Pathoplexus

Zenodo

Repurposing, Focused Rescue, and Accelerated Medchem Database (REFRAMEdb)

Biological and Emerging Infections Research Resources (BEIResources)

Human Cell Atlas (HCA)

MicrobiomeDB

Electron Microscopy Data Bank (EMDB)

Omics Discovery Index (OmicsDI)

Database of Antimicrobial Activity and Structure of Peptides (DBAASP)

ImmuneSpace

Clinical Genome Resource (ClinGen)

bv_brc

Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB)

Vivli

Human Biomolecular Atlas Program (HuBMAP)

Clinical Epidemiology Database (ClinEpiDB)

Qiita

The Network Data Exchange (NDEx)

SAGE Arthritis and Autoimmune and Related Diseases Knowledge Portal (SAGE ARK Portal)

Project Tycho

Harvard Dataverse

Electron Microscopy Public Image Archive (EMPIAR)

Library of Integrated Network-based Cellular Signatures (LINCS)

Malaria Genomic Epidemiology Network (MalariaGEN)

Data Discovery Engine (DDE)

NCBI BioProject

NCBI Sequence Read Archive (NCBI SRA)

accessclinicaldata@NIAID (ACD@NIAID)

Immunology Database and Analysis Portal (ImmPort)

Protein Data Bank (PDB)

bio.tools

National Omics Data Encyclopedia (NODE)

Mendeley Data

Mass Spectrometry Interactive Virtual Environment (MassIVE)

Figshare

NCBI Database of Genotypes and Phenotypes (NCBI dbGaP)

NCBI Gene Expression Omnibus (NCBI GEO)

Dryad Digital Repository (Dryad)

Flow Repository

NICHD Data and Specimen Hub (NICHD DASH)

COVID Rapid Acceleration of Diagnostics (RADx) Data Hub

VDJServer

ProteomeXchange

AmoebaDB

CryptoDB

FungiDB

GiardiaDB

HostDB

MicrosporidiaDB

PiroplasmaDB

PlasmoDB

ToxoDB

TrichDB

TriTrypDB

VectorBase

AccessClinicalData is a NIAID supported IID repository that includes clinical trials data.

AccessClinicalData@NIAID is a NIAID cloud-based, secure data platform that enables sharing of and access to reports and data sets from NIAID COVID-19 and other sponsored clinical trials for the basic and clinical research community.

COVID-19

tuberculosis

Upper Respiratory Tract Infection

HIV infectious disease

pneumonia

Death Domain

infectious disease

drug allergy

Severe acute respiratory syndrome coronavirus 2

Severe acute respiratory syndrome coronavirus

Parallel Study

Randomized Clinical Trial

Double Blind Study

Triple Blind Study

Open Label Study

name

Homo sapiens

Infectious disease

Preclinical and clinical studies

Public health and epidemiology

Medicine

Immunology

Pharmacology

AmoebaDB is a NIAID supported IID repository that includes genomic data.

AmoebaDB is a component website of the Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB) and is constructed using the same infrastructure, data analysis, and loading procedures. VEuPathDB is is one of two bioinformatics Resource Centers (BRCs) funded by the US National Institute of Allergy and Infectious Diseases (NIAID), with additional support from the Wellcome Trust (UK).These resources stem from support initially provided for the Plasmodium Genome Database by the Burroughs Wellcome Fund (2000-2) and a research grant from NIAID (2002-6). The BRC program was initiated in 2004 to provide public access to computational platforms and analysis tools enabling collection, management, integration and mining of genomic information and other large-scale datasets relevant to infectious disease pathogens including their interaction with mammalian hosts and invertebrate vectors of disease.

SAGE ARK Portal is a NIAID supported IID repository that includes immune data.

The SAGE Arthritis and Autoimmune and Related Diseases (ARK Portal) is a public data repository that stores and shares data and research knowledge generated by a network of research teams focused on arthritis and autoimmune and related diseases. The ARK Portal is funded by the National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), and the National Institute of Allergy and Infectious Diseases (NIAID). It is developed and maintained by Sage Bionetworks.

rheumatoid arthritis

systemic lupus erythematosus

osteoarthritis

vitiligo

dermatomyositis

cutaneous lupus erythematosus

Transcriptomics

single cell RNA-seq assay

Proteomics

multimodal

cytometry assay

CITE-seq

Feature Barcoding

sequencing assay

cytometry time of flight assay

single cell immune repertoire sequencing

Other

Genomics

Epigenomics

BEIResources is a NIAID supported IID repository that includes reagent data.

