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As of 2006, there are over 1,000 public and commercial biological databases. These biological databases usually contain genomic, proteomic and metabolomic data, but databases are also used in taxonomy. The data include nucleotide sequences of genes or amino acid sequences of proteins. Furthermore information about function, structure, localisation (both cellular and chromosomeal), clinical effects of mutations as well as similarities of biological sequences and structures can be found.

Contents 1 Overview 2 Example public databases for molecular biology 2.1 Primary sequence databases 2.2 Meta-databases 2.3 Genome Databases 2.4 Genome Browsers 2.5 Protein sequence databases 2.6 Protein structure databases 2.7 Protein-protein interactions 2.8 Metabolic pathway Databases 2.9 Microarray databases 2.10 Mathematical Model Databases 2.11 Specialized databases 3 See also 4 External links

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.

The biological knowledge is distributed amongst many different general and specialized databases. This sometimes makes it difficult to ensure the consistency of information. Biological databases cross-reference other databases with accession numbers as one way of linking their related knowledge together.

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 online databases related to biology and bioinformatics.

(from www.kokocinski.net)

The International Nucleotide Sequence Database (INSD) consists of the following databases.

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.

Strictly speaking a meta-database can be considered a database of databases, rather than any one integration project or technology. They collect data from different sources and usually makes them available in new and more convenient form, or with an emphasis on a particular disease or organism.

1. Entrez[2] (National Center for Biotechnology Information)
2. euGenes (Indiana University)
3. GeneCards (Weizmann Inst.)
4. SOURCE (Stanford University)
5. mGen containing four of the world biggest databases GenBank, Refseq, EMBL and DDBJ - easy and simple program friendly gene extraction
6. Bioinformatic Harvester[3] (Karlsruhe Institute of Technology) - Integrating 26 major protein/gene resources.
7. MetaBase[4] (KOBIC) - A user contributed database of biological databases.

These databases collect organism genome sequences, annotate and analyze them, and provide public access. Some add curation of experimental literature to improve computed annotations. These databases may hold many species genomes, or a single model organism genome.

1. Ensembl provides automatic annotation databases for human, mouse, other vertebrate and eukaryote genomes.
2. JGI Genomes of the DOE-Joint Genome Institute provides databases of many eukaryote and microbial genomes.
3. CAMERA Resource for microbial genomics and metagenomics
4. MGI Mouse Genome (Jackson Lab.)
5. Corn, the Maize Genetics and Genomics Database
6. Saccharomyces Genome Database, genome of the yeast model organism.
7. Wormbase, genome of the model organism Caenorhabditis elegans
8. Zebrafish Information Network, genome of this fish model organism.

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.

1. Integrated Microbial Genomes (IMG) system by the DOE-Joint Genome Institute
2. UCSC Genome Bioinformatics Genome Browser and Tools (UCSC)
3. Ensembl The Ensembl Genome Browser (Sanger Institute and EBI)
4. GBrowse The GMOD GBrowse Project
5. Pathway Tools Genome Browser
6. X:Map A genome browser that shows Affymetrix Exon Microarray hit locations alongside the gene, transcript and exon data on a Google maps api

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

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)

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)
3. Database of Interacting Proteins

1. BioCyc Database Collection including EcoCyc and MetaCyc
2. KEGG PATHWAY Database[9] (Univ. of Kyoto)
3. MANET database [10] (University of Illinois)
4. Reactome[11] (Cold Spring Harbor Laboratory, EBI, Gene Ontology Consortium)

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)

1. [http://www.cellml.org/models (CellML)
2. [http://www.ebi.ac.uk/biomodels/ (Biomodels Database)

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. SHMPD The Singapore Human Mutation and Polymorphism Database
6. NCBI-UniGene (National Center for Biotechnology Information)
7. OMIM Inherited Diseases (Online Mendelian Inheritance in Man)
8. Off. Hum. Genome Db (HUGO Gene Nomenclature Committee)
9. HGMD disease-causing mutations (HGMD Human Gene Mutation Database)
10. PhenCode linking human mutations with phenotype
11. List with SNP-Databases
12. p53 The p53 Knowledgebase
13. Edinburgh Mouse Atlas
14. HvrBase++ Human and primate mitochondrial DNA

• NCBI
• PubMed
• Interactome
• Biological data
• MetaBase

• Genome Proteome Search Engine to search across biological databases
• DBD: Database of Biological Databases/Bioinformatics Databases
• CAMERA Cyberinfrastructure for Metagenomics, free data repository and bioinformatics tools for metagenomics.

Databases supported by Bioinformatic Harvester

NCBI-BLAST | CDD | Ensembl | Entrez | Flybase | Flymine | GFP-cDNA | Genome_browser | GeneCard | Google_Scholar | GoPubMed | HomoloGene | iHOP | IPI | OMIM | Mitocheck | PSORT | PolyMeta | UniProt | SOURCE | SOSUI | RZPD | Sciencenet | STRING | SMART | ZFIN |