Biological database


Biological database

Biological databases are libraries of life sciences information, collected from scientific experiments, published literature, high throughput experiment technology, and computational analyses. They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics. [cite journal |author=Altman RB |title=Building successful biological databases |journal=Brief. Bioinformatics |volume=5 |issue=1 |pages=4–5 |year=2004 |month=March |pmid=15153301 |doi= |url=http://bib.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=15153301] 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.

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. [cite journal |author=Bourne P |title=Will a biological database be different from a biological journal? |journal=PLoS Comput. Biol. |volume=1 |issue=3 |pages=179–81 |year=2005 |month=August |pmid=16158097 |doi=10.1371/journal.pcbi.0010034 |url=] . 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. Cross-references among databases are common, using database accession numbers.

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.

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 [http://www3.oup.co.uk/nar/database/c/ Database Issue of NAR] is freely available, and categorizes many of the publicly available online databases related to biology and bioinformatics.

Example public databases for molecular biology

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

Primary sequence databases

The International Nucleotide Sequence Database (INSD) consists of the following databases.
# [http://www.ddbj.nig.ac.jp/Welcome-e.html DDBJ ] (DNA Data Bank of Japan)
# [http://www.ebi.ac.uk/embl/index.html EMBL Nucleotide DB] (European Molecular Biology Laboratory)
# GenBank [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

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.

# Entrez [http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi] (National Center for Biotechnology Information)
# [http://eugenes.org euGenes] (Indiana University)
# [http://www.genecards.org GeneCards] (Weizmann Inst.)
# [http://genome-www4.stanford.edu/cgi-bin/SMD/source/sourceSearch SOURCE] (Stanford University)
# [http://www.cyber-indian.com/bioperl/index.html mGen] containing four of the world biggest databases GenBank, Refseq, EMBL and DDBJ - easy and simple program friendly gene extraction
# Bioinformatic Harvester [http://harvester.fzk.de] (Karlsruhe Institute of Technology) - Integrating 26 major protein/gene resources.
# MetaBase [http://BioDatabase.Org] (KOBIC) - A user contributed database of biological databases.

Genome 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.
# Ensembl provides automatic annotation databases for human, mouse, other vertebrate and eukaryote genomes.
# [http://genome.jgi.doe.gov/ JGI Genomes] of the DOE-Joint Genome Institute provides databases of many eukaryote and microbial genomes.
# [http://camera.calit2.net/index.php/ CAMERA] Resource for microbial genomics and metagenomics
# [http://www.informatics.jax.org MGI Mouse Genome] (Jackson Lab.)
# [http://www.maizegdb.org/ Corn] , the Maize Genetics and Genomics Database
# Saccharomyces Genome Database, genome of the yeast model organism.
# Wormbase, genome of the model organism Caenorhabditis elegans
# Flybase, genome of the model organism Drosophila melanogaster
# Zebrafish Information Network, genome of this fish model organism.
# [http://troy.bioc.uvic.ca/ Viral Bioinformatics Resource Center] Curated database containing annotated genome data for eleven virus families.
# [http://www.ericbrc.org/ ERIC (Enteropathogen Resource Integration Center)] Curated database containing annotated genome data for five enteropathogens - Escherichia coli, Shigella, Salmonella, Yersinia enterocolitica, and Y. pestis.

Genome Browsers

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.
# [http://img.jgi.doe.gov/ Integrated Microbial Genomes] (IMG) system by the DOE-Joint Genome Institute
# [http://genome.ucsc.edu UCSC Genome Bioinformatics] Genome Browser and Tools (UCSC)
# [http://www.ensembl.org/ Ensembl] The Ensembl Genome Browser (Sanger Institute and EBI)
# [http://www.gmod.org/?q=node/71 GBrowse] The GMOD GBrowse Project
# [http://bioinformatics.ai.sri.com/ptools/ Pathway Tools] Genome Browser
# [http://xmap.picr.man.ac.uk X:Map] A genome browser that shows Affymetrix Exon Microarray hit locations alongside the gene, transcript and exon data on a Google maps api
# [http://troy.bioc.uvic.ca/tools/VGO Viral Genome Organizer (VGO)] A genome browser providing visualization and analysis tools for annotated whole genomes from the eleven virus families in the VBRC (Viral Bioinformatics Resource Center) databases
# [http://apollo.berkeleybop.org/current/index.html Apollo Genome Annotation Curation Tool] A cross-platform, JAVA-based standalone genome viewer with enterprise-level functionality and customizations. The standard for many model organism databases.

Protein sequence databases

# UniProt [http://www.uniprot.org] Universal Protein Resource (UniProt Consortium: EBI, Expasy, PIR)
# [http://www-nbrf.georgetown.edu/pir/searchdb.html PIR] Protein Information Resource (Georgetown University Medical Center (GUMC))
# Swiss-Prot [http://www.expasy.org/sprot/] Protein Knowledgebase (Swiss Institute of Bioinformatics)
# [http://pedant.gsf.de PEDANT] Protein Extraction, Description and ANalysis Tool (Forschungszentrum f. Umwelt & Gesundheit)
# [http://www.expasy.org/prosite/ PROSITE] Database of Protein Families and Domains
# [http://dip.doe-mbi.ucla.edu DIP] Database of Interacting Proteins (Univ. of California)
# [http://www.sanger.ac.uk/Software/Pfam Pfam] Protein families database of alignments and HMMs (Sanger Institute)
# [http://protein.foulouse.inra.fr/prodom/current/html/home.php ProDom] Comprehensive set of Protein Domain Families (INRA/CNRS)
# [http://www.cbs.dtu.dk/services/SignalP/ SignalP 3.0] Server for signal peptide prediction (including cleavage site prediction), based on artificial neural networks and HMMs
# [http://supfam.org/SUPERFAMILY/ SUPERFAMILY] Library of HMMs representing superfamilies and database of (superfamily and family) annotations for all completely sequenced organisms

