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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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DrInsight Resource Report Resource Website 1+ mentions |
DrInsight (RRID:SCR_023871) | software application, software resource, data analysis software, data processing software | Software connectivity mapping based drug repurposing tool that identifies drugs that can potentially reverse query disease phenotype or have similar functions with query drugs. | connectivity mapping based drug repurposing, identifies drugs, reverse query disease phenotype, query drugs, | NIAID U19AI082715 | PMID:30624606 | Free, Available for download, Freely available | https://github.com/cran/DrInsight | SCR_023871 | 2026-07-28 09:45:58 | 1 | ||||||||
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microbeMASST Resource Report Resource Website 1+ mentions |
microbeMASST (RRID:SCR_024713) | software resource, data access protocol, web service | Web taxonomically informed mass spectrometry search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging database of over 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. | Identification of microbial derived metabolites, microbial metabolomics data, microbial metabolite annotation, taxonomy, mass spectrometry search tool, searching tool, bacteria, fungi, metabolomics, microbiome, search known and unknown MS/MS spectra, | is related to: GNPS MASST | NIDDK U24DK133658; NIA U19AG063744; NIGMS 1DP2GM137413; Korean Government ; Austrian Science Fund ; German Research Foundation ; Sao Paulo Research Foundation ; Mexican National Council of Science and Technology ; NIGMS R01GM107550; NSF ; Research Council of Norway ; NIAID R01AI167860; NIDDK T32DK007202; NIGMS 1R01GM132649; NIGMS R35GM142938; NIDDK U01DK119702; NIH Office of the Director S10 OD021750; NLM 1R01LM013115 |
PMID:37577622 | Free, Freely available, | SCR_024713 | 2026-07-28 09:46:09 | 6 | ||||||||
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Sequencing of Idd regions in the NOD mouse genome Resource Report Resource Website 1+ mentions |
Sequencing of Idd regions in the NOD mouse genome (RRID:SCR_001483) | Sequencing of Idd regions in the NOD mouse genome | data or information resource, data set, resource | Genetic variations associated with type 1 diabetes identified by sequencing regions of the non-obese diabetic (NOD) mouse genome and comparing them with the same areas of a diabetes-resistant C57BL/6J reference mouse allowing identification of single nucleotide polymorphisms (SNPs) or other genomic variations putatively associated with diabetes in mice. Finished clones from the targeted insulin-dependent diabetes (Idd) candidate regions are displayed in the NOD clone sequence section of the website, where they can be downloaded either as individual clone sequences or larger contigs that make up the accession golden path (AGP). All sequences are publicly available via the International Nucleotide Sequence Database Collaboration. Two NOD mouse BAC libraries were constructed and the BAC ends sequenced. Clones from the DIL NOD BAC library constructed by RIKEN Genomic Sciences Centre (Japan) in conjunction with the Diabetes and Inflammation Laboratory (DIL) (University of Cambridge) from the NOD/MrkTac mouse strain are designated DIL. Clones from the CHORI-29 NOD BAC library constructed by Pieter de Jong (Children's Hospital, Oakland, California, USA) from the NOD/ShiLtJ mouse strain are designated CHORI-29. All NOD mouse BAC end-sequences have been submitted to the International Nucleotide Sequence Database Consortium (INSDC), deposited in the NCBI trace archive. They have generated a clone map from these two libraries by mapping the BAC end-sequences to the latest assembly of the C57BL/6J mouse reference genome sequence. These BAC end-sequence alignments can then be visualized in the Ensembl mouse genome browser where the alignments of both NOD BAC libraries can be accessed through the Distributed Annotation System (DAS). The Mouse Genomes Project has used the Illumina platform to sequence the entire NOD/ShiLtJ genome and this should help to position unaligned BAC end-sequences to novel non-reference regions of the NOD genome. Further information about the BAC end-sequences, such as their alignment, variation data and Ensembl gene coverage, can be obtained from the NOD mouse ftp site. | genome, sequencing, genome sequencing, insulin-dependent diabetes, c57bl/6j, single nucleotide polymorphism, genetic variation, bacterial artificial chromosome, sequence, gene, animal model, clone, annotation, contig |
