle The citric acid cycle, one of the central metabolic pathways in aerobic organisms. ... This article is about evolution in biology. ... In biology, a species is one of the basic units of biodiversity. ... Oral medication A medication is a licenced drug taken to cure or reduce symptoms of an illness or medical condition. ... This timeline outlines the major events in the development of life on planet Earth. ...

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 publicly available online databases related to computational biology (or bioinformatics). Map of the human X chromosome (from the NCBI website). ...

The Database Issue of NAR

See also: NCBI, PubMed The National Center for Biotechnology Information (NCBI) is part of the US National Library of Medicine (NLM), which is a branch of the US National Institutes of Health. ... Medline is a comprehensive literature database of life sciences and biomedical information. ...

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 publicly available online databases related to computational biology (or bioinformatics). Map of the human X chromosome (from the NCBI website). ...

The Database Issue of NAR

See also: NCBI, PubMed The National Center for Biotechnology Information (NCBI) is part of the US National Library of Medicine (NLM), which is a branch of the US National Institutes of Health. ... Medline is a comprehensive literature database of life sciences and biomedical information. ...

Most important public databases for molecular biology

(from www.kokocinski.net)

Primary sequence databases

The International Nucleotide Sequence Database (INSD) consists of the following databases. The International Nucleotide Sequence Database (INSD) consists of a joint effort to collect and disseminate databases about DNA and RNA sequences. ...

1. DDBJ (DNA Data Bank of Japan)
2. EMBL Nucleotide DB (European Molecular Biology Laboratory)
3. GenBank [1] (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. The European Molecular Biology Laboratory (EMBL) is a molecular biology research institution supported by 19 European countries. ... The GenBank sequence database is an annotated collection of all publicly available nucleotide sequences and their protein translations. ... The National Center for Biotechnology Information (NCBI) is part of the US National Library of Medicine (NLM), which is a branch of the US National Institutes of Health. ... A protein primary structure is a chain of amino acids. ... A crab is an example of an organism. ...

Meta-databases

1. MetaDB (MetaDB: A Metadatabase for the Biological Sciences) containing links and descriptions for over 1200 biological databases.
2. Entrez[2] (National Center for Biotechnology Information)
3. euGenes (Indiana University)
4. GeneCards (Weizmann Inst.)
5. SOURCE (Stanford University)
6. mGen containing four of the world biggest databases GenBank, Refseq, EMBL and DDBJ - easy and simple program friendly gene extraction
7. Harvester (EMBL Heidelberg) Bioinformatic_Harvester Integrating 16 major protein resources.

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 convenient form. The Entrez logo The Entrez Global Query Cross-Database Search System allows access to databases at the National Center for Biotechnology Information (NCBI) website. ... The National Center for Biotechnology Information (NCBI) is part of the US National Library of Medicine (NLM), which is a branch of the US National Institutes of Health. ... Indiana University is the principal campus of the Indiana University system. ... The Koffler accelerator, one of the best-known buildings on campus. ... The Leland Stanford Junior University, commonly known as Stanford University (or simply Stanford), is a private university located approximately 37 miles (60 kilometers) southeast of San Francisco and approximately 20 miles northwest of San José in an unincorporated part of Santa Clara County. ... The European Molecular Biology Laboratory (EMBL) is a molecular biology research institution supported by 19 European countries. ... The Bioinformatic-Harvester is a bioinformatic meta search engine for genes and protein associated information. ...

Genome Browsers

1. UCSC Genome Bioinformatics Genome Browser and Tools (UCSC)
2. Ensembl Genome Browser (Sanger Institute and EBI)
3. Integrated Microbial Genomes Microbial Genome Browser (Joint Genome Institute, Department of Energy)
4. GBrowse The GMOD GBrowse Project
5. Pathway Tools Genome Browser

Genome Browsers enable researchers to visualize and browse entire genomes (most have many complete genomes) with annotated data including gene prediction and structure, proteins, expression, regulation, variation, comparative analysis, etc. Annotated data is usually from multiple diverse sources. The University of California, Santa Cruz, also known as UCSC or UC Santa Cruz, is one of the ten campuses of the University of California. ... The Wellcome Trust Sanger Institute (formally the Sanger Centre) is a genome research centre in Cambridgeshire, England. ... The European Bioinformatics Institute (EBI) part of EMBL is a centre for research and services in bioinformatics. ... The Joint Genome Institute Production Genomics Facility is located in Walnut Creek, California. ... The United States Department of Energy (DOE) is a Cabinet-level department of the United States government responsible for energy policy and nuclear safety. ... The introduction to this article provides insufficient context for those unfamiliar with the subject matter. ... In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). ...

