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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Datamonkey Resource Report Resource Website 1000+ mentions |
Datamonkey (RRID:SCR_010278) | data access protocol, web service, source code, software resource | Web-based suite of phylogenetic analysis tools for use in evolutionary biology. Web application for comparative analysis of sequence alignments using statistical models. Used for analyzing evolutionary signatures in sequence data. Datamonkey 2.0 provides curated collection of methods for interrogating coding-sequence alignments for imprints of natural selection, packaged as a responsive (i.e. can be viewed on tablet and mobile devices), fully interactive, and API-enabled web application. | comparative analysis of sequence alignments, analyzing evolutionary signatures, sequence data, | has parent organization: University of California at San Diego; California; USA | NIGMS R01 GM093939; NIGMS U01 GM110749; NSF ; NIAID AI43638; NIAID AI47745; NIAID AI57167; University of California at San Diego ; Canadian Institutes of Health Research |
PMID:15713735 PMID:20671151 PMID:29301006 |
Free, Available for download, Freely available | nlx_156937 | https://github.com/veg/datamonkey-js | SCR_010278 | , Datamonkey 2.0, datamonkey.org | 2026-07-28 09:42:41 | 1120 | |||||
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Immune Disorder Ontology Resource Report Resource Website |
Immune Disorder Ontology (RRID:SCR_010344) | IMMDIS | controlled vocabulary, data or information resource, ontology | Ontology generated as part of the Bioinformatics Integration Support Contract (BISC) that is based on the National Library of Medicine (NLM) Medical Subject Headings; National Cancer Institute Thesaurus; International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM); ICD-10; and other open source public databases. Specific information may be available about a class, including Preferred_Name, DEFINITION, Synonym, etc. | obo, health, immunology | is listed by: BioPortal | NIAID ; Division of Allergy Immunology and Transplantation |
nlx_157438 | SCR_010344 | 2026-07-28 09:42:43 | 0 | ||||||||
|
E. coli Genome project Resource Report Resource Website 1+ mentions |
E. coli Genome project (RRID:SCR_008139) | database, data or information resource, topical portal, portal | The E. coli Genome Project has the goal of completely sequencing the E. coli and human genomes. They began isolation of an overlapping lambda clonebank of E. coli K-12 strain MG1655. Those clones served as the starting material in our initial efforts to sequence the whole genome. Improvements in sequencing technology have since reached the point where whole-genome sequencing of microbial genomes is routine, and the human genome has in fact been completed. They initiated additional sequencing efforts, concentrating on pathogenic members of the family Enterobacteriaceae -- to which E. coli belongs. They also began a systematic functional characterization of E. coli K-12 genes and their regulation, using the whole genome sequence to address how the over 4000 genes of this organism act together to enable its survival in a wide range of environments. | e. coli, enterobcteriaceae, gene, genome, human, journal aricle, knowledgebase, regulation, sequence, job | has parent organization: University of Wisconsin-Madison; Wisconsin; USA | NIAID ; NHGRI |
nif-0000-20961 | SCR_008139 | E.Coli genome project | 2026-07-28 09:42:17 | 5 | ||||||||
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The Immunology Database and Analysis Portal (ImmPort) Resource Report Resource Website 500+ mentions |
The Immunology Database and Analysis Portal (ImmPort) (RRID:SCR_012804) | ImmPort | service resource, disease-related portal, data or information resource, data repository, database, ontology, controlled vocabulary, storage service resource, topical portal, portal | Data sharing repository of clinical trials, associated mechanistic studies, and other basic and applied immunology research programs. Platform to store, analyze, and exchange datasets for immune mediated diseases. Data supplied by NIAID/DAIT funded investigators and genomic, proteomic, and other data relevant to research of these programs extracted from public databases. Provides data analysis tools and immunology focused ontology to advance research in basic and clinical immunology. | immunology, basic, clinical, data, share, store, analyze, exchange, dataset, immune, mediated, disease, analysis, tool, FASEB list |
is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: NIDDK Research Resources is affiliated with: Cytokine Registry is related to: MetaCyto is related to: The 10000 Immunomes is related to: NIAID |
