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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Collaboratory of AIDS Researchers for Eradciation (CARE)
 
Resource Report
Resource Website
Collaboratory of AIDS Researchers for Eradciation (CARE) (RRID:SCR_013681) CARE data or information resource, organization portal, consortium, portal The Collaboratory of AIDS Researchers for Eradication (CARE) is a consortium of scientific experts in the field of HIV latency from several U.S. and European academic research institutions as well as Merck Research Laboratories working together to find a cure for HIV. AIDS, HIV, drug development, data-sharing enabler, is related to: University of North Carolina at Chapel Hill School of Medicine; North Carolina; USA
is related to: Gladstone Institute of Neurological Disease
is related to: UCSF School of Medicine; California; USA
is related to: Case Western Reserve University; Ohio; USA
is related to: Merck
is related to: UC Davis School of Medicine; California; USA
is related to: University of California at San Diego; California; USA
is related to: University of Utah School of Medicine; Utah; USA
is related to: University of Minnesota Twin Cities; Minnesota; USA
NIAID ;
NIMH
SCR_013681 2026-07-28 09:43:17 0
Immune Tolerance Network TrialShare
 
Resource Report
Resource Website
10+ mentions
Immune Tolerance Network TrialShare (RRID:SCR_013699) ITN TrialShare, TrialShare service resource, data or information resource, data repository, clinical trial, storage service resource Immune tolerance data management and visualization portal for studies sponsored by Immune Tolerance Network (ITN) and collaborating investigators. Data from published studies are accessible to any user; data from current in-progress studies are accessible to study investigators and collaborators. Includes links to published Figures, tools for visualization and analysis of data, and ability to query study data by subject, group, or any other study parameter. clinical trial, clinical data, biological specimens, is recommended by: National Library of Medicine
is related to: Immune Tolerance Network (ITN)
Type 1 diabetes, Diabetes, Allergy, Asthma, Autoimmune disease, Transplantation, Immunological disorder NIAID Restricted https://www.itntrialshare.org/login/home/login.view?returnUrl=%2Fproject%2Fhome%2Fstart.view%3F SCR_013699 , ITN, TrialShare, Trial Share, Immune Tolerance Network 2026-07-28 09:43:37 27
VDJ Server
 
Resource Report
Resource Website
10+ mentions
VDJ Server (RRID:SCR_014356) software application, web application, data analysis software, software resource, data processing software, collaboration tool A web application immune repertoire management, analysis, and archiving. Users can collaborate and share data either privately or publicly. Users can perform a variety of tasks, such as create and share projects with other users, conduct pre-processing tasks on single end reads, run IgBlast, and obtain basic repertoire characterization results for B cell receptor and T cell receptor repertoires. omics data, web application, scalable resource, immune repertoire has parent organization: University of Texas Southwestern Medical Center; Texas; USA
has parent organization: J. Craig Venter Institute
has parent organization: Yale University; Connecticut; USA
NIAID 1R01A1097403 Free, Open source analysis software is available for local use http://wiki.vdjserver.org/vdjserver/index.php/VDJServer_Wiki SCR_014356 VDJServer 2026-07-28 09:43:25 16
Pathosystems Resource Integration Center
 
Resource Report
Resource Website
1000+ mentions
Pathosystems Resource Integration Center (RRID:SCR_004154) PATRIC service resource, data or information resource, data analysis service, database, production service resource, analysis service resource, bioinformatics resource center A Bioinformatics Resource Center bacterial bioinformatics database and analysis resource that provides researchers with an online resource that stores and integrates a variety of data types (e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data) and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. The PATRIC project includes three primary collaborators: the University of Chicago, the University of Manchester, and New City Media. The University of Chicago is providing genome annotations and a PATRIC end-user genome annotation service using their Rapid Annotation using Subsystem Technology (RAST) system. The National Centre for Text Mining (NaCTeM) at the University of Manchester is providing literature-based text mining capability and service. New City Media is providing assistance in website interface development. An FTP server and download tool are available. genomics, genome, transcriptomics, protein-protein interaction, sequence typing, proteobacteria, brucella, rickettsia, coxiella, coronavirus, calicivirus, lyssavirus, virus, hepatitis a, hepatitis e, pathway, proteome, metabolic pathway, drug, vaccine, diagnostics, FASEB list is listed by: OMICtools
has parent organization: Virginia Polytechnic Institute and State University; Virginia; USA
NIAID PMID:24225323
PMID:17142235
Free, Public, Acknowledgement requested r3d100010142, OMICS_01658, nlx_17476 http://patricbrc.vbi.vt.edu/portal/portal/patric/Home, https://doi.org/10.17616/R3WS3X http://patric.vbi.vt.edu/ SCR_004154 PathoSystems Resource Integration Center, PATRIC, Pathosystems Resource Integration Center 2026-07-28 09:40:53 1083
HCV Databases
 
