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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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NSR Physiome Project Resource Report Resource Website 1+ mentions |
NSR Physiome Project (RRID:SCR_007379) | NSR Physiome Project | data or information resource, portal, professional program, simulation software, software application, software resource, topical portal, training resource | Database of physiological, pharmacological, and pathological information on humans and other organisms and integration through computational modeling. Models include everything from diagrammatic schema, suggesting relationships among elements composing a system, to fully quantitative, computational models describing the behavior of physiological systems and an organism''s response to environmental change. Each mathematical model is an internally self-consistent summary of available information, and thereby defines a working hypothesis about how a system operates. Predictions from such models are subject to test, with new results leading to new models.BR /> A Tool developed for the NSR Physiome project is JSim, an open source, free software. JSim is a Java-based simulation system for building quantitative numeric models and analyzing them with respect to experimental reference data. JSim''s primary focus is in physiology and biomedicine, however its computational engine is quite general and applicable to a wide range of scientific domains. JSim models may intermix ODEs, PDEs, implicit equations, integrals, summations, discrete events and procedural code as appropriate. JSim''s model compiler can automatically insert conversion factors for compatible physical units as well as detect and reject unit unbalanced equations. JSim also imports the SBML and CellML model archival formats. All JSim models are open source. Goals of the Physiome Project: - To develop and database observations of physiological phenomenon and interpret these in terms of mechanism (a fundamentally reductionist goal). - To integrate experimental information into quantitative descriptions of the functioning of humans and other organisms (modern integrative biology glued together via modeling). - To disseminate experimental data and integrative models for teaching and research. - To foster collaboration amongst investigators worldwide, to speed up the discovery of how biological systems work. - To determine the most effective targets (molecules or systems) for therapy, either pharmaceutic or genomic. - To provide information for the design of tissue-engineered, biocompatible implants. | physiome, computational modeling, cell, organ, organism, human, model, physiological, pharmacological, pathological, model repository, sbml, cellml, biophysics, biochemistry, database, proteome, jsim simulation analysis system, data analysis tool, parameter optimization tool, integrating biological system | has parent organization: University of Washington; Seattle; USA | NSF BE08407; NHLBI T15 HL88516-01; NSF BES-0506477; NHLBI R01HL073598; NIBIB R01EB001973 |
nif-0000-00532 | SCR_007379 | National Simulation Resource Physiome Project | 2026-09-12 12:56:54 | 3 | |||||||
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VISTA Enhancer Browser Resource Report Resource Website 100+ mentions |
VISTA Enhancer Browser (RRID:SCR_007973) | VISTA Enhancer Browser | data or information resource, data repository, database, service resource, storage service resource | Resource for experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation in other vertebrates or epigenomic evidence (ChIP-Seq) of putative enhancer marks. Central public database of experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to particular tissue, or download entire collections of enhancers with defined tissue specificity or conservation depth. | human, noncoding fragment, mutant mouse strain, molecular neuroanatomy resource, image, telencephalon, development, genome, enhancer, dna fragment, embryo, embryonic mouse, brain, neural tube, eye, ear, heart, tail, limb, nose, cranial nerve, trigeminal, dorsal root ganglia, face, branchial arch, gene expression, annotation, vector, transgenic embryo, lacz reporter vector, lacz, biomaterial supply resource, in vivo, image collection, transcriptional enhancer, chip-seq, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: NIF Data Federation is related to: One Mind Biospecimen Bank Listing is related to: OMICtools has parent organization: Lawrence Berkeley National Laboratory |
