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Biological database

 
Wikipedia: 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.

Contents

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.


Output

Biological data comes in many formats. These formats include text, sequence data, protein structure, links. Each of these can be found from certain sources. For example,

Text formats are provided by PubMed and OMIM.

Sequence Data are provide by GeneBank, in terms of DNA, and UniProt, in terms of protein.

Protein Structures are provided by PDB, SCOP, and CATH.

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)
  4. UniProtKB (Universal Protein Resource Knowledgebase)

The four largest databases are GeneBank, (the U.S.’s collection of various biological data), EMBL, (Europe’s collection of nucleotide sequence data), DDBJ, (DNA Data Bank of Japan), and UniProt, (Universal Protein Resource). GeneBank, is a service provided by NCBI, which stores sequence data and “biological sequence related data.” EMBL is a service provided by EBI, the European Bioinformatics Institute, and provides a collection of nucleotide sequence data, as its name suggests. DDBJ is a nucleotide database. UniProt is a high-quality and comprehensive universal protein resource. It provides translations of sequences from EMBL, GeneBank, and DDBJ, in its UniProt Knowledgebase (UniProtKB).

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.

Note that GeneBank, EMBL, and DDBJ work very closely with one-another, and as a result what one can find from one of these sources they can find from any of the other two and vice-versa.

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. Xenbase, genome of the model organism Xenopus tropicalis and Xenopus laevis
  13. Wormbase, genome of the model organism Caenorhabditis elegans
  14. Zebrafish Information Network, genome of this fish model organism.
  15. TAIR, The Arabidopsis Information Resource.
  16. UCSC Malaria Genome Browser, genome of malaria causing species (Plasmodium falciparumata and others)
  17. 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

Signaling Pathway Databases

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

Main article: 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. GyDB
  11. WikiProfessional

Problems Associated with Protein Databases

Since discovery in the area of protein structure has not evolved quite as quickly as discoveries in the area sequence data, due to the 3D nature of protein structure, less information is available for it. Nonetheless, data can be accessed through the RCSB Protein Data Bank at (http://www.pdb.org), SCOP-Structural Classification of Proteins- at ([13]), and CATH at ([14]).

Frequently Used

Also, species specific databases are also available for some species, mainly those that are often used in research. These databases provided extensive detail for the species in question. For example, Colibase ([15]) is an E. coli database. Other popular species specific databases include, Flybase ([16]) for drosophila, and Wormbase ([17]) for nematodes.

Harvesting

It is impossible to attain all the necessary information in one place with the large amount of information present. However, there is a web-site which is working on doing just that. There web-page can be found at, http://harvester.embl.de/.

Be Careful

Note, with the large amount of information available, one must be wary of false data.

References

  1. ^ Altman RB (March 2004). "Building successful biological databases". Brief. Bioinformatics 5 (1): 4–5. doi:10.1093/bib/5.1.4. PMID 15153301. http://bib.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=15153301. 
  2. ^ Bourne P (August 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. 

http://www.avatar.se/molbioinfo2001/databases.html</ref>

See also

v • d • e
Databases supported by Bioinformatic Harvester
NCBI-BLAST  · CDD  · Ensembl  · Entrez  · Flybase  · Flymine  · GFP-cDNA  · Genome browser  · GeneCard  · Google Scholar  · GoPubMed  · Harvester42  · HomoloGene  · iHOP  · IPI  · OMIM  · MGI  · Mitocheck  · PSORT  · Polymer  · RGD  · UniProt  · SOURCE  · SOSUI  · RZPD  · Sciencenet  · STRING  · SMART  · TAIR  · WikiProfessional  · ZFIN

External links


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