Specialized databases

1. CGAP Cancer Genes (National Cancer Institute)
2. Clone Registry Clone Collections (National Center for Biotechnology Information)
3. DBGET H.sapiens (Univ. of Kyoto)
4. GDB Hum. Genome Db (Human Genome Organisation)
5. I.M.A.G.E Clone Collections (Image Consortium)
6. MGI Mouse Genome (Jackson Lab.)
7. SHMPD The Singapore Human Mutation and Polymorphism Database
8. NCBI-UniGene (National Center for Biotechnology Information)
9. OMIM Inherited Diseases (Online Mendelian Inheritance in Man)
10. Off. Hum. Genome Db (HUGO Gene Nomenclature Committee)
11. List with SNP-Databases
12. p53 The p53 Knowledgebase

The National Cancer Institute (NCI) is the United States federal governments principal agency for cancer research and training, and the first institute of the present-day National Institutes of Health. ... The National Center for Biotechnology Information (NCBI) is part of the US National Library of Medicine (NLM), which is a branch of the US National Institutes of Health. ... The Clocktower Kyoto University (Japanese: 京都大学, Kyōto Daigaku; abbreviated to 京大, Kyōdai) in Kyoto, Japan, is the second oldest university and one of the leading research universities in the country. ... The Human Genome Organisation (HUGO) is an organization involved in the Human Genome Project, a project about mapping the human genome. ... The Jackson Laboratory was founded in Bar Harbor, Maine in 1929 by C. C. Little. ...

Pathway Databases

1. BioCyc Database Collection including EcoCyc and MetaCyc
2. KEGG PATHWAY Database[3] (Univ. of Kyoto)
3. Reactome[4] (Cold Spring Harbor Laboratory, EBI, Gene Ontology Consortium)

The BioCyc database collection describes genome and pathway information for hundreds of organisms. ... EcoCyc is a bioinformatics database for the bacterium Escherichia coli K-12. ... The MetaCyc database contains extensive information on metabolic pathways and enzymes from many organisms. ... KEGG PATHWAY Database is one of the important databases in bioinformatics. ... The Clocktower Kyoto University (Japanese: 京都大学, Kyōto Daigaku; abbreviated to 京大, Kyōdai) in Kyoto, Japan, is the second oldest university and one of the leading research universities in the country. ... Reactome is an online bioinformatics database of human biology described in molecular terms. ... The Cold Spring Harbor Laboratory (CSHL) is a research and educational institution, consisting of science laboratories located in Cold Spring Harbor, New York on Long Island, USA. The Laboratory has research programs focusing on cancer, neurobiology, plant genetics, genomics and bioinformatics, and has a broad educational mission, including the recently... The European Bioinformatics Institute (EBI) part of EMBL is a centre for research and services in bioinformatics. ...

Protein sequence databases

1. UniProt[5] Universal Protein Resource (UniProt Consortium: EBI, Expasy, PIR)
2. PIR Protein Information Resource (Georgetown University Medical Center (GUMC))
3. Swiss-Prot[6] Protein Knowledgebase (Swiss Institute of Bioinformatics)
4. PEDANT Protein Extraction, Description and ANalysis Tool (Forschungszentrum f. Umwelt & Gesundheit)
5. PROSITE Database of Protein Families and Domains
6. DIP Database of Interacting Proteins (Univ. of California)
7. Pfam Protein families database of alignments and HMMs (Sanger Institute)
8. ProDom Comprehensive set of Protein Domain Families (INRA/CNRS)
9. SignalP Server for signal peptide prediction

