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 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

Primary databases
International Nucleotide Sequence Database (INSD) consists of the following databases.

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

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

Amino acid / protein databases

Protein sequence databases

Protein structure databases

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

Protein model databases

Protein-protein and other molecular interactions

Protein expression databases

Signal transduction pathway databases

Metabolic pathway and protein function databases

Additional databases

Exosomal databases

Mathematical model databases

Taxonomic databases

Main article: List of biodiversity databases

Radiologic databases

Antimicrobial resistance databases

Wiki-style databases

Specialized databases


  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". 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". Retrieved 2019-05-27.
  10. ^ Dash S, Campbell JD, Cannon EK, Cleary AM, Huang W, Kalberer SR, et al. (January 2016). "Legume information system ( 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". 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. ^ 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.
  14. ^ 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.
  15. ^ 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.
  16. ^ 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.
  17. ^ 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. PMID 32663312.
  18. ^ (IHEC) data portal
  19. ^ CEEHRC
  20. ^ Blueprint
  21. ^ EGA
  22. ^ DEEP
  23. ^ CREST
  24. ^ "Sharing epigenomes globally". Nature Methods. 15 (3): 151. 2018. doi:10.1038/nmeth.4630. ISSN 1548-7105.
  25. ^ 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.