Immune mediated disease | NIH ; NIAID ; DAIT ; NIAID HHSN266200400076C; NIAID HHSN272201200028C |
PMID:24791905 | nlx_152691, r3d100012529 | http://www.immport.org/immport-open/public/home/home, http://www.immport.org/ | http://www.immport.org | SCR_012804 | Immunology Data and Analysis Portal, ImmPort system, ImmPort, Immunology Database and Analysis Portal | 2026-07-28 09:43:08 | 987 | |||
|
SALSA Resource Report Resource Website 10+ mentions |
SALSA (RRID:SCR_022013) | software application, software resource, data analysis software, data processing software | Software tool for scaffold long read assemblies with Hi-C data. | scaffolding, Hi-C data, scaffold long read assemblies | NHGRI R44 HG009584; NIAID R01 AI100947; Ministry of Health and Welfare ; Republic of Korea |
DOI:10.1371/journal.pcbi.1007273 DOI:10.1186/s12864-017-3879-z |
Free, Available for download, Freely available | SCR_022013 | SALSA2 | 2026-07-28 09:45:23 | 40 | ||||||||
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Stitchr Resource Report Resource Website 1+ mentions |
Stitchr (RRID:SCR_022139) | software application, data analysis software, sequence analysis software, software resource, data processing software | Software Python tool for stitching coding T cell receptors nucleotide sequences from V,J,CDR3 information. Produces complete coding sequences representing fully spliced TCR cDNA given minimal V,J,CDR3 information. | Stitch together coding TCR nucleotide sequences, Python, T cell receptors nucleotide, V and J gene symbols, hypervariable CDR3 amino acid sequence, fully spliced TCR cDNA | NCI R01 CA164273; NIAID R43 AI120313; NCI R43 CA232942; Emily Venanzi Fund |
PMID:35325179 | Free, Available for download, Freely available | SCR_022139 | 2026-07-28 09:45:37 | 3 | |||||||||
|
Harmony Resource Report Resource Website 100+ mentions |
Harmony (RRID:SCR_022206) | software application, software resource, data analysis software, data processing software | Software R package to project cells into shared embedding in which cells group by cell type rather than dataset specific conditions. Harmony simultaneously accounts for multiple experimental and biological factors. Used for integration of single cell data. | cells grouping, cell type, experimental factors, biological factors, single cell data integration | is used by: harmonypy | NIAID U19 AI111224; NIH R01 AR063759; NIH UH2 AR067677; NIH T32 AR007530 |
PMID:31740819 | Free, Available for download, Freely available | SCR_022206 | Harmony for immunogenomics | 2026-07-28 09:45:38 | 171 | |||||||
|
MCScanX Resource Report Resource Website 100+ mentions |
MCScanX (RRID:SCR_022067) | software application, data analysis software, software resource, data processing software, software toolkit | Software toolkit for detection and evolutionary analysis of gene synteny and collinearity. | gene synteny and collinearity, detection and evolutionary analysis, | NSF DBI 0849896; NSF MCB 0821096; NSF MCB 1021718; NIAID R01 AI068908 |
PMID:22217600 | Free, Available for download, Freely available | SCR_022067 | Multiple Collinearity Scan toolkit X version | 2026-07-28 09:45:36 | 257 | ||||||||
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National Swine Resource and Research Center Resource Report Resource Website 50+ mentions |
National Swine Resource and Research Center (RRID:SCR_006855) | NSRRC | cell repository, organism supplier, biomaterial supply resource, material resource | Provides access to critically needed swine models of human health and disease as well as a central resource for reagents, creation of new genetically modified swine, and information and training related to use of swine models in biomedical research. | RIN, Resource Information Network, pig, fetal fibroblast, live animal, tissue, fibroblast, fetus, genetically modified pig, biomaterial manufacture, genome, genotyping, genetics, reproduction, breeding, health monitoring, cryopreservation, phenotyping, consulting, RRID Community Authority |
is used by: Integrated Animals is listed by: One Mind Biospecimen Bank Listing is listed by: Resource Information Network is related to: One Mind Biospecimen Bank Listing has parent organization: University of Missouri; Missouri; USA |
NIH Office of the Director U42 OD011140; NIAID ; NHLBI |
Public, To investigators, Application required | nif-0000-12086 | SCR_006855 | National Swine Resource Research Center | 2026-07-28 09:41:44 | 79 | ||||||
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Add Health (National Longitudinal Study of Adolescent Health) Resource Report Resource Website 10+ mentions |