lists: VEGA is listed by: NIDDK Information Network (dkNET) has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Type 1 diabetes, Diabetes | NIAID AI 15416; NIDDK ; JDRF |
PMID:23729657 | Free, Freely available | nlx_152738 | http://www.sanger.ac.uk/resources/mouse/nod/ | SCR_001483 | Sequencing of Insulin-dependent diabetes regions in the NOD mouse genome | 2026-07-28 09:40:12 | 1 | |||
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Ontodog: A Web-based Ontology View Generator Resource Report Resource Website 10+ mentions |
Ontodog: A Web-based Ontology View Generator (RRID:SCR_005061) | Ontodog | service resource, source code, production service resource, software resource | Ontodog is a web-based ontology view generator. It can generate inSubset annotation ontology, user preferred label annotation ontology and subset of source ontology. Simply provide Ontodog input term file (Microsoft Excel file or tab-delimited text file), select one source ontology or enter your own source ontology and SPARQL endpoint, then set the settings for Ontodog output files and get the OWL (RDF/XML) Output files. Ontodog performs the basic ontology modularization-like function, i.e.,it automatically extracts all axioms and related terms associated with user-specified signature term(s). In addition, Ontodog includes extra features: (1) extracting all instance data associated with the retrieved class terms and annotations; and (2) recursively extracting all axioms and related terms indirectly associated with signature terms. More features are being added to Ontodog, such as relabeling preferred names for various ontology terms to fit in with the needs from a specific community. The Ontodog input data requires a source ontology and a list of user-specified signature terms in tab-delimited format. Ontodog provides the template files for generating the signature terms as the input terms file to download. There are several output options that the users can choose based on their needs. With more and more ontologies being developed, Ontodog offers a timely web-based package of solutions for ontology view generation. Ontodog provides an efficient approach to promote ontology sharing and interoperability. It is easy to use and does not require knowledge of SPARQL, script programming, and command line operation. Ontodog is developed to serve the ontology community for ontology reuse. It is freely available under the Apache License 2.0. The source code is made available under Apache License 2.0. | ontology, interoperability | has parent organization: University of Michigan Medical School; Michigan; USA | Rackham Pilot Research ; NIAID R01AI081062; NIGMS 5R01GM93132-1 |
nlx_144053 | SCR_005061 | 2026-07-28 09:41:09 | 17 | ||||||||
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CEDAR Workbench Resource Report Resource Website 1+ mentions |
CEDAR Workbench (RRID:SCR_016270) | data or information resource, web application, portal, software resource | Web application for creating, collecting, testing, and sharing metadata. It provides templates for metadata models or structures, and is capable of testing those models quickly using real data. | metadata, share, collect, capture, model, structure, workspace, workflow, pipeline | has parent organization: Center for Expanded Data Annotation and Retrieval | NIAID U54 AI117925 | Freely available, Account required, Tutorial available | SCR_016270 | CEDAR suite, Center for Expanded Data Annotation and Retrieval Workbench, CEDAR tools | 2026-07-28 09:44:13 | 1 | ||||||||
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NIH-CIDI Segmentation of PET Images based on Affinity Propagation Clustering Resource Report Resource Website 1+ mentions |
NIH-CIDI Segmentation of PET Images based on Affinity Propagation Clustering (RRID:SCR_014151) | software application, software resource, data processing software, segmentation software, image analysis software | A MATLAB GUI for segmenting and quantifying PET images with multi-focal and diffuse uptakes. It imports a PET image and allows the user to draw region of interests (ROIs) in 2D or 3D to roughly separate the object of interest from the background. The areas are then segmented using a PET image segmentation method based on Affinity Propagation clustering to cluster the image intensities into meaningful groups. For quantification, the Standardized Uptake Value measurements of the binary or the user defined ROI are SUVmax, SUVmean, and Volume (mm^3) and can be exported into an excel sheet. | matlab gui, pet image, region of interest, 2d, 3d, segmentation, affinity propagation clustering | Howard Hughes Medical Institute ; Center for Infectious Disease Imaging ; NIAID Intramural research program ; NIBIB ; NIH Directors New Innovator Award OD006492; NIAD R01AI079590; NIAID R01A1035272 |
