Databases and public repositories

On this page you will find descriptions and links to databases and data repositories relevant for research on pathogen data. We have selected these resources because they are public and freely available.

The Pathogens Portal

The Pathogens Portal

A web portal for accessing open data on emerging and endemic pathogens. Developed and maintaned by EMBL-EBI.

European Nucleotide Archive

European Nucleotide Archive

The European Nucleotide Archive (ENA) is a repository providing free and unrestricted access to annotated DNA and RNA sequences.

DataverseNO

DataverseNO

DataverseNO is a national research data repository hosted by UiT The Arctic University of Norway. It allows researchers to store, share, and publish their research data in a secure and organized manner.

Recommended Databases

TagsLinkDescriptionDomains
COVID-19 Data Portal
Covid-19
SARS-CoV-2
covid19dataportal.org
Raw and assembled sequence and analysis of SARS-CoV-2 and other coronaviruses
Bacteria
pubMLST
MLST
pubmlst.org
Public databases for molecular typing and microbial genome diversity including multiple pathogen species
Bacteria
BIGSdb-Pasteur
MLST
bigsdb.pasteur.fr
Web platform with collections of curated databases of bacterial isolates, genomes and genotypes
Bacteria
NDARO
AMR
bigsdb.pasteur.fr
National Database of Antibiotic Resistant Organisms (NDARO), a centralized hub for researchers to access AMR data
Bacteria
CARD database
AMR
card.mcmaster.ca
The Comprehensive Antibiotic Resistance Database (CARD) is a bioinformatic database of resistance genes, their products and associated phenotypes.
Bacteria
The Pseudomonas Genome Database
Pseudomonas
Genomes
pseudomonas.com
High quality genome annotation of pseudomonas strains, including pathway annotations and AMR Gene Predictions
Bacteria
PLSDB
Plasmids
covid19.sfb.uit.no
Bacterial plasmids retrieved from the NCBI nucleotide database with additional annotations consist of resistance and virulence factors
Bacteria
COVID-19 (SARS-CoV-2 Database)
Covid-19
Genomes
bv-brc.org
Covid-19
Virus
BV-BRC
Genomes
Proteins
Experimental data
Plasmids
Metagenomes
bv-brc.org
Bacterial and Viral Bioinformatics Resource Center (BV-BRC) encompasses integrated datasets from mainly pathogenic bacteria, archaea, viruses, and eukaryotes
Virus
Bacteria
Archaea
Eukaryote
Virus-Host DB
Pathogen-host
genome.jp
Virus-Host DB organizes data about the relationships between viruses and their hosts, represented in the form of pairs of NCBI taxonomy IDs for viruses and their hosts
Virus
EuPathDB
Genomes
Genes
Pathogen-host
veupathdb.org
The Eukaryotic Pathogen Database (EuPathDB) is an integrated database covering numerous eukaryotic pathogens including Plasmodium and Trypanosoma
Eukaryote
PHI-base
Pathogen-host
Genes
phi-base.org.
PHI-base is to provide expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions that are of medical and agronomical importance
Fungi
Bacteria