List of biological databases

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]

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.

Nucleic acid databasesEdit

DNA databasesEdit

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

  • 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.[4][5]

Gene expression databases (mostly microarray data)Edit

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 databasesEdit

RNA databasesEdit

Amino acid / protein databasesEdit

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

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

Taxonomic databasesEdit

  • BacDive: bacterial metadatabase that provides strain-linked information about bacterial and archaeal biodiversity, including taxonomy information
  • EzTaxon-e: database for the identification of prokaryotes based on 16S ribosomal RNA gene sequences

Radiologic databasesEdit

Antimicrobial resistance databasesEdit

Wiki-style databasesEdit

Specialized databasesEdit

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 (13 October 2018). "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. ^ Powell, Sean; Forslund, Kristoffer; Szklarczyk, Damian; Trachana, Kalliopi; Roth, Alexander; Huerta-Cepas, Jaime; Gabaldón, Toni; Rattei, Thomas; Creevey, Chris; Kuhn, Michael; Jensen, Lars J. (2013-12-01). "eggNOG v4.0: nested orthology inference across 3686 organisms". Nucleic Acids Research. 42 (D1): D231–D239. doi:10.1093/nar/gkt1253. ISSN 0305-1048. PMC 3964997. PMID 24297252.
  5. ^ Huerta-Cepas, Jaime; Szklarczyk, Damian; Heller, Davide; Hernández-Plaza, Ana; Forslund, Sofia K; Cook, Helen; Mende, Daniel R; Letunic, Ivica; Rattei, Thomas; Jensen, Lars J; von Mering, Christian (2018-11-12). "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. ISSN 0305-1048. PMC 6324079. PMID 30418610.
  6. ^ ArrayExpress
  7. ^ GEO
  8. ^ "The Human Protein Atlas". www.proteinatlas.org. Retrieved 2019-05-27.
  9. ^ Dash S, Campbell JD, Cannon EK, Cleary AM, Huang W, Kalberer SR, Karingula V, Rice AG, Singh J, Umale PE, Weeks NT, Wilkey AP, Farmer AD, Cannon SB (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.
  10. ^ "Saccharomyces Genome Database | SGD". www.yeastgenome.org. Retrieved 2018-09-04.
  11. ^ Grant, David; Nelson, Rex T.; Cannon, Steven B.; Shoemaker, Randy C. (2010). "SoyBase, the USDA-ARS soybean genetics and genomics database". Nucleic Acids Research. 38 (Suppl 1) (Database issue): D843–D846. doi:10.1093/nar/gkp798. PMC 2808871. PMID 20008513.
  12. ^ Mir S, Alhroub Y, Anyango S, Armstrong DR, Berrisford JM, Clark AR, Conroy MJ, Dana JM, Deshpande M, Gupta D, Gutmanas A, Haslam P, Mak L, Mukhopadhyay A, Nadzirin N, Paysan-Lafosse T, Sehnal D, Sen S, Smart OS, Varadi M, Kleywegt GJ, Velankar S (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.
  13. ^ 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.
  14. ^ 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.
  15. ^ Hermjakob, H., Montecchi-Palazzi, L., Lewington, C., Mudali, S., Kerrien, S., Orchard, S., Vingron, M., Roechert, B., Roepstorff, P., Valencia, A., Margalit, H., Armstrong, J., Bairoch, A., Cesareni, G., Sherman, D., & Apweiler, R. (2004). IntAct: an open source molecular interaction database. Nucleic acids research, 32(Database issue), D452–D455. https://doi.org/10.1093/nar/gkh052
  16. ^ Kerrien, S., Aranda, B., Breuza, L., Bridge, A., Broackes-Carter, F., Chen, C., Duesbury, M., Dumousseau, M., Feuermann, M., Hinz, U., Jandrasits, C., Jimenez, R. C., Khadake, J., Mahadevan, U., Masson, P., Pedruzzi, I., Pfeiffenberger, E., Porras, P., Raghunath, A., Roechert, B., … Hermjakob, H. (2012). The IntAct molecular interaction database in 2012. Nucleic acids research, 40(Database issue), D841–D846. https://doi.org/10.1093/nar/gkr1088
  17. ^ Hounkpe, Bidossessi Wilfried; Chenou, Francine; de-Lima, Franciele; De-Paula, Erich Vinicius (2020-07-14). "HRT Atlas v1.0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets". Nucleic Acids Research: gkaa609. doi:10.1093/nar/gkaa609. ISSN 0305-1048. 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, Héctor; Cantón, Francisco R.; Aledo, Juan Carlos (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