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Biological database

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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. [1] 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. [2]. 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 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 www.kokocinski.net)

Primary sequence databases

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.

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.

  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.
  8. ConsensusPathDB - A molecular functional interaction database, integrating information from 12 other 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.

  1. CAMERA Resource for microbial genomics and metagenomics
  2. Corn, the Maize Genetics and Genomics Database
  3. Ensembl provides automatic annotation databases for human, mouse, other vertebrate and eukaryote genomes.
  4. ERIC (Enteropathogen Resource Integration Center) Curated database containing annotated genome data for five enteropathogens - Escherichia coli, Shigella, Salmonella, Yersinia enterocolitica, and Y. pestis.
  5. Flybase, genome of the model organism Drosophila melanogaster
  6. MGI Mouse Genome (Jackson Lab.)
  7. JGI Genomes of the DOE-Joint Genome Institute provides databases of many eukaryote and microbial genomes.
  8. National Microbial Pathogen Data Resource. A manually curated database of annotated genome data for the pathogens Campylobacter, Chlamydia, Chlamydophila, Haemophilus, Listeria, Mycoplasma, Neisseria, Staphylococcus, Streptococcus, Treponema, Ureaplasma, and Vibrio.
  9. Saccharomyces Genome Database, genome of the yeast model organism.
  10. Viral Bioinformatics Resource Center Curated database containing annotated genome data for eleven virus families.
  11. The SEED platform for microbial genome analysis includes all complete microbial genomes, and most partial genomes. The platform is used to annotate microbial genomes using subsystems.
  12. Wormbase, genome of the model organism Caenorhabditis elegans
  13. Zebrafish Information Network, genome of this fish model organism.
  14. TAIR, The Arabidopsis Information Resource.
  15. UCSC Malaria Genome Browser, genome of malaria causing species (Plasmodium falciparumata and others)
  16. RGD Rat Genome Database: Genomic and phenotype data for Rattus norvegicus

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.

  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
  7. 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
  8. 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.
  9. SEED viewer for visualizing and interrogating the SEED database of complete microbial genomes
  10. Integrated Genome Browser (IGB) A cross-platform, Java-based desktop genome viewer.
  11. Argo Genome Browser A fre and open source standalone Java-based genome browser for visualizing and manually annotating whole genomes.

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. PRINTS PRINTS is a compendium of protein fingerprints (Manchester University)
  9. ProDom Comprehensive set of Protein Domain Families (INRA/CNRS)
  10. SignalP 3.0 Server for signal peptide prediction (including cleavage site prediction), based on artificial neural networks and HMMs
  11. SUPERFAMILY Library of HMMs representing superfamilies and database of (superfamily and family) annotations for all completely sequenced organisms
  12. Annotation Clearing House a project from the National Microbial Pathogen Data Resource

Protein structure Databases

  1. Protein Data Bank[7] (PDB) (Research Collaboratory for Structural Bioinformatics (RCSB))
  2. Protein Model Portal[8] (PMP) Meta database that combines several databases of protein structure models (Biozentrum, Basel, Switzerland)
  3. CATH Protein Structure Classification
  4. SCOP Structural Classification of Proteins
  5. SWISS-MODEL Server and Repository for Protein Structure Models
  6. ModBase Database of Comparative Protein Structure Models (Sali Lab, UCSF)

Protein-protein interactions

  1. BioGRID [9] 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. DIP Database of Interacting Proteins
  4. BIND Biomolecular Interaction Network Database

Metabolic pathway Databases

  1. BioCyc Database Collection including EcoCyc and MetaCyc
  2. KEGG PATHWAY Database[10] (Univ. of Kyoto)
  3. MANET database [11] (University of Illinois)
  4. Reactome[12] (Cold Spring Harbor Laboratory, EBI, Gene Ontology Consortium)

Microarray databases

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

Mathematical Model Databases

  1. Biomodels Database
  2. CellML

PCR / Real time PCR primer Databases

  1. PathoOligoDB: A free QPCR oligo database for pathogens

Specialized databases (in alphabetical order)

Wiki style databases

  1. Gene Wiki
  2. OpenWetWare
  3. PDBWiki
  4. Proteopedia
  5. Topsan
  6. WikiGenes
  7. WikiPathways
  8. YTPdb
  9. CHDwiki
  10. WikiProfessional

References

  1. ^ Altman RB (2004). "Building successful biological databases". Brief. Bioinformatics. 5 (1): 4–5. doi:10.1093/bib/5.1.4. PMID 15153301. {{cite journal}}: Unknown parameter |month= ignored (help)
  2. ^ Bourne P (2005). "Will a biological database be different from a biological journal?". PLoS Comput. Biol. 1 (3): 179–81. doi:10.1371/journal.pcbi.0010034. PMID 16158097. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: unflagged free DOI (link)

See also

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