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

accessclinicaldata@NIAID

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.

AmoebaDB

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

SAGE ARK Portal

Genomics

Epigenomics

BacDive is a BMBF supported IID repository that includes phenotypic data.

The Bacterial Diversity Metadatabase BacDive is the worldwide largest database for standardized bacterial phenotypic information. Its mission is to mobilize research data on strain level from internal files in culture collections (e.g. CABI, CIP, CCUG, DSMZ) as well as from primary literature and make it freely accessible. Today BacDive offers data on 93,254 bacterial and archaeal strains, including 19,313 type strains and thereby covers approx. 90% of the validly described species. Within over 600 data fields the topics taxonomy, morphology, physiology, origin, molecular data, and cultivation conditions are covered. The database offers systematic access to phenotypic data. BacDive thereby enables queries like "show me all strains that grow under certain conditions” by using the Advanced search or queries like “show me all strains isolated from a marine environment” by using the Isolation source search. With currently 15,357 API® tests for 27,634 strains, BacDive also offers the worldwide largest API® test collection, which can be queried using the API test finder tool.

cystic fibrosis

Obesity

pertussis

endocarditis

Legionnaires' disease

Norrie disease

hereditary sensory and autonomic neuropathy

Streptomyces sp.

Arthrobacter sp.

Escherichia coli

Sorangium cellulosum

Nannocystis exedens

Bacillus cereus

Streptomyces parvisporogenes

bacterium

Lysinibacillus mangiferihumi

Lysinibacillus varians

BacDive

Antarctica

Middle and South America

Africa

Europe

Australia and Oceania

North America

Arctic

Asia

Arabidopsis thaliana

Zea mays

Solanum tuberosum

Oryza sativa

Solanum lycopersicum

Glycine max

Sphagnum papillosum

Salmo salar

Artemisia annua

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

Zika virus

BEI Resources

Mustela putorius furo

Mus musculus

Aedes aegypti

Cavia porcellus

Hemibela hemicalypta

Anopheles gambiae

Macaca mulatta

Bos taurus

Ricinus communis

NCBI BioSample is a NIH supported generalist repository that includes other data.

neoplasm

severe accute respiratory syndrome

prostate cancer

Healthy

breast neoplasm

lung neoplasm

Neoplasm Invasiveness

C57BL/6J

bacterium 7BL

human gut metagenome

metagenome

uncultured bacterium

Illumina MiniSeq

Illumina MiSeq

Illumina NovaSeq 6000

Illumina HiSeq 2000

Illumina HiSeq 2500

NextSeq 500

Illumina HiSeq 4000

Illumina HiSeq X Ten

16s ribosomal gene sequencing assay

pyrosequencing

BioSample

Zungaro sp. 6J

Gallus gallus

Sus scrofa

Hordeum vulgare subsp. vulgare

Echium vulgare subsp. vulgare

Rattus norvegicus

BioStudies is a repository that includes life sciences data by organising links to data in other databases at EMBL-EBI or elsewhere.

The mission of BioStudies is to provide access to all the data outputs of a life sciences study from a single place, by organising links to data in other databases at EMBL-EBI or elsewhere, as well as hosting data and metadata that do not fit anywhere else. The database accepts submissions via an online tool, or in a simple tab-delimited format. BioStudies provides rich mechanisms for defining and using metadata guidelines specific for a particular data source such as a project or a community, and organises datasets in collections.

Saccharomyces cerevisiae

Caenorhabditis elegans

Schizosaccharomyces pombe

Candida albicans

Salmonella typhimurium

Pseudomonas aeruginosa

Escherichia coli str. K-12 substr. MG1655

assay

RNA assay

assay array

transcription profiling by array assay

DNA assay

RNA-seq of coding RNA

ChIP-seq assay

genotyping by high throughput sequencing assay

comparative genomic hybridization by array assay

BioStudies

Drosophila melanogaster

Danio rerio

Gene expression

Cell biology

Oncology

Developmental biology

Epigenetics

Animal study

Gene regulation

Biology

Topic

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.

disease

Lung Carcinoma

Alzheimer disease

bio.tools

human

mouse

Human

vector

binary

SARS-CoV-2

plants

bacteria

viruses

metagenomes

Machine learning

Molecular interactions, pathways and networks

Small molecules

RNA-Seq

Sequencing

Sequence analysis

Genotype and phenotype

Workflows

Genome

Bacterial and Viral Bioinformatics Resource Center (BV-BRC) is a NIAID supported IID repository that includes genomic data.

The Bacterial and Viral Bioinformatics Resource Center (BV-BRC) is an information system designed to support research on bacterial and viral infectious diseases. The BV-BRC combines the data and tools from the Legacy BRC resources: PATRIC, the bacterial BRC, and IRD and ViPR, the viral BRCs.

Bacterial and Viral Bioinformatics Resource Center

Data Sources