Resource Report
Resource Website
50+ mentions
HCV Databases (RRID:SCR_002863) HCV Databases disease-related portal, data or information resource, topical portal, portal The Hepatitis C Virus (HCV) Database Project strives to present HCV-associated genetic and immunologic data in a user-friendly way, by providing access to the central database via web-accessible search interfaces and supplying a number of analysis tools. hcv, hepatitis c virus, hepatitis c, database, data analysis service, sequence, immunology, annotation, FASEB list has parent organization: HIV Databases
is parent organization of: HCV Sequence Database
is parent organization of: HCV Immunology Database
Hepatitis C NIAID Free, Freely available nif-0000-02944 SCR_002863 Hepatitis C Virus Database, Hepatitis C Virus Database Project, HCV Database, Hepatitis C Virus Databases, Hepatitis C Virus (HCV) Database Project 2026-07-28 09:40:41 66
PaVE
 
Resource Report
Resource Website
100+ mentions
PaVE (RRID:SCR_016599) PaVE service resource, web application, data or information resource, data analysis service, database, software resource, production service resource, analysis service resource Collection of curated papillomavirus genomic sequences, accompanied by web-based sequence analysis tools. Database and web applications support the storage, annotation, analysis, and exchange of information. data, curated, papilloma, virus, genomic, sequence, analysis, storage, annotation, FASEB list is listed by: NIAID NIAID ZIA AI001071 PMID:28053164 Open source SCR_016599 PapillomaVirus Episteme, Papillomavirus Episteme 2026-07-28 09:44:18 125
HASP
 
Resource Report
Resource Website
HASP (RRID:SCR_016615) HASP software application, data or information resource, database, software resource, data processing software, data visualization software Web server to visualize phylogenetic, biochemical, and immunological hemagglutinin data in the three-dimensional context of homology models. Database and structural visualization platform for comparative models of influenza A hemagglutinin proteins. structural, visualization, phylogenetic, biochemical, immunological, hemagglutinin, data, 3D, is listed by: NIAID
is listed by: NIDDK Information Network (dkNET)
NIAID DOI:10.1186/1471-2105-14-197 Free, Freely available SCR_016615 HemAgglutinin Structure Prediction, Hemagglutinin Structure Prediction 2026-07-28 09:44:19 0
Phenograph
 
Resource Report
Resource Website
100+ mentions
Phenograph (RRID:SCR_016919) PhenoGraph software application, software resource, data analysis software, data processing software Software tool as clustering method designed for high dimensional single cell data. Algorithmically defines phenotypes in high dimensional single cell data. Used for large scale analysis of single cell heterogeneity. high, dimention, single, cell, data, phenotype, analysis, heterogeneity uses: Python Programming Language
is related to: Rphenograph
NIGMS R00 GM104148;
NICHD DP1 HD084071;
NCI R01 CA164729;
NCI U54 CA121852;
NCI R01 CA130826;
NCI U54 CA143907;
US Department of Health and Human Services HHSN272200700038C;
NIH N01 HV00242;
NCI P01 CA034233;
NIAID U19 AI057229;
NCI U54 CA149145;
US FDA HHSF223201210194C;
US DOD W81XWH1210591;
Entertainment Industry Foundation ;
Rachford and Carlota Harris Endowed Professorship ;
CIRM DR1 01477;
CIRM RB201592;
Stand Up To Cancer Phillip A. Sharp Award SU2CAACRPS04;
Packard Fellowship for Science and Engineering ;
NIH Office of the Director DP2 OD002414
PMID:26095251 Free, Available for download, Freely available https://github.com/JinmiaoChenLab/Rphenograph https://github.com/jacoblevine/PhenoGraph SCR_016919 2026-07-28 09:44:26 213
CheckMyMetal
 
