Table 1. Overview of some representative databases, registries and other tools to find life science data.
A more complete list can be found at FAIRsharing.
| Database/
registry |
Name | Description | Datatypes | URL |
|---|---|---|---|---|
| Database | Gene Ontology | Repository of functional roles of gene products,
including: proteins, ncRNAs, and complexes. |
Functional roles as determined experimentally or
through inference. Includes evidence for these roles and links to literature |
http://geneontology.org/ |
| Database | Kyoto
Encyclopedia of Genes and Genomes (KEGG) |
Repository for pathway relationships of
molecules, genes and cells, especially molecular networks |
Protein, gene, cell, and genome pathway
membership data |
http://www.genome.jp/kegg/ |
| Database | OrthoDB | Repository for gene ortholog information | Protein sequences and orthologous group
annotations for evolutionarily related species groups |
http://www.orthodb.org/ |
| Database
with analysis layer |
eggNOG | Repository for gene ortholog information with
functional annotation prediction tool |
Protein sequences, orthologous group
annotations and phylogenetic trees for evolutionarily related species groups |
http://eggnogdb.embl.de/ |
| Database | European
Nucleotide Archive (ENA) |
Repository for nucleotide sequence information | Raw next-generation sequencing data, genome
assembly and annotation data |
http://www.ebi.ac.uk/ena |
| Database | Sequence Read
Archive (SRA) |
Repository for nucleotide sequence information | Raw high-throughput DNA sequencing and
alignment data |
https://www.ncbi.nlm.nih.gov/sra/ |
| Database | GenBank | Repository for nucleotide sequence information | Annotated DNA sequences | https://www.ncbi.nlm.nih.gov/genbank/ |
| Database | ArrayExpress | Repository for genomic expression data | RNA-seq, microarray, CHIP-seq, Bisulfite-seq and
more (see https://www.ebi.ac.uk/arrayexpress/ help/experiment_types.html for full list) |
https://www.ebi.ac.uk/arrayexpress/ |
| Database | Gene
Expression Omnibus (GEO) |
Repository for genetic/genomic expression data | RNA-seq, microarray, real-time PCR data on
gene expression |
https://www.ncbi.nlm.nih.gov/geo/ |
| Database | PRIDE | Repository for proteomics data | Protein and peptide identifications, post-translational
modifications and supporting spectral evidence |
https://www.ebi.ac.uk/pride/archive/ |
| Database | Protein Data
Bank (PDB) |
Repository for protein structure information | 3D structures of proteins, nucleic acids and
complexes |
https://www.wwpdb.org/ |
| Database | MetaboLights | Repository for metabolomics experiments and
derived information |
Metabolite structures, reference spectra and
biological characteristics; raw and processed metabolite profiles |
http://www.ebi.ac.uk/metabolights/ |
| Ontology/
database |
ChEBI | Ontology and repository for chemical entities | Small molecule structures and chemical
properties |
https://www.ebi.ac.uk/chebi/ |
| Database | Taxonomy | Repository of taxonomic classification information | Taxonomic classification and nomenclature data
for organisms in public NCBI databases |
https://www.ncbi.nlm.nih.gov/taxonomy |
| Database | BioStudies | Repository for descriptions of biological studies,
with links to data in other databases and publications |
Study descriptions and supplementary files | https://www.ebi.ac.uk/biostudies/ |
| Database | Biosamples | Repository for information about biological
samples, with links to data generated from these samples located in other databases |
Sample descriptions | https://www.ebi.ac.uk/biosamples/ |
| Database
with analysis layer |
IntAct | Repository for molecular interaction information | Molecular interactions and evidence type | http://www.ebi.ac.uk/intact/ |
| Database | UniProtKB
(SwissProt and TrEMBL) |
Repository for protein sequence and function
data. Combines curated (UniProtKB/SwissProt) and automatically annotated, uncurated (UniProtKB/TrEMBL) databases |
Protein sequences, protein function and
evidence type |
http://www.uniprot.org/ |
| Database | European
Genome- Phenome Archive |
Controlled-access repository for sequence and
genotype experiments from human participants whose consent agreements authorise data release for specific research use |
Raw, processed and/or analysed sequence and
genotype data along with phenotype information |
https://www.ebi.ac.uk/ega/ |
| Database
with analysis layer |
EBI
Metagenomics |
Repository and analysis service for
metagenomics and metatranscriptomics data. Data is archived in ENA |
Next-generation sequencing metagenomic
and metatranscriptomic data; metabarcoding (amplicon-based) data |
https://www.ebi.ac.uk/metagenomics/ |
| Database
with analysis layer |
MG-RAST | Repository and analysis service for
metagenomics data. |
Next-generation sequencing metagenomic and
metabarcoding (amplicon-based) data |
http://metagenomics.anl.gov/ |
| Registry | Omics DI | Registry for dataset discovery that currently
spans 11 data repositories: PRIDE, PeptideAtlas, MassIVE, GPMDB, EGA, Metabolights, Metabolomics Workbench, MetabolomeExpress, GNPS, ArrayExpress, ExpressionAtlas |
Genomic, transcriptomic, proteomic and
metabolomic data |
http://www.omicsdi.org |
| Registry | DataMed | Registry for biomedical dataset discovery that
currently spans 66 data repositories |
Genomic, transcriptomic, proteomic,
metabolomic, morphology, cell signalling, imaging and other data |
https://datamed.org |
| Registry | Biosharing | Curated registry for biological databases, data
standards, and policies |
Information on databases, standards and
policies including fields of research and usage recommendations by key organisations |
https://biosharing.org/ |
| Registry | re3data | Registry for research data repositories across
multiple research disciplines |
Information on research data repositories, terms
of use, research fields |
http://www.re3data.org |