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

For DNA barcoding databases with a taxonomic focus, see #Taxonomic databases.

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]

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

For rRNA databases with a taxonomic focus, see #Taxonomic databases.

Amino acid / protein databases

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 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

Taxonomic databases

Main article: List of biodiversity databases

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.

Image databases

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 databases

Exosomal databases

Mathematical model databases

Radiologic databases

Databases on antimicrobial resistance rates and antibiotic consumption

Databases on antimicrobial resistance mechanisms

Wiki-style databases

Specialized databases

References

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  22. ^ (IHEC) data portal
  23. ^ CEEHRC
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  25. ^ EGA
  26. ^ DEEP
  27. ^ CREST
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