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 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.

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
  • 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)
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
  • 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
  • PomBase database: manually curated phenotypic data for the yeast Schizosaccharomyces pombe

RNA databases

Amino acid / protein databases

Protein sequence databases

Protein structure databases
  • Protein Data Bank (PDB), comprising:
    • Protein DataBank in Europe (PDBe)[12]
    • ProteinDatabank in Japan (PDBj)[13]
    • Research Collaboratory for Structural Bioinformatics (RCSB)[14]
  • Structural Classification of Proteins (SCOP)

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

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
  • Biomodels Database: published mathematical models describing biological processes

Taxonomic databases
Main article: List of biodiversity 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

Antimicrobial resistance databases

Wiki-style databases

Specialized databases
  • 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
  • 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:[15] integrates epigenomic reference data from well-known national endeavors such as the Canadian CEEHRC,[16] European Blueprint,[17] European Genome-phenome Archive (EGA[18]), US ENCODE and NIH Roadmap, German DEEP,[19] Japanese CREST,[20] Korean KNIH, Singapore's GIS and China's EpiHK[21]
  • 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[22]
  • 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.

References
  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.
  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.
  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. (IHEC) data portal
  16. CEEHRC
  17. Blueprint
  18. EGA
  19. DEEP
  20. CREST
  21. "Sharing epigenomes globally". Nature Methods. 15 (3): 151. 2018. doi:10.1038/nmeth.4630. ISSN 1548-7105.
  22. 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.
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