Available to the research community | http://www.nitrc.org/projects/ap_seg_2013_nih | SCR_014151 | 2026-07-28 09:43:22 | 1 | |||||||||
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Differential Gene Correlation Analysis Resource Report Resource Website 1+ mentions |
Differential Gene Correlation Analysis (RRID:SCR_020964) | DGCA | software application, software resource, data analysis software, data processing software | Software R package to perform differential gene correlation analysis. Performs differential correlation analysis on input matrices, with multiple conditions specified by design matrix. | Differential gene, gene, gene correlation, correlation analysis, input matrices, differential correlations, identifier pairs, gene expression data, calculate differential correlations | is listed by: CRAN | NIA F30 AG052261; NIA R01 AG046170; NCI R01 CA163772; NIAID U01 AI111598 |
PMID:27846853 | Free, Available for download, Freely available | https://github.com/andymckenzie/DGCA | SCR_020964 | 2026-07-28 09:44:59 | 1 | ||||||
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celltrackR Resource Report Resource Website 1+ mentions |
celltrackR (RRID:SCR_021021) | software application, data analysis software, software resource, data processing software, software toolkit | Software R package to analyze immune cell migration data. Supports pipeline for track analysis by providing methods for data management, quality control, extracting and visualizing migration statistics, clustering tracks, and simulating cell migration.Available measures include displacement, confinement ratio, autocorrelation, straightness, turning angle, and fractal dimension. Measures can be applied to entire tracks, steps, or subtracks with varying length. | Immune cell migration data, dimensional space, cell analysis, cell migration, cell tracks, cell migration data, displacement, confinement ratio, autocorrelation, turning angle, fractal dimension | is listed by: CRAN | NIAID U01 AI095550; NIAID R01 AI077600 |
DOI:10.1101/670505v1 | Free, Available for download, Freely available | https://github.com/ingewortel/celltrackR | SCR_021021 | 2026-07-28 09:45:01 | 7 | |||||||
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ImmuneSpace Resource Report Resource Website 10+ mentions |
ImmuneSpace (RRID:SCR_010508) | data or information resource, organization portal, portal | A consortium of university groups to characterize human immune populations. The Human Immunology Project Consortium (HIPC) program, established in 2010 by the NIAID Division of Allergy, Immunology, and Transplantation, is a major collaborative effort that is generating large amounts of cross-center and cross-assay data including high-dimensional data to characterize the status of the immune system in diverse populations under both normal conditions and in response to stimuli. This large data problem has given birth to ImmuneSpace, a powerful data management and analysis engine where datasets can be easily explored and analyzed using state-of-the-art computational tools. | immunology | has parent organization: Human Immunology Project Consortium | NIAID | nlx_158717 | SCR_010508 | immune space, Immunespace.org | 2026-07-28 09:42:49 | 12 | ||||||||
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Minimum Information about Biosynthetic Gene cluster Resource Report Resource Website 50+ mentions |
Minimum Information about Biosynthetic Gene cluster (RRID:SCR_023660) | MIBiG | project portal, data or information resource, database, portal | MIBiG is genomic standards consortium project and biosynthetic gene cluster database used as reference dataset. Provides community standard for annotations and metadata on biosynthetic gene clusters and their molecular products. Standardised data format that describes minimally required information to uniquely characterise biosynthetic gene clusters. MIBiG 2.0 is expended repository for biosynthetic gene clusters of known function. MIBiG 3.0 is database update comprising large scale validation and re-annotation of existing entries and new entries. Community driven effort to annotate experimentally validated biosynthetic gene clusters. | Genomic standards consortium project, community standard, annotations and metadata standards, biosynthetic gene clusters, sequence framework, biosynthetic gene cluster data, | Netherlands Organization for Scientific Research VENI grant ; NSF CAREER Award ; UK Biotechnology and Biological Sciences Research Council ; Novo Nordisk Foundation ; NIH U41 AT008718; Danish National Research Foundation ; NCCIH U24 AT010811; NCCIH F32 AT011475; Natural Sciences and Engineering Council of Canada Discovery grant ; European Union Horizon 2020 projects CARTNET ; Horizon 2020 Marie Skłodowska-Curie ; U.S. Department of Energy ; Portuguese Science and Technology Foundation ; U.S. National Science Foundation ; National Research Foundation of Korea ; NIGMS GM134688; NIAID R01AI155694; Netherlands eScience Center Accelerating Scientific Discoveries Grant ; Funds of the Chemical Industry Germany ; UK government Department for Environment ; Food and Rural Affairs ; German Chemical Industry ; Natural Sciences and Engineering Council of Canada |