Add Health (National Longitudinal Study of Adolescent Health) (RRID:SCR_007434) | Add Health | data or information resource, database | Longitudinal study of a nationally representative sample of adolescents in grades 7-12 in the United States during the 1994-95 school year. Public data on about 21,000 people first surveyed in 1994 are available on the first phases of the study, as well as study design specifications. It also includes some parent and biomarker data. The Add Health cohort has been followed into young adulthood with four in-home interviews, the most recent in 2008, when the sample was aged 24-32. Add Health combines longitudinal survey data on respondents social, economic, psychological and physical well-being with contextual data on the family, neighborhood, community, school, friendships, peer groups, and romantic relationships, providing unique opportunities to study how social environments and behaviors in adolescence are linked to health and achievement outcomes in young adulthood. The fourth wave of interviews expanded the collection of biological data in Add Health to understand the social, behavioral, and biological linkages in health trajectories as the Add Health cohort ages through adulthood. The restricted-use contract includes four hours of free consultation with appropriate staff; after that, there''s a fee for help. Researchers can also share information through a listserv devoted to the database. | adolescent, longitudinal, adult human, interview, social, behavior, health, early adult human, FASEB list | has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA | Aging | NICHD ; NCI ; CDC ; NIAID ; NIMHD ; NIDCD ; NIGMS ; NIMH ; NINR ; NIA ; NIAAA ; NIDA ; NSF ; NIH ; Department of Health and Human Services ; MacArthur Foundation ; Robert Wood Johnson Foundation |
Restricted use | nif-0000-00621 | SCR_007434 | National Longitudinal Study of Adolescent Health | 2026-07-28 09:41:48 | 37 | |||||
|
CharProtDB: Characterized Protein Database Resource Report Resource Website |
CharProtDB: Characterized Protein Database (RRID:SCR_005872) | CharProtDB | data or information resource, database | The Characterized Protein Database, CharProtDB, is designed and being developed as a resource of expertly curated, experimentally characterized proteins described in published literature. For each protein record in CharProtDB, storage of several data types is supported. It includes functional annotation (several instances of protein names and gene symbols) taxonomic classification, literature links, specific Gene Ontology (GO) terms and GO evidence codes, EC (Enzyme Commisssion) and TC (Transport Classification) numbers and protein sequence. Additionally, each protein record is associated with cross links to all public accessions in major protein databases as ��synonymous accessions��. Each of the above data types can be linked to as many literature references as possible. Every CharProtDB entry requires minimum data types to be furnished. They are protein name, GO terms and supporting reference(s) associated to GO evidence codes. Annotating using the GO system is of importance for several reasons; the GO system captures defined concepts (the GO terms) with unique ids, which can be attached to specific genes and the three controlled vocabularies of the GO allow for the capture of much more annotation information than is traditionally captured in protein common names, including, for example, not just the function of the protein, but its location as well. GO evidence codes implemented in CharProtDB directly correlate with the GO consortium definitions of experimental codes. CharProtDB tools link characterization data from multiple input streams through synonymous accessions or direct sequence identity. CharProtDB can represent multiple characterizations of the same protein, with proper attribution and links to database sources. Users can use a variety of search terms including protein name, gene symbol, EC number, organism name, accessions or any text to search the database. Following the search, a display page lists all the proteins that match the search term. Click on the protein name to view more detailed annotated information for each protein. Additionally, each protein record can be annotated. | protein, annotation, functional annotation, taxonomic classification, literature, gene ontology, evidence code, enzyme commission, transport classification, protein sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: J. Craig Venter Institute |
NHGRI R01 HG004881; NIAID contract HHSN266200100038C |