Resource Report
Resource Website
1+ mentions
CheckMyMetal (RRID:SCR_016887) CMM software resource, data access protocol, web service Metal binding site validation server. Used for systematic inspection of the metal-binding architectures in macromolecular structures. The validation parameters that CMM examines cover the entire binding environment of the metal ion, including the position, charge and type of atoms and residues surrounding the metal. metal, binging, site, validation, server, systematic, inspection, macromolecular, structure, ion, charge, position, atom NIGMS GM117325;
NHGRI HG008424;
NIAID HHSN272201200026C
PMID:28291757 Free, Freely available SCR_016887 2026-07-28 09:44:25 5
ImmuneDB
 
Resource Report
Resource Website
1+ mentions
ImmuneDB (RRID:SCR_017125) service resource, data or information resource, data analysis service, database, production service resource, analysis service resource Software system for storing and analyzing high throughput B and T cell immune receptor sequencing data. Comprised of web interface and of Python analysis tools to process raw reads for gene usage, infer clones, aggregate data, and run downstream analyses, or in conjunction with other AIRR tools using its import and export features. collect, store, analysis, B cell, T cell, immune, receptor, sequencing, data, process, raw, read is used by: AIRR Data Commons NIAID P01 AI106697;
NIAID P30 AI0450080;
NIDDK UC4 DK112217;
NCI P30 CA016520
PMID:30298069 Free, Available for download, Freely available https://github.com/arosenfeld/immunedb SCR_017125 2026-07-28 09:44:31 8
immuneXpresso
 
Resource Report
Resource Website
immuneXpresso (RRID:SCR_017578) software application, service resource, data or information resource, software resource, text-mining software Software tool as text-mining engine that structures and standardizes knowledge of immune intercellular communication. Knowledgebase contains interactions and separate mentions of cells or cytokines in context of thousands of diseases. Intercellular interactions were text-mined from all available PubMed abstracts across disease conditions. Structure, standardize, immune, cellular, interaction, cytokine, disease, cell, PubMed, abstract is listed by: NIDDK Information Network (dkNET)
is listed by: OMICtools
NIH ;
NIAID ;
Rappaport Family Institute for Research in the Medical Sciences
PMID:29912209 Free, Freely available SCR_017578 2026-07-28 09:44:35 0
Database of Immune Cell Epigenomes
 
Resource Report
Resource Website
50+ mentions
Database of Immune Cell Epigenomes (RRID:SCR_018259) DICE data or information resource, database, data access protocol, software resource, web service Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics. Collection of identified cis-eQTLs for 12,254 unique genes, which represent 61% of all protein-coding genes expressed in human cell types. Datasets to help reveal effects of disease risk associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis. Data set, immune cell expression, expression quantitative trait loci, epigenomics, data, cis-eQLC, gene, protein coding gene, human cell type, genetic polymorphism disease, immune cell, pathogenesis has parent organization: La Jolla Institute for Immunology William K. Bowes Jr Foundation ;
NIAID R24 AI108564;
NCRR S10 RR027366;
NIH Office of the Director S10 OD016262
PMID:30449622 Free, Freely available SCR_018259 Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics 2026-07-28 09:44:39 59
outbreak.info
 
Resource Report
Resource Website
100+ mentions
outbreak.info (RRID:SCR_018282) data or information resource, topical portal, portal Resource to aggregate all outbreak information into single location during outbreaks of emerging diseases, such as COVID-19. COVID-19 data collection, single location, outbreak information, emerging disease is listed by: Data and Computational Resources to Address COVID-19
has parent organization: Scripps Research Institute
COVID-19 NIAID Free, Freely available SCR_018282 2026-07-28 09:44:43 113
TimeZone
 
Resource Report
Resource Website
1+ mentions
TimeZone (RRID:SCR_018564) software application, software resource, data analysis software, data processing software Software package to detect footprints of positive selection for functionally adaptive point mutations in microbial genomes. Detect footprint, positive selection, functionally adaptive, point mutation, microbial genome NIGMS R01 GM084318;
NIAID RC4 AI092828
PMID:23471110 Free, Available for download, Freely available SCR_018564 2026-07-28 09:44:46 1
EpiModel
 