PMID:36399496 DOI:10.1093/nar/gkz882 |
Free, Freely available | SCR_023660 | MIBiG 3.0, MIBiG 2.0 | 2026-07-28 09:45:58 | 55 | |||||||
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Recombination Detection Program Resource Report Resource Website 100+ mentions |
Recombination Detection Program (RRID:SCR_018537) | RDP | software application, software resource, data analysis software, data processing software | Software package to analyse nucleotide sequence data and identify evidence of genetic recombination. RDP3 is version of RDP program for characterizing recombination events in DNA-sequence alignments. RDP4 is version of RDP program for detection and analysis of recombination patterns in virus genomes. | DNA sequence, alignment, phylogenetic tree, nucleotide analysis, sequence data analysis, genetic recombination identification, DNA sequence alignment, recombinant pattern analysis, virus genome | Wellcome Trust ; Fund for Scientific Research Flanders ; South African Centre of High Performance Computing ; European Research Council ; Spanish Ministry of Science and Education ; South African National Research Foundation ; University of Cape Town ; Polyomielitis Research Foundation ; Carnergie Corporation ; NIAID AI090970; NIGMS U01 GM110749; NIAID AI100665 |
PMID:27774277 PMID:20798170 |
Free, Available for download, Freely available | SCR_018537 | Recombination Detection Program, RDP4, RDP3 | 2026-07-28 09:44:46 | 483 | |||||||
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Tracer Resource Report Resource Website 1000+ mentions |
Tracer (RRID:SCR_019121) | software application, data analysis software, software resource, data processing software, data visualization software | Open source software tool for analysing trace files generated by Bayesian MCMC runs. Software package for visualising and analysing MCMC trace files generated through Bayesian phylogenetic inference. Provides kernel density estimation, multivariate visualisation, demographic trajectory reconstruction, conditional posterior distribution summary and more. | Analysing trace files, files generated by Bayesian MCMC runs, MCMC trace files, conditional posterior distribution summary, demographic trajectory reconstruction, Bayesian phylogenetic inference, kernel density estimation, multivariate visualisation | Wellcome Trust ; European Union Seventh Framework Programme ; NSF DMS 1264153; NIAID R01 AI107034; NIAID U19 AI135995 |
PMID:29718447 | Free, Available for download, Freely available | https://github.com/beast-dev/tracer, http://gensoft.pasteur.fr/docs/Tracer/v1.6, http://beast.community/tracer, https://github.com/beast-dev/tracer/releases/tag/v1.7.1 | SCR_019121 | Tracer v1.7.1, Tracer v1.6 | 2026-07-28 09:44:56 | 1582 | |||||||
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DatA Tag Suite Resource Report Resource Website |
DatA Tag Suite (RRID:SCR_019236) | DATS | narrative resource, data or information resource, standard specification, software resource, software toolkit | Software suite to enable discoverability of datasets. Enables submission of metadata on datasets to DataMed. Has core set of elements, which are generic and applicable to any type of dataset, and extended set that can accommodate more specialized data types. Platform independent model developed by NIH BD2K bioCADDIE project for DataMed Data Discovery Index prototype being developed. Also available as annotated serialization in schema.org, which in turn is widely used by major search engines like Google, Microsoft, Yahoo and Yandex. | Data processing, data discovery, metadata submission, DataMed, data, discovery | NIAID U24 AI117966; ELIXIR EXCELERATE ; ELIXIR-UK |
PMID:28585923 | Free, Freely available | SCR_019236 | 2026-07-28 09:44:55 | 0 | ||||||||
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ArchR Resource Report Resource Website 100+ mentions |