PMID:22140108 | biotools:charprotdb, nlx_149421 | https://bio.tools/charprotdb | SCR_005872 | Characterized Protein Database | 2026-07-28 09:41:22 | 0 | |||||
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ApiDB CryptoDB Resource Report Resource Website 10+ mentions |
ApiDB CryptoDB (RRID:SCR_013455) | ApiDB CryptoDB | data or information resource, database | An integrated genomic and functional genomic database for the parasite Cryptosporidium. CryptoDB integrates whole genome sequence and annotation along with experimental data and environmental isolate sequences provided by community researchers. The database includes supplemental bioinformatics analyses and a web interface for data-mining. Organisms included in CryptoDB are Cryptosporidium parvum, Cryptosporidium hominis, Cryptosporidium muris and environmental isolate sequences from numerous species. CryptoDB is allied with the databases PlasmoDB and ToxoDB via ApiDB, an NIH/NIAID-funded Bioinformatics Resource Center. Tools include: * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Cryptosporidium Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * CryptoCyc: Explore Automatically Defined Metabolic Pathways * Searches via Web Services: Web service access to our data | cryptosporidium parvum, cryptosporidium, cryptosporidium genome, cryptosporidium orf, cryptosporidium sage tag alignments, cryptosporidium snp, genomic sequence, dna motif, snp, est, orf, data set, bio.tools |
uses: SynView is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Eukaryotic Pathogen Database Resources |
NIAID contract HHSN266200400037C | PMID:16381902 | nif-0000-02698, biotools:cryptodb, r3d100012265 | https://bio.tools/cryptodb | http://cryptodb.org/ | SCR_013455 | CryptoDB, Cryptosporidium Genomics Resource | 2026-07-28 09:43:29 | 25 | ||||
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Cytokine Registry Resource Report Resource Website 1+ mentions |
Cytokine Registry (RRID:SCR_014368) | data or information resource, database | A registry of cytokines, chemokines, and receptors generated for the purpose of collecting, integrating, and mapping between entity names and synonyms from several resources. These resources include MeSH, the Protein Ontology, EntrezGene, HGNC, MGI, UniProt and others. | cytokine, registry, innate immune system, chemokine, receptor |
uses: UniProt uses: MeSH uses: Plant Ontology uses: Mouse Genome Informatics (MGI) uses: HGNC uses: Entrez Gene is affiliated with: The Immunology Database and Analysis Portal (ImmPort) has parent organization: University of California at San Francisco; California; USA |
NIAID ; NIH ; Department of Health and Human Services |
Acknowledgement required, Registry file is available for download | SCR_014368 | ImmPort Cytokine Registry | 2026-07-28 09:43:28 | 1 | ||||||||
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EPIMHC Resource Report Resource Website 1+ mentions |
EPIMHC (RRID:SCR_016279) | data or information resource, database | Database of naturally processed MHC-restricted peptide ligands and epitopes for customized computational vaccinology. | mhc, peptide, ligand, eiptope, vaccine, vaccinology, virology, t cell, immunogenic, molecule, virus | NIAID AI50900; NIAID AI43649; Molecular Immunology Foundation |
PMID:15657103 | Freely available, The research community can contribute to this resource | SCR_016279 | EPIMHC Database | 2026-07-28 09:44:16 | 4 | ||||||||
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Database of Antimicrobial Activity and Structure of Peptides Resource Report Resource Website 10+ mentions |
Database of Antimicrobial Activity and Structure of Peptides (RRID:SCR_016600) | DBAASP | data or information resource, database | Collection of manually curated data regarding structure and antimicrobial activity of natural and synthetic peptides. Provides the information and analytical resources to develop antimicrobial compounds with the high therapeutic index. | data, collection, structure, antimicrobial, activity, natural, synthetic, peptide, sequence | NIAID G2102; Shota Rustaveli National Science Foundation FR397718014; International Science and Technology Center |
PMID:26578581 PMID:27060142 |
Free, Freely available | SCR_016600 | DataBase of Antimicrobial Activity and Structure of Peptides, Database of Antimicrobial Activity and Structure of Peptides | 2026-07-28 09:44:22 | 42 | |||||||
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ImmGen Resource Report Resource Website 100+ mentions |