American Heart Association ; DOE contract DE-AC02-05CH11231; DOE DE020060; NHGRI HG003988; NHLBI HL066681; NIDCR ; NINDS NS062859 |
PMID:17130149 | Free, Freely available | nif-0000-03637, OMICS_01568, biotools:vista_enhancer_browser | https://bio.tools/vista_enhancer_browser | SCR_007973 | 2026-09-12 12:56:58 | 249 | |||||
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Ribosomal Database Project Resource Report Resource Website 1000+ mentions |
Ribosomal Database Project (RRID:SCR_006633) | RDP | data or information resource, database, resource | A database which provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences. It specifically contains information on quality-controlled, aligned and annotated bacterial and archaean 16S rRNA sequences, fungal 28S rRNA sequences, and a suite of analysis tools for the scientific community. Most of the RDP tools are now available as open source packages for users to incorporate in their local workflow. | microbiome, database, rrna gene sequence, rrna, ribosome, genome browser, high-throughput sequencing, bacteria, archaea, fungi, FASEB list |
is listed by: OMICtools is listed by: Human Microbiome Project has parent organization: Michigan State University; Michigan; USA is parent organization of: RDPipeline |
DOE DE-FG02-99ER62848; DOE DE-SC0004601; DOE DE-FC02-07ER64494; NIEHS P42 ES004911; NSF DBI-0328255; USDA 2008-35107-04542; NHLBI U01HL098961; NIDDK UH3 DK083993 |
PMID:24288368 PMID:17586664 |
Open source | r3d100012372, nif-0000-03404, OMICS_01513 | https://doi.org/10.17616/R3C087 | SCR_006633 | Ribosomal Database Project | 2026-09-12 12:56:42 | 1724 | ||||
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Macaque.org Resource Report Resource Website 1+ mentions |
Macaque.org (RRID:SCR_002767) | Macaque.org | data or information resource, disease-related portal, laboratory portal, organization portal, portal, research forum portal, topical 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 | 2026-09-12 12:55:46 | 3 | |||||
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SNPHunter Resource Report Resource Website |
SNPHunter (RRID:SCR_002968) | data analysis software, data processing software, resource, sequence analysis software, software application, software resource | A tool for SNP Search and downloading with local management. It also offers flanking sequence downloading and automatic SNP filtering. It requires Windows and .NET Framework. | population, genetics, software, management, single nucleotide polymorphism, population genetics, training tools, data acquisition |
is listed by: 3DVC has parent organization: Harvard University; Cambridge; United States |
NIH ; NHGRI R01HG002518; NIDDK R01DK062290; NIDDK R01DK066401; NHLBI R01HL073882 |
DOI:10.1186/1471-2105-6-60 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30137 | http://www.hsph.harvard.edu/ppg/software.htm | SCR_002968 | SNPHunter - dbSNP Search & Management, Program for Population Genetics Software | 2026-09-12 12:55:49 | 0 | |||||
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Lifestyle Interventions for Expectant Moms (LIFE-Moms) Resource Report Resource Website |
Lifestyle Interventions for Expectant Moms (LIFE-Moms) (RRID:SCR_014376) | LIFE-Moms | data or information resource, organization portal, portal, resource | A consortium whose overall goal is to identify effective behavioral and lifestyle interventions that will improve weight, glycemic control and other pregnancy-related outcomes in obese and overweight pregnant women, and determine whether these interventions reduce obesity and metabolic abnormalities in their children. The study/consortium is comprised of seven clinical centers, with each clinical center conducting its own trial. Additional information on the consortium and individual trials is located in the Consortium Summaries tab. | pregnant, pregnancy, obesity, metabolic abnormality, behavioral intervention, lifestyle intervention, clinical trial |
is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources |
Obesity | NIDDK ; NHLBI ; NICHD ; National Center for Complementary and Integrative Health ; Office of Research on Womens Health ; Office of Behavioral and Social Sciences Research |