UniProt is the universal protein database, a central repository of protein data created by combining Swiss-Prot, TrEMBL and PIR. This makes it the worlds most comprehensive resource on protein information. ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... The European Bioinformatics Institute (EBI) part of EMBL is a centre for research and services in bioinformatics. ... The introduction of this article does not provide enough context for readers unfamiliar with the subject. ... Georgetown University, incorporated as the The President and Directors of the College of Georgetown, is a private university in the United States, located in Georgetown, a historic neighborhood of Washington, D.C. Founded on January 23, 1789 by Archbishop John Carroll, it is both the oldest Roman Catholic and oldest... Swiss-Prot is a curated biological database of protein sequences created in 1986 by Amos Bairoch during his PhD and developed by the Swiss Institute of Bioinformatics and the European Bioinformatics Institute. ... The Swiss Institute of Bioinformatics (SIB) is an academic not-for-profit foundation established on March 30, 1998 whose mission is: to promote research, develop databanks and computer technologies, and be involved with teaching and service activities in the field of bioinformatics in Switzerland with international collaborations. ... A protein family is a group of evolutionarily related proteins. ... Within a protein, a structural domain (domain) is an element of overall structure that is self-stabilizing and often folds independently of the rest of the protein chain. ... The University of California (UC) is a public university system in the state of California. ... The Wellcome Trust Sanger Institute (formally the Sanger Centre) is a genome research centre in Cambridgeshire, England. ... The Institut National de la Recherche Agronomique (INRA) is a French public research institute dedicated to scientific studies surrounding the problems of agriculture. ... The Centre national de la recherche scientifique (CNRS) is the largest and most prominent public research organization in France. ... A signal peptide is a short (15-60 amino acids long) peptide chain that directs the post transrational transport of a protein. ...

Protein structure databases

Protein structure databases: Proteins are amino acid chains, made up from 20 different L-α-amino acids, also referred to as residues, that fold into unique three-dimensional protein structures. ...

1. Protein Data Bank[7] (PDB) (Research Collaboratory for Structural Bioinformatics (RCSB))
2. CATH Protein Structure Classification
3. SCOP Structural Classification of Proteins
4. SWISS-MODEL Server and Repository for Protein Structure Models
5. ModBase Database of Comparative Protein Structure Models (Sali Lab, UCSF)

The Protein Data Bank (PDB) is a repository for 3-D structural data of proteins and nucleic acids. ... UCSF in 1908, with the streetcar that used to run on Parnassus Avenue The University of California, San Francisco (UCSF) is one of the worlds leading centers of health sciences research, patient care, and education. ...

Microarray-databases

Microarray-databases: A DNA microarray (also DNA chip or gene chip in common speech) is a piece of glass or plastic on which pieces of DNA have been affixed in a microscopic array. ...

1. ArrayExpress (European Bioinformatics Institute)
2. Gene Expression Omnibus (National Center for Biotechnology Information)
3. maxd (Univ. of Manchester)
4. SMD (Stanford University)
5. GPX(Scottish Centre for Genomic Technology and Informatics)

The European Bioinformatics Institute (EBI) part of EMBL is a centre for research and services in bioinformatics. ... The National Center for Biotechnology Information (NCBI) is part of the US National Library of Medicine (NLM), which is a branch of the US National Institutes of Health. ... The University of Manchester is a large university located in Manchester, England. ... The Leland Stanford Junior University, commonly known as Stanford University (or simply Stanford), is a private university located approximately 37 miles (60 kilometers) southeast of San Francisco and approximately 20 miles northwest of San José in an unincorporated part of Santa Clara County. ...

Protein-Protein Interactions

Protein-protein interactions: Protein-protein interactions refer to the association of protein molecules and the study of these associations from the perspective of biochemistry, signal transduction and networks. ...

1. BioGRID[8] A General Repository for Interaction Datasets (Samuel Lunenfeld Research Institute)
2. STRING: STRING is a database of known and predicted protein-protein interactions. (EMBL)

The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein interactions created in 2003 (originally referred to as simply the General Repository for Interaction Datasets (GRID) by Mike Tyers, Bobby-Joe Breitkreutz, and Chris Stark at the Samuel Lunenfeld Research Institute at Mount Sinai... Mount Sinai Hospital The Samuel Lunenfeld Research Institute of Mount Sinai Hospital (Toronto), Ontario, Canada was established in 1985 by an endowment from the Lunenfeld and Kunin families. ... The European Molecular Biology Laboratory (EMBL) is a molecular biology research institution supported by 19 European countries. ...

See also

• Interactome
• Biological data