ArchR (RRID:SCR_020982) | software application, data analysis software, software resource, data processing software, software toolkit | Software R package for processing and analyzing single-cell ATAC-seq data. Used for integrative single cell chromatin accessibility analysis.Provides intuitive, user focused interface for complex single cell analysis, including doublet removal, single cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing. | single-cell ATAC-seq data analysis, single-cell ATAC-seq data processing, single cell chromatin accessibility analysis, doublet removal, single cell clustering, cell type identification, unified peak set generation, cellular trajectory identification, transcription factor footprinting | NHGRI RM1 HG007735; NHGRI UM1 HG009442; NCI R35 CA209919; NHGRI UM1 HG009436; NCI U2C CA233311; NIAID U19 AI057266; NIA K99 AG059918; American Society of Hematology Scholar Award ; International Collaborative Award ; Defense Advanced Research Project Agency ; Ray and Dagmar Dolby Family Fund ; Stanford Cancer Institute-Goldman Sachs Foundation Cancer Research Award |
PMID:33633365 | Free, Available for download, Freely available | https://github.com/GreenleafLab/ArchR, https://www.archrproject.com/, https://github.com/GreenleafLab/ArchR_2020 | SCR_020982 | 2026-07-28 09:45:04 | 358 | ||||||||
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DAVID Resource Report Resource Website 10000+ mentions |
DAVID (RRID:SCR_001881) | DAVID | data or information resource, database, data access protocol, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. Bioinformatics resource system including web server and web service for functional annotation and enrichment analyses of gene lists. Consists of comprehensive knowledgebase and set of functional analysis tools. Includes gene centered database integrating heterogeneous gene annotation resources to facilitate high throughput gene functional analysis. | functional domain, annotation, motif, protein, ontology enrichment, gene, high-throughput, functional classification, functional annotation, clustering, genome, pathway, gene-disease association, interaction, functional domain, motif, visualization, FASEB list |
is listed by: OMICtools is listed by: 3DVC is listed by: LabWorm is listed by: SoftCite is related to: Gene Ontology is related to: BioCarta Pathways is related to: KEGG has parent organization: NCI-Frederick |
NIAID NO1-CO-56000; NCI |
PMID:19131956 PMID:12734009 PMID:35325185 PMID:22543366 PMID:17980028 PMID:17576678 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30408, nif-0000-10451, OMICS_02220, SCR_003033 | http://david.abcc.ncifcrf.gov/ | SCR_001881 | DAVID Bioinformatics Resources, Visualization and Integrated Discovery Bioinformatics Resources, Database for Annotation Visualization and Integrated Discovery, The Database for Annotation, The Database for Annotation Visualization and Integrated Discovery Bioinformatics Resources | 2026-07-28 09:40:27 | 18488 | ||||
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HIV Databases Resource Report Resource Website 100+ mentions |
HIV Databases (RRID:SCR_000614) | data or information resource, database, software resource | Contains comprehensive data on HIV genetic sequences and immunological epitopes. This collection of databases contains tools to visualize and analyze HIV-related data. | HIV, AIDS, HIV genetic sequences and immunological epitopes data, tools to visualize and analyze HIV-related data, FASEB list |
has parent organization: Los Alamos National Laboratory is parent organization of: Nonhuman Primate HIV/SIV Vaccine Trials Database is parent organization of: HCV Databases is parent organization of: HIV Molecular Immunology Database is parent organization of: HIV Sequence Database is parent organization of: HFV Database |
HIV, AIDS, SIV | NIAID | SCR_014940, nlx_151409 | SCR_000614 | 2026-07-28 09:40:01 | 495 | ||||||||
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Human Immunology Project Consortium Resource Report Resource Website 10+ mentions |
Human Immunology Project Consortium (RRID:SCR_001491) | HIPC | data or information resource, organization portal, consortium, portal | Consortium established to capitalize on recent advances in immune profiling methods in order to create a novel public resource that characterizes diverse states of the human immune system following infection; prior to and following vaccination against an infectious disease; or prior to and following treatment with an immune adjuvant that targets a known innate immune receptor(s). Through this program, well-characterized human cohorts are studied using a variety of modern analytic tools, including multiplex transcriptional, cytokine, and proteomic assays; multiparameter phenotyping of leukocyte subsets; assessment of leukocyte functional status; and multiple computational methods. Centralized