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 2016 issue has a list of about 180 such databases and updates to previously described databases.[2]

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.

Model organism databases

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

  • 23andme's database
  • HapMap
  • OMIM (Online Mendelian Inheritance in Man): inherited diseases
  • RefSeq
  • SNP / Disease Databases

Gene expression databases (mostly microarray data)

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

RNA databases

Amino acid / protein databases

Protein sequence databases

Protein structure databases

  • Protein Data Bank (PDB), comprising:
    • Protein DataBank in Europe (PDBe)
    • ProteinDatabank in Japan (PDBj)
    • Research Collaboratory for Structural Bioinformatics (RCSB)

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

Protein model databases

  • ModBase: database of comparative protein structure models (Sali Lab, UCSF)
  • Protein Model Portal (PMP): meta database that combines several databases of protein structure models (Biozentrum, Basel, Switzerland)
  • Similarity Matrix of Proteins (SIMAP): database of protein similarities computed using FASTA
  • Swiss-model: server and repository for protein structure models

Protein-protein and other molecular interactions

Additional databases

Signal transduction pathway databases

Metabolic pathway and protein function databases

Exosomal databases

Mathematical model databases

Taxonomic databases

  • 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 databases

Wiki-style databases

Specialized databases

References

  1. Wren JD, Bateman A (2008). "Databases, data tombs and dust in the wind". Bioinformatics. 24 (19): 2127–8. doi:10.1093/bioinformatics/btn464. PMID 18819940.
  2. "Nucleic Acids Research Database issue 2016". Nucleic Acids Research. Oxford University Press. Retrieved 26 Oct 2016.
  3. ArrayExpress
  4. GEO
  5. Dash, Sudhansu; Campbell, Jacqueline D.; Cannon, Ethalinda K. S.; Cleary, Alan M.; Huang, Wei; Kalberer, Scott R.; Karingula, Vijay; Rice, Alex G.; Singh, Jugpreet (2016-01-04). "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–D1188. doi:10.1093/nar/gkv1159. ISSN 0305-1048. PMC 4702835. PMID 26546515.
  6. (IHEC) data portal
  7. CEEHRC
  8. Blueprint
  9. EGA
  10. DEEP
  11. CREST
  12. "Sharing epigenomes globally". Nature Methods. 15 (3): 151–151. 2018. doi:10.1038/nmeth.4630. ISSN 1548-7105.
  13. dbGaP
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