Мы используем файлы cookie.
Продолжая использовать сайт, вы даете свое согласие на работу с этими файлами.
Biological database
List of biological databases
Другие языки:

    List of biological databases

    Подписчиков: 0, рейтинг: 0

    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.

    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.[metadatabase is a database model for metadata management, global query of independent database, and distributed data processing. The word metadatabase is an addition to the dictionary]. originally ,metadata was only common term referring simply to data about data such a tags ,keywords, and markup headers.

    Model organism databases

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

    Nucleic acid databases

    DNA databases

    For DNA barcoding databases with a taxonomic focus, see #Taxonomic databases.

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

    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:

    • 23andMe's database
    • 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

    Gene expression databases (mostly microarray data)

    Main article: Microarray 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

    RNA databases

    For rRNA databases with a taxonomic focus, see #Taxonomic databases.

    Amino acid / protein databases

    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.

    Sequence databases
    Database Short Name Database Name
    CCDS The Consensus CDS protein set database
    DDBJ DNA Data Bank of Japan
    ENA European Nucleotide Archive
    GenBank GenBank nucleotide sequence database
    Refseq NCBI Reference Sequence Database
    UniGene Database of computationally identifies transcripts from the same locus
    UniProtKB Universal Protein Resource (UniProt)
    3D structure protein databases
    Database Short Name Database Name
    DisProt Database of Protein Disorder
    MobiDB Database of intrinsically disordered and mobile proteins
    ModBase Database of Comparative Protein Structure Models
    PDBsum Pictorial database of 3D structures in the Protein Data Bank
    ProteinModelPortal Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase
    SMR Database of annotated 3D protein structure models

    Protein sequence databases

    Protein structure databases

    For more protein structure databases, see also Protein structure database.

    Protein model databases

    • ModBase: database of comparative protein structure models (Sali Lab, UCSF)
    • Similarity Matrix of Proteins (SIMAP): database of protein similarities computed using FASTA
    • Swiss-model: server and repository for protein structure models
    • AAindex: database of amino acid indices, amino acid mutation matrices, and pair-wise contact potentials

    Protein-protein and other molecular interactions

    Protein expression databases

    Signal transduction pathway databases

    Metabolic pathway and protein function databases

    Taxonomic databases

    Main article: List of biodiversity 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:

    Radiologic databases

    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

    Radiologic databases

    Databases on antimicrobial resistance rates and antibiotic consumption

    Databases on antimicrobial resistance mechanisms

    Wiki-style databases

    Specialized databases

    • Barcode of Life Data Systems: database of DNA barcodes
    • Bacterial Pesticidal Protein Database
    • The Cancer Genome Atlas (TCGA): provides data from hundreds of cancer samples obtained using high-throughput techniques such as gene expression profiling, copy number variation profiling, SNP genotyping, genome-wide DNA methylation profiling, microRNA profiling, and exon sequencing of at least 1,200 genes
    • Cellosaurus: a knowledge resource on cell lines
    • CTD (Comparative Toxicogenomics Database): describes chemical-gene-disease interactions
    • DiProDB: a database to collect and analyse thermodynamic, structural and other dinucleotide properties
    • Housekeeping and Reference Transcript Atlas (HRT Atlas) web-based tool for searching cell specific candidate reference genes/transcripts suitable for qPCR experiment normalization. HRT Atlas also describes a complete list of human and mouse housekeeping genes and transcripts
    • Dryad: repository of data underlying scientific publications in the basic and applied biosciences
    • Edinburgh Mouse Atlas
    • EPD Eukaryotic Promoter Database
    • FINDbase (the Frequency of INherited Disorders database)
    • GigaDB: repository of large scale datasets underlying scientific publications in the biological and biomedical research
    • HGNC (HUGO Gene Nomenclature Committee): a resource for approved human gene nomenclature
    • International Human Epigenome Consortium: integrates epigenomic reference data from well-known national endeavors such as the Canadian CEEHRC, European Blueprint, European Genome-phenome Archive (EGA), US ENCODE and NIH Roadmap, German DEEP, Japanese CREST, Korean KNIH, Singapore's GIS and China's EpiHK
    • MethBase: database of DNA methylation data visualized on the UCSC Genome Browser
    • Minimotif Miner: database of short contiguous functional peptide motifs
    • Oncogenomic databases: a compilation of databases that serve for cancer research
    • PubMed: references and abstracts on life sciences and biomedical topics
    • RIKEN integrated database of mammals
    • TDR Targets: a chemogenomics database focused on drug discovery in tropical diseases
    • TRANSFAC: a database about eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles
    • JASPAR: a database of manually curated, non-redundant transcription factor binding profiles.
    • MetOSite: a database about methionine sulfoxidation sites and its functional roles in proteins
    • Healthcare Cost and Utilization Project (HCUP) is the largest collection of hospital care data in the United States. It includes hundreds of millions of inpatient, outpatient, and emergency records.
    • LEXAS curates descriptions of biological experiments from PMC articles.
    • Bovine Metabolome Database is a free web database that lists known bovine metabolites

    External links


    Новое сообщение