research resources and a comprehensive, centralized database will be constructed for use by the greater scientific community. The information gained from the program will provide a comprehensive understanding of the human immune system and its regulation, and will reveal novel associations between components of the immune system and other biological systems, identify novel immune mediators and pathways, establish predictors of vaccine safety in different populations, and enable the rapid evaluation of different vaccine formulations and administration regimens in human populations. | immune profiling, immune system, infection, vaccine, infectious disease, immune adjuvant, immune receptor, multiplex assay, phenotyping, systems biology, mass spectrometry, regulation, mediator, pathway, database, leukocyte, transcriptome, proteome | is parent organization of: ImmuneSpace | Infection, Vaccination, Treatment with immune adjuvant | NIAID | Free, Freely available | SciRes_000173 | SCR_001491 | immune profiling, immuneprofiling.org | 2026-07-28 09:40:17 | 17 | |||||
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HCV Sequence Database Resource Report Resource Website 10+ mentions |
HCV Sequence Database (RRID:SCR_006019) | HCV Sequence Database | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | The HCV sequence database collects and annotates sequence data and provides them to the public via a website that contains a user-friendly search interface and a large number of sequence analysis tools, based on the model of the highly regarded Los Alamos HIV database. The hepatitis C virus (HCV) is a significant threat to public health worldwide. The virus is highly variable and evolves rapidly, making it an elusive target for the immune system and for vaccine and drug design. At present, some 30 000 HCV sequences have been published. This central website provides annotated sequences and analysis tools that will be helpful to HCV scientists worldwide. Things you can do: * Find sequences in the database * Download sequences from the database * Retrieve data about the sequences * Analyze sequences * Work with the sequences using our tools * Download ready-made alignments The HCV sequence database was officially launched in September 2003. Since then, its usage has steadily increased and is now at an average of approximately 280 visits per day from distinct IP addresses. | hepatitis c virus, sequence, annotation | has parent organization: HCV Databases | Hepatitis C | NIAID | PMID:15377502 | Public | nlx_151411 | SCR_006019 | Hepatitis C Sequence Database, Hepatitis C Virus Sequence Database, Los Alamos hepatitis C sequence database | 2026-07-28 09:41:30 | 19 | ||||
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Ontobee Resource Report Resource Website 50+ mentions |
Ontobee (RRID:SCR_006321) | Ontobee | service resource, data or information resource, database, ontology, controlled vocabulary | Web-based linked data server and browser specifically designed for ontology terms, it supports ontology visualization, query, and development. Ontobee provides a web interface for displaying the details and hierarchy of a specific ontology term. Meanwhile, Ontobee provides a RDF source code for the particular web page, which supports remote query of the ontology term and the Semantic Web. Ontobee provides an efficient and publicly available method to promote ontology sharing, interoperability, and data integration. | visualization, query, development, ontology, ontology sharing, interoperability, data integration, sparql, FASEB list |
lists: Porifera Ontology lists: Chemical Methods Ontology is related to: eagle-i research resource ontology has parent organization: University of Michigan Medical School; Michigan; USA |
NIAID R01AI081062 | Public | nlx_152048 | SCR_006321 | 2026-07-28 09:41:34 | 68 | |||||||
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xCell Resource Report Resource Website 50+ mentions |
xCell (RRID:SCR_026446) | software toolkit, web application, source code, software resource | Software R package for generating cell type scores and R scripts for development of xCell. Web tool that performs cell type enrichment analysis from gene expression data for immune and stroma cell types. Used for Cell types enrichment analysis. | Cell types enrichment analysis, cell type, enrichment analysis, generating cell type scores and R scripts, development of xCell, | Gruss Lipper Postdoctoral Fellowship ; NCI U24 CA195858; NIAID |
PMID:29141660 | Free, Available for download, Freely available | http://xCell.ucsf.edu/ | SCR_026446 | 2026-07-27 09:37:38 | 62 |
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