ImmGen (RRID:SCR_021792) | data or information resource, database | Project combines immunology and computational biology laboratories in effort to establish complete road map of gene-expression and regulatory networks in all immune cells. Project will generate, with rigorously standardized conditions, complete compendium of genome-wide data sets showing expression of protein-coding genes for all defined cell populations of mouse immune system. | gene expression, regulatory networks, all immune cells, protein coding genes, mouse immune system | NIAID R24 AI072073 | PMID:18800157 PMID:32978299 |
Free, Freely available | SCR_021792 | Immunological Genome Project | 2026-07-28 09:45:33 | 258 | ||||||||
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ATHLATES Resource Report Resource Website 1+ mentions |
ATHLATES (RRID:SCR_023689) | software toolkit, software resource | Software package for determining HLA genotypes for individuals from Illumina exome sequencing data. Program applies assembly, allele identification and allelic pair inference to short read sequences, and applies it to data from Illumina platforms. | Illumina, HLA genotypes determination, Illumina exome sequencing data, allele identification, allelic pair inference, short read sequence, | Washington University School of Medicine ; NIAID ; National Institutes of Health ; Department of Health and Human Services |
PMID:23748956 | Free, Available for download, Freely available | SCR_023689 | 2026-07-28 09:45:58 | 3 | |||||||||
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DICOMConvert Resource Report Resource Website |
DICOMConvert (RRID:SCR_014100) | software application, standalone software, software resource | A DICOM image converter based on the ITK IO mechanism for reading and writing images. The formats currently supported by the converter are DICOM to: Analyze (*.hdr); MetaImage (*.mhd); Nrrd (*.nhdr, *.nrrd). | standalone software, dicom, image converter |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: National Institutes of Health |
Center for Infectious Disease Imaging ; NIAID ; NIBIB |
Available for download | SCR_014100 | Dicom Converter | 2026-07-28 09:43:24 | 0 | ||||||||
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Cooperative Study Group for Autoimmune Disease Prevention Resource Report Resource Website |
Cooperative Study Group for Autoimmune Disease Prevention (RRID:SCR_006803) | CSGADP | knowledge environment, resource | Collaborative network of investigators with a focus on prevention of autoimmune disease, defined as halting the development of autoimmune disease prior to clinical onset by means other than global immunosuppression, and an emphasis on Type 1 diabetes. Its mission is to engage in scientific discovery that significantly advances knowledge for the prevention and regulation of autoimmune disease. The specific goals enunciated in pursuit of this mission are: * To create improved models of disease pathogenesis and therapy to better understand immune mechanisms that will provide opportunities for prevention strategies * To use these models as validation platforms with which to test new tools applicable to human studies * To encourage core expertise and collaborative projects designed for rapid translation from animal to human studies, emphasizing the development of surrogate markers for disease progression and/or regulation which can be utilized in the context of clinical trials | prevention, clinical, immune, model, disease pathogenesis, therapy |
is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources |
Type 1 diabetes, Diabetes, Autoimmune disease | NIAID ; NIDDK ; NICHD ; NIH Office of Research on Womens Health ; Juvenile Diabetes Research Foundation International |
nlx_152797 | SCR_006803 | 2026-07-28 09:41:43 | 0 | |||||||
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CIBERSORT Resource Report Resource Website 1000+ mentions |
CIBERSORT (RRID:SCR_016955) | software application, data analytics software, software resource | Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets. | estimation, abundance, cell, type, mixed, population, gene, expression, data, tissue, complex, analysis, RNA, biomarker, therapeutic, target, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Stanford University; Stanford; California |
Doris Duke Charitable Foundation ; Damon Runyon Cancer Research Foundation ; B&J Cardan Oncology Research Fund ; Ludwig Institute for Cancer Research ; NCI U01 CA154969; NIAID U19 AI090019; NCI T32 CA09302; US Department of Defense ; Siebel Stem Cell Institute ; Thomas and Stacey Siebel Foundation |
PMID:25822800 | Not freely available for download or distribution, Available for non commercial users, Registration required | biotools:CIbERSORt | https://bio.tools/CIBERSORT | SCR_016955 | 2026-07-28 09:44:25 | 1239 |
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