Resource Report
Resource Website
1+ mentions
EpiModel (RRID:SCR_018539) software application, data analysis software, software resource, data processing software, software toolkit Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics. Infectious disease, mathematical modeling, simulation, analysis, infectious disease dynamic, bio.tools is listed by: Debian
is listed by: bio.tools
NICHD R01 HD068395;
NIMH R21 MH112449;
NICHD R21 HD075662;
NIDA P30 DA027828;
NIAID P30 AI050409;
NIAID P30 AI027757;
NICHD T32 HD007543
PMID:29731699 Free, Available for download, Freely available biotools:epimodel https://bio.tools/epimodel SCR_018539 2026-07-28 09:44:46 7
GOnet
 
Resource Report
Resource Website
1+ mentions
GOnet (RRID:SCR_018977) service resource, software resource, data access protocol, web service Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists. Gene Ontology, interactive analysis, data, gene, protein, gene list, protein list, analysis, bio.tools is listed by: Debian
is listed by: bio.tools
works with: Gene Ontology
NIH Common Fund ;
NIGMS ;
NHGRI R24 HG010032;
NIAID U19 AI118610;
NIAID U19 AI118626
PMID:30526489 biotools:GOnet https://github.com/mikpom/gonet, https://bio.tools/GOnet SCR_018977 2026-07-28 09:45:02 3
NMPDR
 
Resource Report
Resource Website
1+ mentions
NMPDR (RRID:SCR_007821) NMPDR service resource, data or information resource, data analysis service, database, production service resource, analysis service resource The National Microbial Pathogen Data Resource provides curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio; as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma. This edition of the NMPDR includes 47 archaeal, 725 bacterial, and 29 eukaryal genomes with 3,257,100 genetic features, of which 1,338,895 are in FIGfams curated using 616 active subsystems. ''''''Notice to NMPDR Users'''''' - The NMPDR BRC contract ended in December 2009. At that time we ceased maintenance of the NMPDR web resource and data. Bacterial data from NMPDR has been transferred to PATRIC (http://www.patricbrc.org), a new consolidated BRC for all NIAID category A-C priority pathogenic bacteria. NMPDR was a collaboration among researchers from the Computation Institute of the University of Chicago, the Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the National Center for Supercomputing Applications (NCSA) at the University of Illinois. has parent organization: University of Chicago; Illinois; USA NIAID contract HHSN266200400042C PMID:17145713 nif-0000-03193 http://www.nmpdr.org SCR_007821 NMPDR - National Microbial Pathogen Data Resource, National Microbial Pathogen Data Resource, NMPDR BRC, NMPDR Bioinformatics Resource Center 2026-07-28 09:41:54 3
ERIC
 
Resource Report
Resource Website
500+ mentions
ERIC (RRID:SCR_007644) ERIC service resource, data or information resource, data analysis service, database, production service resource, analysis service resource ERIC is a resource of annotated enterobacterial genomes. Information is available and accessed through a open web portal uniting biological data and analysis tools. ERIC contains information on Escherichia, Shigella, Salmonella, Yersinia, and other microorgansims. ERIC has recently been moved over to PATRIC: The PATRIC BRC is now responsible for all bacterial species in the NIAID Category A-C Priority Pathogen lists for biodefense research, and pathogens causing emerging/reemerging infectious diseases. For ERIC users, we understand that the resource was valuable to your work. As such, we will be doing our very best to create a useful PATRIC resource to continue supporting your work. We realize that the transition will cause disruptions. However, it is a priority for us to work with established BRC users and communities to identify and prioritize our transition efforts. We have concentrated on the transfer of genomic data for this initial release. We anticipate adding new data, tools, and website features over the next several months. We look forward to working with you during the next 5 years., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. enterobacteria, enterobacteria pathogen, biodefense, disease bioinformatics, human disease, pathogen, pathogenic bacteria, cronobacter, enterobacter, erwinia, klebsiella, pectobacterium, photorhabdus, proteus, serratia, escherichia, shigella, salmonella, yersinia, citrobacter, FASEB list has parent organization: Virginia Polytechnic Institute and State University; Virginia; USA NIAID THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-02813 http://www.ericbrc.org SCR_007644 Enteropathogen Resource Integration Center (ERIC), Enteropathogen Resource Integration Center 2026-07-28 09:42:08 950
Macaque.org
 