Synopses available, Users may access trial data at clinicaltrial.gov | http://www.niddk.nih.gov/research-funding/research-resources/Pages/default.aspx | SCR_014376 | Lifestyle Interventions for Expectant Moms | 2026-09-12 12:58:16 | 0 | |||||
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variancePartition Resource Report Resource Website 50+ mentions |
variancePartition (RRID:SCR_019204) | data analysis software, data analytics software, data processing software, software application, software resource | Software R package to quantify and interpret divers of variation in multilevel gene expression experiments.Provides statistical and visualization framework for studying drivers of variation in RNA-seq datasets in many types of high throughput genomic assays including RNA-seq gene-, exon- and isoform-level quantification, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays and epigenomic sequencing assays. | Repeated measures, variation in gene expression, RNA-seq datasets, high throughput genomic assays, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays, epigenomic sequencing assays, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is related to: CRAN |
Icahn School of Medicine at Mount Sinai ; NHLBI U01 HL107388 |
PMID:27884101 | Free, Available for download, Freely available | biotools:variancepartition | https://bio.tools/variancepartition | SCR_019204 | 2026-09-12 12:59:10 | 62 | ||||||
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LINCS Joint Project - Breast Cancer Network Browser Resource Report Resource Website 1+ mentions |
LINCS Joint Project - Breast Cancer Network Browser (RRID:SCR_016181) | LJP-BCNB, LJP, BCNB | data access protocol, service resource, software resource, web service | Interactive on line tool where signatures are tagged with user selected metadata and external transcript signatures are projected onto network. Browser to visualize signatures from breast cancer cell lines treated with single molecule perturbations. | breast, cancer, tissue, cluster, drug, perturbation, cell, line, gene, expression |
is related to: L1000 Characteristic Direction Signature Search Engine is related to: LINCS Project |
Breast cancer | NCI U54 CA189201; NHGRI U54 HG006093; NHLBI U54 HL127365; NHLBI U54 HL127624 |
PMID:29084964 | Free, Freely available | https://github.com/MaayanLab/LJP | SCR_016181 | LINCS Joint Project, Breast Cancer Network Browser | 2026-09-12 12:58:36 | 1 | ||||
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CycIF.org Resource Report Resource Website 10+ mentions |
CycIF.org (RRID:SCR_016267) | CycIF.org | data or information resource, experimental protocol, immuno detection protocol, immunofluorescence, narrative resource, web page | Web page for cyclic immunofluorescence. It lists several downloadable data and software pertaining to cyclic immunofluorescence. | immunofluorescence, cyclic, cycif, data, software, single cell, numeric, dataset, intratumoural, heterogeneity | has parent organization: LINCS Data Portal | NHLBI U54 HL127365 | PMID:26399630 | Public | SCR_016267 | cycif.org | 2026-09-12 12:58:37 | 16 | ||||||
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star-for-criu Resource Report Resource Website 1+ mentions |
star-for-criu (RRID:SCR_016294) | alignment software, data processing software, image analysis software, software application, software resource | Software as an Hot Start software container for STAR alignment using CRIU (Checkpoint Restore in Userspace) tool to freeze the running container. Can be deployed to align RNA sequencing data. Used in the processing of biomedical big data for better reproducibility and reliability. | hot, start, container, star, aligner, sequencing, data, processing, biomedical, cloud, reproducibility, RNA, analysis, computing, environment | is related to: Systems Transcriptional Activity Reconstruction | AMEDD Advanced Medical Technology Initiative ; NHLBI U54 HL127624; NIGMS R01 GM126019 |
Free, Freely available, Available for download | https://github.com/paizhang/Hotstarting-For-STAR-Alignment | SCR_016294 | 2026-09-12 12:58:37 | 1 | ||||||||
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Sleep Heart Health Study Resource Report Resource Website 50+ mentions |