BEI Resources was established by the National Institute of Allergy and Infectious Diseases (NIAID) to provide reagents, tools and information for studying Category A, B, and C priority pathogens, emerging infectious disease agents, non-pathogenic microbes and other microbiological materials of relevance to the research community.  BEI Resources acquires, authenticates and produces reagents that scientists need to carry out basic research and develop improved diagnostic tests, vaccines, and therapies. By centralizing these functions within BEI Resources, access to and use of these materials in the scientific community is monitored and quality control of the reagents is assured. In addition to supplying the infectious disease community with materials, BEI Resources also encourages and supports the deposit of materials from researchers and institutions. Depositing materials with BEI Resources has many advantages to the researcher and the research community including secure storage, community access and distribution; all while protecting the intellectual property rights of the depositor. The BEI Resources repository will be maintained as a resource for researchers as long as there is need.  Your deposit into BEI Resources is a long term investment to aid future research. BEI Resources has been managed under contract by American Type Culture Collection (ATCC) since 2003.  A seven-year contract to continue managing BEI Resources was awarded to ATCC in May 2016. The scope of the contract has expanded to a more comprehensive catalog of research materials, including those deposited by other Government-supported research projects, to be made available to the biodefense and emerging infectious disease scientific communities. Fungal, Parasite, Vector and other relevant Materials have been added to the existing Bacterial, Viral and Toxin reagents which cover NIAID Category A, B and C Priority Pathogens and NIAID designated emerging infectious disease agents and organisms.

influenza

plasma cell myeloma

severe acute respiratory syndrome

pulmonary tuberculosis

vaccinia

arbovirus infection

malaria

AIDS

diarrheal disease

Mycobacterium tuberculosis

Staphylococcus aureus

Human immunodeficiency virus

Influenza A virus

Plasmodium falciparum

Salmonella enterica I

Escherichia coli

Zika virus

Mustela putorius furo

Mus musculus

Aedes aegypti

Cavia porcellus

Hemibela hemicalypta

Anopheles gambiae

Macaca mulatta

Bos taurus

Ricinus communis

bio.tools is an ELIXIR supported tool repository that includes information about software tools, databases and services.

The use of bioinformatics is ubiquitous within the life sciences. In bio.tools, we are striving to provide a comprehensive registry of software and databases, facilitating researchers from across the spectrum of biological and biomedical science to find, understand, utilise and cite the resources they need in their day-to-day work.  Everything from simple command-line tools and online services, through to databases and complex, multi-functional analysis workflows is included. Resources are described in a rigorous semantics and syntax, providing end-users with the convenience of concise, consistent and therefore comparable information.  Each bio.tools entry is assigned a human-readable, unique identifier based on the resource name, e.g. biotools:signalp. These identifiers provide a persistent reference to our Tool Cards of essential information, as well as a means to trace resources and integrate bio.tools data with other resources.  bio.tools was supported by ELIXIR through the ELIXIR-EXCELERATE grant, which was funded by the European Union Horizon 2020 program under grant agreement 676559.

neoplasm

breast neoplasm

disease

Lung Carcinoma

Alzheimer disease

human

mouse

Human

vector

binary

SARS-CoV-2

plants

bacteria

viruses

metagenomes

Machine learning

Molecular interactions, pathways and networks

Gene expression

Small molecules

RNA-Seq

Sequencing

Sequence analysis

Genotype and phenotype

Workflows

Topic

ClinEpiDB is a NIAID supported IID repository that includes epidemiological data.

ClinEpiDB, launched in February 2018, is an open-access exploratory data analysis platform. We integrate data from high quality epidemiological studies, and offer tools and visualizations to explore the data within the browser in a point and click interface. We enable investigators to maximize the utility and reach of their data and to make optimal use of data released by others. ClinEpiDB is led by a team of scientists and developers based at the University of Pennsylvania, the University of Georgia, Imperial College London, and several other academic institutions. Currently, we are funded by the Bill and Melinda Gates Foundation for resource development and data integration, and by NIAID for integration of data from the International Centers of Excellence in Malaria Research (ICEMR).

Data Sources