Protein structure Databases

# Protein Data Bank [http://www.rcsb.org/pdb/] (PDB) (Research Collaboratory for Structural Bioinformatics (RCSB))
# [http://www.cathdb.info/ CATH] Protein Structure Classification
# [http://scop.mrc-lmb.cam.ac.uk/scop/ SCOP] Structural Classification of Proteins
# [http://swissmodel.expasy.org//SWISS-MODEL.html SWISS-MODEL] Server and Repository for Protein Structure Models
# [http://salilab.org/modbase ModBase] Database of Comparative Protein Structure Models (Sali Lab, UCSF)

Protein-protein interactions

# BioGRID [http://www.thebiogrid.org] A General Repository for Interaction Datasets (Samuel Lunenfeld Research Institute)
# [http://string.embl.de STRING: STRING is a database of known and predicted protein-protein interactions.] (EMBL)
# [http://dip.doe-mbi.ucla.edu/ DIP Database of Interacting Proteins]

Metabolic pathway Databases

# BioCyc Database Collection including EcoCyc and MetaCyc
# KEGG PATHWAY Database [http://www.genome.ad.jp/kegg/pathway.html] (Univ. of Kyoto)
# MANET database [http://www.manet.uiuc.edu/] (University of Illinois)
# Reactome [http://www.reactome.org] (Cold Spring Harbor Laboratory, EBI, Gene Ontology Consortium)

Microarray databases

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

Mathematical Model Databases

# [http://www.cellml.org/models CellML]
# [http://www.ebi.ac.uk/biomodels/ Biomodels Database]

PCR / Real time PCR primer Databases

# [http://www.pathooligodb.com/ PathoOligoDB: A free QPCR oligo database for pathogens ]

Specialized databases

# [http://biomovie.ethz.ch BIOMOVIE] (ETH Zurich) movies related to biology and biotechnology
# [http://cgap.nci.nih.gov/Genes/GeneFinder CGAP Cancer Genes] (National Cancer Institute)
# [http://www.ncbi.nlm.nih.gov/genome/clone Clone Registry Clone Collections] (National Center for Biotechnology Information)
# [http://www.genome.ad.jp/dbget-bin/www_bfind?h.sapiens DBGET H.sapiens] (Univ. of Kyoto)
# [http://www.gdb.org/gdb GDB Hum. Genome Db] (Human Genome Organisation)
# [http://shmpd.bii.a-star.edu.sg SHMPD] The Singapore Human Mutation and Polymorphism Database
# [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene NCBI-UniGene] (National Center for Biotechnology Information)
# [http://www.ncbi.nlm.nih.gov/Omim OMIM Inherited Diseases] (Online Mendelian Inheritance in Man)
# [http://www.gene.ucl.ac.uk/nomenclature Off. Hum. Genome Db] (HUGO Gene Nomenclature Committee)
# [http://www.hgmd.cf.ac.uk/ HGMD disease-causing mutations] (HGMD Human Gene Mutation Database)
# [http://www.bx.psu.edu/phencode/ PhenCode] linking human mutations with phenotype
# [http://hgvbase.cgb.ki.se/databases.htm List with SNP-Databases]
# [http://p53.bii.a-star.edu.sg p53] The p53 Knowledgebase
# [http://genex.hgu.mrc.ac.uk/ Edinburgh Mouse Atlas]
# [http://www.hvrbase.org/ HvrBase++] Human and primate mitochondrial DNA
# [http://www.polygenicpathways.co.uk/ PolygenicPathways] Genes and risk factors implicated in Alzheimer's disease, Bipolar disorder or Schizophrenia
# [http://www.broad.mit.edu/cmap/ Connectivity map] Transcriptional expression data and correlation tools for drugs
# [http://ctd.mdibl.org/ CTD] The Comparative Toxicogenomics Database describes chemical-gene-disease interactions

Wiki style databases

# [http://ecoliwiki.net/ EcoliWiki]
# Gene Wiki
# [http://openwetware.org/ OpenWetWare]
# [http://pdbwiki.org/ PDBWiki]
# [http://www.proteopedia.org/ Proteopedia]
# [http://www.topsan.org/ Topsan]
# [http://www.wikigenes.org/ WikiGenes]
# [http://www.wikipathways.org/ WikiPathways]
# WikiProfessional

=References=

ee also

*NCBI
*dbSNP
*PubMed
*Interactome
*Biological data
*MetaBase

External links

* [http://www.gpse.org Genome Proteome Search Engine] to search across biological databases
* [http://www.biodbs.info DBD: Database of Biological Databases]
* [http://camera.calit2.net/index.php CAMERA] Cyberinfrastructure for Metagenomics, free data repository and bioinformatics tools for metagenomics.


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