Sleep Heart Health Study (RRID:SCR_016559) | SHHS | data or information resource, disease-related portal, portal, topical portal | Portal for a multi-cohort study focused on sleep-disordered breathing and cardiovascular outcomes implemented by the National Heart Lung and Blood Institute. Recorded signals are: EEG, ECG, EOG, SaO2, HR, EOG, EMG, respiratory inductance plethysmography, respiration (thermistor), position, light. | dataset, analysis, sleep, apnea, breathing, disorder, cardiovascular, disease, EEG, ECG, respiration, PSG | is listed by: National Sleep Research Resource (NSRR) | sleep disorder, sleep apnea, cardiovascular disease | NHLBI U01 HL53916; NHLBI U01 HL53931; NHLBI U01 HL53934; NHLBI U01 HL53937; NHLBI U01 HL53938; NHLBI U01 HL53941; NHLBI U01 HL64360 |
PMID:9493915 | Free, Freely available, Registration required for membership | SCR_016559 | Sleep Heart Health Study | 2026-09-12 12:58:41 | 84 | |||||
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SINCERA Pipeline Resource Report Resource Website 1+ mentions |
SINCERA Pipeline (RRID:SCR_016563) | SINCERA | data analysis software, data analytics software, data processing software, software application, software resource | Software tool implemented in R S4 as an analytic pipeline for processing single-cell RNA-seq data from a whole organ or sorted cells. Used for Single Cell RNA-Seq profiling analysis. | single, cell, RNA seq, data, sorted, whole, organ, profiling, analysis | NHLBI R01 HL105433; NHLBI U01 HL110964; NHLBI U01 HL122642 |
PMID:26600239 | Free, Available for download, Freely available | https://research.cchmc.org/pbge/sincera.html | SCR_016563 | SINCERA, SINgle CEll RNA seq profiling Analysis | 2026-09-12 12:58:41 | 5 | ||||||
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exRNA Atlas Resource Report Resource Website 10+ mentions |
exRNA Atlas (RRID:SCR_017221) | analysis service resource, application programming interface, atlas, consortium, controlled vocabulary, data access protocol, data analysis service, data or information resource, data repository, database, expression atlas, ontology, organization portal, portal, production service resource, service resource, software resource, storage service resource | Software tool as data and metadata repository of Extracellular RNA Communication Consortium. Atlas includes small RNA sequencing and qPCR derived exRNA profiles from human and mouse biofluids. All RNAseq datasets are processed using version 4 of exceRpt small RNAseq pipeline. Atlas accepts submissions for RNAseq or qPCR data. | Differential, expression, RNA, sequencing, qPCR, data, visualization, extracellular, exRNA, atlas, repository, dataset |
is recommended by: National Library of Medicine has parent organization: Baylor College of Medicine; Houston; Texas has parent organization: exRNA |
gastric cancer, colon carcinoma, colorectal cancer, prostate carcinoma, pancreatic carcinoma, multiple sclerosis, glioblastoma multiforme, ulcerative colitis, Alzheimer's disease, ischemic stroke, intraparenchymal hemorrhage of brain, asthma, cardiovascular disorder, myocardial infarction, lupus, nephrotic syndrome, transplanted kidney present, liver disease, transplanted liver present, pre-eclampsia, Parkinson disease, intraventricular brain hemorrhage, subarachnoid hemorrhage | American Cancer Society ResearchProfessor Award ; Frank McGraw Memorial Chair in CancerResearch ; NCATS UH3 TR000906; NCATS UH3 TR000943; NCI CA217685; NCI R01 CA163849; NCI R35 CA209904; NCI U19 CA179512; NHLBI K23 HL127099; NHLBI R01 HL122547; NHLBI R01 HL136685; NIA R01 AG059729; NIDA U54 DA036134; NIDDK P30 DK63720; NIGMS R25 GM056929 |
PMID:30951672 | Restricted | SCR_017221 | 2026-09-12 12:58:50 | 29 | |||||||
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piNET Resource Report Resource Website 1+ mentions |
piNET (RRID:SCR_018693) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values. | Analysis, visualization, proteomics data, integrated annotation, quantitative proteomics data, PTM network, LINCS library integration, genetic perturbation signature, peptide, protein, post translational modification site, PTM site, data | is related to: LINCS Project | NCATS UL1 TR001425; NCI T32 CA236764; NHLBI U54 HL127624; NIEHS P30 ES006096; NIGMS U01 GM120953; NIMH R01 MH107487 |
DOI:10.1093/nar/gkaa436 | Free, Freely available | SCR_018693 | 2026-09-12 12:59:04 | 4 | ||||||||
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Drug Gene Budger Resource Report Resource Website |
