List of biological databases

Summary

Biological databases are stores of biological information.[1] 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.[2] Omics Discovery Index can be used to browse and search several biological databases.

Meta databasesEdit

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 databasesEdit

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

Nucleic acid databasesEdit

DNA databasesEdit

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:[clarification needed]

  • 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.[5][6]

Other databases

Gene expression databases (mostly microarray data)Edit

Genome databasesEdit

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 databasesEdit

RNA databasesEdit

Amino acid / protein databasesEdit

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.[13] 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.[13]

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 databasesEdit

Protein structure databasesEdit

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

Protein model databasesEdit

  • 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 interactionsEdit

Protein expression databasesEdit

Signal transduction pathway databasesEdit

Metabolic pathway and protein function databasesEdit

Taxonomic databasesEdit

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 databasesEdit

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:[18]

Additional databasesEdit

Exosomal databasesEdit

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

Mathematical model databasesEdit

Radiologic databasesEdit

Databases on antimicrobial resistance rates and antibiotic consumptionEdit

Databases on antimicrobial resistance mechanismsEdit

Wiki-style databasesEdit

Specialized databasesEdit

  • Barcode of Life Data Systems: database of DNA barcodes
  • 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) [21] 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:[22] integrates epigenomic reference data from well-known national endeavors such as the Canadian CEEHRC,[23] European Blueprint,[24] European Genome-phenome Archive (EGA[25]), US ENCODE and NIH Roadmap, German DEEP,[26] Japanese CREST,[27] Korean KNIH, Singapore's GIS and China's EpiHK[28]
  • 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[29]
  • 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

ReferencesEdit

  1. ^ Wren JD, Bateman A (October 2008). "Databases, data tombs and dust in the wind". Bioinformatics. 24 (19): 2127–8. doi:10.1093/bioinformatics/btn464. PMID 18819940.
  2. ^ "Volume 46 Issue D1 | Nucleic Acids Research | Oxford Academic". academic.oup.com. Retrieved 2018-09-04.
  3. ^ Lock A, Rutherford K, Harris MA, Hayles J, Oliver SG, Bähler J, Wood V (January 2019). "PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information". Nucleic Acids Research. 47 (D1): D821–D827. doi:10.1093/nar/gky961. PMC 6324063. PMID 30321395.
  4. ^ Zhu B, Stülke J (January 2018). "SubtiWiki in 2018: from genes and proteins to functional network annotation of the model organism Bacillus subtilis". Nucleic Acids Research. 46 (D1): D743–D748. doi:10.1093/nar/gkx908. PMC 5753275. PMID 29788229.
  5. ^ Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, et al. (January 2014). "eggNOG v4.0: nested orthology inference across 3686 organisms". Nucleic Acids Research. 42 (Database issue): D231-9. doi:10.1093/nar/gkt1253. PMC 3964997. PMID 24297252.
  6. ^ Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, et al. (January 2019). "eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses". Nucleic Acids Research. 47 (D1): D309–D314. doi:10.1093/nar/gky1085. PMC 6324079. PMID 30418610.
  7. ^ ArrayExpress
  8. ^ GEO
  9. ^ "The Human Protein Atlas". www.proteinatlas.org. Retrieved 2019-05-27.
  10. ^ Dash S, Campbell JD, Cannon EK, Cleary AM, Huang W, Kalberer SR, et al. (January 2016). "Legume information system (LegumeInfo.org): a key component of a set of federated data resources for the legume family". Nucleic Acids Research. 44 (D1): D1181-8. doi:10.1093/nar/gkv1159. PMC 4702835. PMID 26546515.
  11. ^ "Saccharomyces Genome Database | SGD". www.yeastgenome.org. Retrieved 2018-09-04.
  12. ^ Grant D, Nelson RT, Cannon SB, Shoemaker RC (January 2010). "SoyBase, the USDA-ARS soybean genetics and genomics database". Nucleic Acids Research. 38 (Database issue): D843-6. doi:10.1093/nar/gkp798. PMC 2808871. PMID 20008513.
  13. ^ a b Chen C, Huang H, Wu CH (2017). Wu CH, Arighi CN, Ross KE (eds.). "Protein Bioinformatics Databases and Resources". Methods in Molecular Biology. New York, NY: Springer New York. 1558: 3–39. doi:10.1007/978-1-4939-6783-4_1. ISBN 978-1-4939-6781-0. PMC 5506686. PMID 28150231.
  14. ^ Mir S, Alhroub Y, Anyango S, Armstrong DR, Berrisford JM, Clark AR, et al. (January 2018). "PDBe: towards reusable data delivery infrastructure at protein data bank in Europe". Nucleic Acids Research. 46 (D1): D486–D492. doi:10.1093/nar/gkx1070. PMC 5753225. PMID 29126160.
  15. ^ Kinjo AR, Bekker GJ, Suzuki H, Tsuchiya Y, Kawabata T, Ikegawa Y, Nakamura H (January 2017). "Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures". Nucleic Acids Research. 45 (D1): D282–D288. doi:10.1093/nar/gkw962. PMC 5210648. PMID 27789697.
  16. ^ Rose PW, Prlić A, Altunkaya A, Bi C, Bradley AR, Christie CH, et al. (January 2017). "The RCSB protein data bank: integrative view of protein, gene and 3D structural information". Nucleic Acids Research. 45 (D1): D271–D281. doi:10.1093/nar/gkw1000. PMC 5210513. PMID 27794042.
  17. ^ Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, et al. (January 2004). "IntAct: an open source molecular interaction database". Nucleic Acids Research. 32 (Database issue): D452-5. doi:10.1093/nar/gkh052. PMC 308786. PMID 14681455.
  18. ^ a b Ellenberg J, Swedlow JR, Barlow M, Cook CE, Sarkans U, Patwardhan A, et al. (November 2018). "A call for public archives for biological image data". Nature Methods. 15 (11): 849–854. doi:10.1038/s41592-018-0195-8. PMC 6884425. PMID 30377375.
  19. ^ Tendler BC, Hanayik T, Ansorge O, Bangerter-Christensen S, Berns GS, Bertelsen MF, et al. (March 2022). "The Digital Brain Bank, an open access platform for post-mortem imaging datasets". eLife. 11: e73153. doi:10.7554/eLife.73153. PMC 9042233. PMID 35297760.
  20. ^ Iudin A, Korir PK, Salavert-Torres J, Kleywegt GJ, Patwardhan A (May 2016). "EMPIAR: a public archive for raw electron microscopy image data". Nature Methods. 13 (5): 387–388. doi:10.1038/nmeth.3806. PMID 27067018.
  21. ^ Hounkpe BW, Chenou F, de Lima F, De Paula EV (January 2021). "HRT Atlas v1.0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets". Nucleic Acids Research. 49 (D1): D947–D955. doi:10.1093/nar/gkaa609. PMC 7778946. PMID 32663312.
  22. ^ (IHEC) data portal
  23. ^ CEEHRC
  24. ^ Blueprint
  25. ^ EGA
  26. ^ DEEP
  27. ^ CREST
  28. ^ "Sharing epigenomes globally". Nature Methods. 15 (3): 151. 2018. doi:10.1038/nmeth.4630. ISSN 1548-7105.
  29. ^ Valverde H, Cantón FR, Aledo JC (November 2019). "MetOSite: an integrated resource for the study of methionine residues sulfoxidation". Bioinformatics. 35 (22): 4849–4850. doi:10.1093/bioinformatics/btz462. PMC 6853639. PMID 31197322.

External linksEdit

  • Nucleic Acid Research Molecular Biology Database Collection – over 1,600 databases