List of biological databases GudangMovies21 Rebahinxxi LK21

      Biological databases are stores of biological information. The journal Nucleic Acids Research regularly publishes special issues on biological databases and has a list of such databases. The 2018 issue has a list of about 180 such databases and updates to previously described databases. Omics Discovery Index can be used to browse and search several biological databases. Furthermore, the NIAID Data Ecosystem Discovery Portal developed by the National Institute of Allergy and Infectious Diseases (NIAID) enables searching across databases.


      Meta databases


      Meta databases are databases of databases that collect data about data to generate new data. They are capable of merging information from different sources and making it available in a new and more convenient form, or with an emphasis on a particular disease or organism. Originally, metadata was only a common term referring simply to data about data such as tags, keywords, and markup headers.

      ConsensusPathDB: a molecular functional interaction database, integrating information from 12 others
      Entrez (National Center for Biotechnology Information)
      Neuroscience Information Framework (University of California, San Diego): integrates hundreds of neuroscience relevant resources; many are listed below


      Model organism databases


      Model organism databases provide in-depth biological data for intensively studied organisms.

      PomBase: the knowledgebase for the fission yeast Schizosaccharomyces pombe
      SubtiWiki: integrated database for the model bacterium Bacillus subtilis
      TAIR: the knowledgebase for the plant Arabidopsis thaliana


      Nucleic acid databases




      = DNA databases

      =

      The primary databases make up the International Nucleotide Sequence Database (INSD). The include:

      DNA Data Bank of Japan (National Institute of Genetics)
      EMBL (European Bioinformatics Institute)
      GenBank (National Center for Biotechnology Information)
      DDBJ (Japan), GenBank (USA) and European Nucleotide Archive (Europe) are repositories for nucleotide sequence data from all organisms. All three accept nucleotide sequence submissions, and then exchange new and updated data on a daily basis to achieve optimal synchronisation between them. These three databases are primary databases, as they house original sequence data. They collaborate with Sequence Read Archive (SRA), which archives raw reads from high-throughput sequencing instruments.
      Secondary databases are:

      HapMap
      OMIM (Online Mendelian Inheritance in Man): inherited diseases
      RefSeq
      1000 Genomes Project: launched in January 2008. The genomes of more than a thousand anonymous participants from a number of different ethnic groups were analyzed and made publicly available.
      EggNOG Database: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. It provides multiple sequence alignments and maximum-likelihood trees, as well as broad functional annotation.
      Other databases

      Nucleosome positioning region database


      = Gene expression databases

      =
      Generic gene expression databases
      Microarray gene expression databases


      = Genome databases

      =
      These databases collect 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.


      = Phenotype databases

      =
      PHI-base: pathogen-host interaction database. It links gene information to phenotypic information from microbial pathogens on their hosts. Information is manually curated from peer-reviewed literature.
      RGD Rat Genome Database: genomic and phenotype data for Rattus norvegicus
      PomBase database: manually curated phenotypic data for the yeast Schizosaccharomyces pombe


      = RNA databases

      =

      miRBase: the microRNA database
      PolymiRTS: a database of DNA variations in putative microRNA target sites
      PolyQ: database of polyglutamine repeats in disease and non-disease associated proteins
      Rfam: a database of RNA families
      IRESbase: A comprehensive database of experimentally validated internal ribosome entry sites.


      Amino acid / protein databases


      (See also: List of proteins in the human body)
      Several publicly available data repositories and resources have been developed to support and manage protein related information, biological knowledge discovery and data-driven hypothesis generation. The databases in the table below are selected from the databases listed in the Nucleic Acids Research (NAR) databases issues and database collection and the databases cross-referenced in the UniProtKB. Most of these databases are cross-referenced with UniProt / UniProtKB so that identifiers can be mapped to each other.
      Proteins in human:
      There are about ~20,000 protein coding genes in the standard human genome. (Roughly ~1200 already have Wikipedia articles - the Gene Wiki - about them) if we are Including splice variants, there could be as many as 500,000 unique human proteins


      = Different types of Protein databases

      =


      Signal transduction pathway databases


      NCI-Nature Pathway Interaction Database
      Netpath: curated resource of signal transduction pathways in humans
      Reactome: navigable map of human biological pathways, ranging from metabolic processes to hormonal signalling (Ontario Institute for Cancer Research, European Bioinformatics Institute, NYU Langone Medical Center, Cold Spring Harbor Laboratory)
      WikiPathways


      Metabolic pathway and protein function databases




      Taxonomic databases



      Numerous databases collect information about species and other taxonomic categories. The Catalogue of Life is a special case as it is a meta-database of about 150 specialized "global species databases" (GSDs) that have collected the names and other information on (almost) all described and thus "known" species.

      BacDive: bacterial metadatabase that provides strain-linked information about bacterial and archaeal biodiversity, including taxonomy information
      Catalogue of Life: a meta-database of all species on earth
      EzTaxon-e: database for the identification of prokaryotes based on 16S ribosomal RNA gene sequences
      NCBI Taxonomy: a taxonomic database operated by NCBI and concentrating on all taxa for which DNA sequences are available (those sequences are stored by GenBank, another database operated by NCBI).


      Image databases


      Images play a critical role in biomedicine, ranging from images of anthropological specimens to zoology. However, there are relatively few databases dedicated to image collection, although some projects such as iNaturalist collect photos as a main part of their data. A special case of "images" are 3-dimensional images such as protein structures or 3D-reconstructions of anatomical structures. Image databases include, among others:

      Allen Brain Atlas
      Digital Brain Bank
      Electron Microscopy Public Image Archive (EMPIAR)
      Image Data Resource
      Morphobank
      Morphosource


      = Radiologic databases

      =
      The Cancer Imaging Archive (TCIA)
      Neuroimaging Informatics Tools and Resources Clearinghouse


      Additional databases




      = Exosomal databases

      =
      ExoCarta
      Extracellular RNA Atlas: a repository of small RNA-seq and qPCR-derived exRNA profiles from human and mouse biofluids


      = Mathematical model databases

      =
      Biomodels Database: published mathematical models describing biological processes


      = Databases on antimicrobial resistance rates and antibiotic consumption

      =
      CIPARS
      EARS-Net
      ESAC-Net


      = Databases on antimicrobial resistance mechanisms

      =


      Wiki-style databases


      Gene Wiki
      WikiSpecies
      WikiProfessional


      Specialized databases




      References




      External links


      Nucleic Acid Research Molecular Biology Database Collection – over 1,600 databases
      Nucleic Acid Research (NAR) Database Summary Paper Category List

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    list of biological databases
    List of Biological Databases | PDF | National Center For Biotechnology ...

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