Drug Gene Budger (RRID:SCR_016489) | DGB | data access protocol, service resource, software resource, web service | Web based application to assist researchers with identifying drugs and small molecules that are predicted to maximally influence expression of mammalian gene of interest. Used to identify drugs and small molecules to regulate expression of target genes for research purpose only. Application for ranking drugs to modulate specific gene based on transcriptomic signatures. | identify, drug, small, molecule, predict, influence, expression, mammalian, gene, regulate, target |
is related to: LINCS Project has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA works with: CMAP works with: Gene Expression Omnibus (GEO) |
BD2K-LINCS Data Coordination and Integration Center Mount Sinai Knowledge Management Center for IDG ; NCI U24 CA224260; NHLBI U54 HL127624 |
PMID:30169739 | Restricted | SCR_016489 | Drug Gene Budger | 2026-09-12 12:58:40 | 0 | ||||||
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Apnea, Bariatric surgery, and CPAP study Resource Report Resource Website 1+ mentions |
Apnea, Bariatric surgery, and CPAP study (RRID:SCR_016575) | ABC study | data or information resource, disease-related portal, portal, topical portal | Portal for randomized controlled trial to compare effectiveness of bariatric surgery versus continuous positive airway pressure (CPAP) therapy for obstructive sleep apnea. Signals included in the polysomnography (PSG) montage are EEG, EMG, EOG, ECG, SpO2, airflow, CPAP pressure, CPAP flow, plethysmography, position, pulse, light, respiratory effort, snore. | dataset, bariatric, surgery, continuous, positive, airway, pressure, therapy, sleep, apnea, obesity II | is listed by: National Sleep Research Resource (NSRR) | class II obesity, obstructive sleep apnea | NHLBI K24 HL127307; NHLBI R01 HL106410 |
DOI:10.1164/rccm.201708-1637LE | Free, Available for public download, Registration required | SCR_016575 | and Cpap study, Bariatric surgery, Apnea | 2026-09-12 12:58:41 | 1 | |||||
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Best Apnea Interventions for Research (BestAIR) sleep study Resource Report Resource Website 1+ mentions |
Best Apnea Interventions for Research (BestAIR) sleep study (RRID:SCR_016583) | BestAIR | data or information resource, disease-related portal, portal, topical portal | Portal for sleep study to address challenges in conducting future large-scale trials of sleep apnea treatment. Includes data from sleep apnea patients with cardiovascular disease or risk factors. Signals included in the polysomnography (PSG) montage are ECG, SpO2, airflow, nasal pressure, position, pulse, respiratory effort, snore, tidal volume. | data, analysis, sleep, apnea, treatment, cardiovascular, disease, risk, factor, polysomnography, ECG, SpO2 | is listed by: National Sleep Research Resource (NSRR) | sleep apnea, cardiovascular disease | NHLBI U34 HL105277; Philips Respironics ; ResMed Foundation |
DOI:10.5665/sleep.4266 | SCR_016583 | bestair, , Best Apnea Interventions for Research, Bestair | 2026-09-12 12:58:41 | 3 | ||||||
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TopDom Resource Report Resource Website 10+ mentions |
TopDom (RRID:SCR_016964) | TOPDOM | data analysis software, data processing software, software application, software resource, software toolkit | Software tool to identify Topological Domains, which are basic builiding blocks of genome structure. Detects topological domains in a linear time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | identify, topological, domain, genome, structure, linear, time, data, analysis |
has parent organization: University of Southern California; Los Angeles; USA works with: CCTOP |
Arnold and Mabel Beckman foundation ; NHLBI U01 HL108634; NIDDK U54 DK107981; NSF CAREER 0747475; NSF CAREER 1150287; Pew Charitable Trusts |
PMID:26704975 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016964 | TOPological DOMains, Topological Domains, TopDom_v0.0.2, TopDom_v0.0.1 | 2026-09-12 12:58:46 | 11 | ||||||
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CardioVascular Research Grid (CVRG) Resource Report Resource Website 1+ mentions |
CardioVascular Research Grid (CVRG) (RRID:SCR_004472) | CVRG | analysis service resource, atlas, data analysis service, data or information resource, data repository, image repository, production service resource, service resource, storage service resource | Infrastructure for sharing cardiovascular data and data analysis tools. Human ExVivo heart data set and canine ExVivo normal and failing heart data sets are available. Canine hearts atlas and human InVivo atlases are available. | human, heart, canine, ex vivo, in vivo, protein microarray, cardiomyopathy, electrocardiogram, heart fiber, data sharing, microarray, data analysis tool, data analysis, mri, diffusion magnetic resonance imaging, diffusion weighted imaging, dti, cardiovascular, source code, web service, imaging |