Resource Report
Resource Website
1+ mentions
Macaque.org (RRID:SCR_002767) Macaque.org research forum portal, disease-related portal, data or information resource, organization portal, laboratory portal, topical portal, portal THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on June 8, 2020.Macaque genomic and proteomic resources and how they are providing important new dimensions to research using macaque models of infectious disease. The research encompasses a number of viruses that pose global threats to human health, including influenza, HIV, and SARS-associated coronavirus. By combining macaque infection models with gene expression and protein abundance profiling, they are uncovering exciting new insights into the multitude of molecular and cellular events that occur in response to virus infection. A better understanding of these events may provide the basis for innovative antiviral therapies and improvements to vaccine development strategies. genomic, hiv, infection, proteomic, virus, simian immunodeficiency virus, influenza virus, animal model has parent organization: University of Washington; Seattle; USA Viral infection, Infectious disease NCRR ;
NIAID ;
NHLBI ;
NIDA
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-24370 SCR_002767 Macaque.org 2026-07-28 09:40:31 3
miniTUBA
 
Resource Report
Resource Website
miniTUBA (RRID:SCR_003447) miniTUBA analysis service resource, service resource, storage service resource, production service resource miniTUBA is a web-based modeling system that allows clinical and biomedical researchers to perform complex medical/clinical inference and prediction using dynamic Bayesian network analysis with temporal datasets. The software allows users to choose different analysis parameters (e.g. Markov lags and prior topology), and continuously update their data and refine their results. miniTUBA can make temporal predictions to suggest interventions based on an automated learning process pipeline using all data provided. Preliminary tests using synthetic data and laboratory research data indicate that miniTUBA accurately identifies regulatory network structures from temporal data. miniTUBA represents in a network view possible influences that occur between time varying variables in your dataset. For these networks of influence, miniTUBA predicts time courses of disease progression or response to therapies. minTUBA offers a probabilistic framework that is suitable for medical inference in datasets that are noisy. It conducts simulations and learning processes for predictive outcomes. The DBN analysis conducted by miniTUBA describes from variables that you specify how multiple measures at different time points in various variables influence each other. The DBN analysis then finds the probability of the model that best fits the data. A DBN analysis runs every combination of all the data; it examines a large space of possible relationships between variables, including linear, non-linear, and multi-state relationships; and it creates chains of causation, suggesting a sequence of events required to produce a particular outcome. Such chains of causation networks - are difficult to extract using other machine learning techniques. DBN then scores the resulting networks and ranks them in terms of how much structured information they contain compared to all possible models of the data. Models that fit well have higher scores. Output of a miniTUBA analysis provides the ten top-scoring networks of interacting influences that may be predictive of both disease progression and the impact of clinical interventions and probability tables for interpreting results. The DBN analysis that miniTUBA provides is especially good for biomedical experiments or clinical studies in which you collect data different time intervals. Applications of miniTUBA to biomedical problems include analyses of biomarkers and clinical datasets and other cases described on the miniTUBA website. To run a DBN with miniTUBA, you can set a number of parameters and constrain results by modifying structural priors (i.e. forcing or forbidding certain connections so that direction of influence reflects actual biological relationships). You can specify how to group variables into bins for analysis (called discretizing) and set the DBN execution time. You can also set and re-set the time lag to use in the analysis between the start of an event and the observation of its effect, and you can select to analyze only particular subsets of variables. analysis, analyze, bayesian, causation, clinical, linear, medical, structure, temporal, network analysis, network, molecule, information refining, gene expression regulation, bioinformatics, statistical package, interaction network, prediction, pathway, inference, biomedical, intervention is listed by: Biositemaps
has parent organization: National Center for Integrative Biomedical Informatics
has parent organization: University of Michigan; Ann Arbor; USA
Society of University Surgeons Foundation ;
NIDA U54DA021519;
NIAID 1R21AI057875-01;
NIGMS K08 GM074678-01A1
PMID:17644819 Free, Freely available nif-0000-33272 SCR_003447 miniTUBA - Medical Inference by Network Integration of Temporal Data using Bayesian Analysis tool, Medical Inference by Network Integration of Temporal Data using Bayesian Analysis tool, Medical Inference by Network Integration of Temporal Data using Bayesian Analysis tool (miniTUBA), The Medical Inference by Network Integration of Temporal Data using Bayesian Analysis tool 2026-07-28 09:40:48 0

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