is recommended by: National Library of Medicine is related to: Galaxy is related to: XNAT - The Extensible Neuroimaging Archive Toolkit is related to: NIH Data Sharing Repositories has parent organization: Johns Hopkins University; Maryland; USA is parent organization of: Cardiac Electrophysiology Ontology is parent organization of: Electrocardiography Ontology |
Normal, Failing heart, Cardiomyopathy, Ischemic cardiomyopathy, Non-ischemic cardiomyopathy | NHLBI R24 HL085343 | Free, Freely Available | r3d100012849, nlx_143758 | https://doi.org/10.17616/R3323J | SCR_004472 | The Cardiovascular Research Grid, Cardio Research Grid | 2026-09-12 12:56:13 | 4 | ||||
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Mouse Phenome Database (MPD) Resource Report Resource Website 100+ mentions |
Mouse Phenome Database (MPD) (RRID:SCR_003212) | MPD | data or information resource, data repository, database, experimental protocol, narrative resource, service resource, storage service resource | Database enables integration of genomic and phenomic data by providing access to primary experimental data, data collection protocols and analysis tools. Data represent behavioral, morphological and physiological disease-related characteristics in naive mice and those exposed to drugs, environmental agents or other treatments. Collaborative standardized collection of measured data on laboratory mouse strains to characterize them in order to facilitate translational discoveries and to assist in selection of strains for experimental studies. Includes baseline phenotype data sets as well as studies of drug, diet, disease and aging effect., protocols, projects and publications, and SNP, variation and gene expression studies. Provides tools for online analysis. Data sets are voluntarily contributed by researchers from variety of institutions and settings, or retrieved by MPD staff from open public sources. MPD has three major types of strain-centric data sets: phenotype strain surveys, SNP and variation data, and gene expression strain surveys. MPD collects data on classical inbred strains as well as any fixed-genotype strains and derivatives that are openly acquirable by the research community. New panels include Collaborative Cross (CC) lines and Diversity Outbred (DO) populations. Phenotype data include measurements of behavior, hematology, bone mineral density, cholesterol levels, endocrine function, aging processes, addiction, neurosensory functions, and other biomedically relevant areas. Genotype data are primarily in the form of single-nucleotide polymorphisms (SNPs). MPD curates data into a common framework by standardizing mouse strain nomenclature, standardizing units (SI where feasible), evaluating data (completeness, statistical power, quality), categorizing phenotype data and linking to ontologies, conforming to internal style guides for titles, tags, and descriptions, and creating comprehensive protocol documentation including environmental parameters of the test animals. These elements are critical for experimental reproducibility. | female, genomic location, genotype, inbred strain, male, mouse strain, phenome, phenotype, qtl, reference data, single-nucleotide polymorphism, strain allele, strain characteristic, strain, trait, gene expression, variation, hypothesis testing, data set, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: Integrated Datasets is used by: NIH Heal Project is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Special Mouse Strains Resource is related to: Vertebrate Trait Ontology is related to: GenomeMUSter has parent organization: Jackson Laboratory |
NHGRI HG003057; NHLBI HL66611; NIA AG025707; NIA AG038070; NIDA ; NIDA DA028420; NIMH MH071984 |
PMID:24243846 PMID:22102583 PMID:18987003 PMID:17151079 |
Free, Freely available | biotools:mpd, nif-0000-03160, r3d100010101 | https://bio.tools/mpd, https://doi.org/10.17616/R3PC7F | http://www.jax.org/phenome | SCR_003212 | Mouse Phenome Database | 2026-09-12 12:55:53 | 230 |
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