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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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PhenoSys Resource Report Resource Website 10+ mentions |
PhenoSys (RRID:SCR_004072) | PhenoSys | commercial organization | A research- and development-oriented company based in Berlin that engineers and markets technology for animal behavior research offering unique, automated instrumentation. This includes specialized applications of virtual reality and touch screen technology for animal behavior environments and RFID (transponder) operated devices in home cage environments. Their experimental systems are used for behavioral phenotyping, brain research, experimental psychology, and the diagnostic characterization of animal models for translational medicine. | animal behavior, behavior, virtual reality, learning, memory, cognition, navigation, touchscreen, tracking, emotion, group, group cage, multi-cage, olfactometer, odor, olfactory, sensory, behavioral biology, phenotype | nlx_158513 | SCR_004072 | PhenoSys GmbH | 2026-02-07 02:06:37 | 37 | |||||||||
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Abgent Resource Report Resource Website 50+ mentions |
Abgent (RRID:SCR_008393) | commercial organization | Antibody supplier. | antibody, peptide, synthesis, protein, primary antibody, reagent, peptide synthesis, cell signaling, post-translational modification, stem cell, neuronal development, neurodegenerative disease, gene regulation, development, autophagy, apoptosis, stem cell, phosphorylation, cell function, gene, regulation, research, library, human, kinome, cdna clone, rnai, tissue, cell | is listed by: ScienceExchange | nif-0000-30051, SciEx_4353 | https://www.abcepta.com/ | SCR_008393 | Abgent Antibodies and Peptides, Abcepta | 2026-02-07 02:07:27 | 67 | ||||||||
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IITC Life Sciences Plantar Test Apparatus Resource Report Resource Website 1+ mentions |
IITC Life Sciences Plantar Test Apparatus (RRID:SCR_012152) | Plantar Test Apparatus | instrument resource | The IITC Plantar Analgesia Meter for thermal paw can be used on 12 mice, 6 rats and other animals (cats, rabbits) unrestrained when testing for narcotic drugs. Experiments are easy to perform, simply slide the test head under test subject, align the heat source via our exclusive guide light (idle state) by the attached, adjustable, angled mirror on test head to test subject and perform tests. | testing apparatus, hargreaves, paw radiant heat assay, toe toaster, hargreaves method, hardware, instrument, equipment | rid_000075 | https://www.iitcinc.com/pdf/Plantar%20Test%20Hargreaves.pdf | SCR_012152 | Plantar Test Apparatus for Mice and Rats, Plantar Test Apparatus (Hargreaves Method) for Mice and Rats | 2026-02-07 02:08:25 | 2 | ||||||||
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Flash Gviewer Resource Report Resource Website 1+ mentions |
Flash Gviewer (RRID:SCR_012870) | Flash GViewer | software resource | Flash GViewer is a customizable Flash movie that can be easily inserted into a web page to display each chromosome in a genome along with the locations of individual features on the chromosomes. It is intended to provide an overview of the genomic locations of a specific set of features - eg. genes and QTLs associated with a specific phenotype, etc. rather than as a way to view all features on the genome. The features can hyperlink out to a detail page to enable to GViewer to be used as a navigation tool. In addition the bands on the chromosomes can link to defineable URL and new region selection sliders can be used to select a specific chromosome region and then link out to a genome browser for higher resolution information. Genome maps for Rat, Mouse, Human and C. elegans are provided but other genome maps can be easily created. Annotation data can be provided as static text files or produced as XML via server scripts. This tool is not GO-specific, but was built for the purpose of viewing GO annotation data. Platform: Online tool | visualization, chromosome, video, gene, qtl, genome, navitgation, phenotype, ontology or annotation visualization |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Medical College of Wisconsin; Wisconsin; USA |
Free for academic use | nlx_149333 | http://gmod.org/flashgviewer | SCR_012870 | 2026-02-07 02:08:47 | 2 | |||||||
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IITC Life Sciences Rotarod Test Resource Report Resource Website 1+ mentions |
IITC Life Sciences Rotarod Test (RRID:SCR_015698) | instrument resource | Kit for assessing motor function and endurance in mice and rats. IITC’s Rotarod Test is capable of having up to five mice or rats tested at a time standard. | motor function, endurance, mouse, rat, drug resistance, material resource, hardware, instrument, equipment, USEDit |
is listed by: USEDit is related to: ANY-maze |
Commercially available | https://www.iitcinc.com/pdf/Rotarod.pdf | SCR_015698 | IITC Rotarod Test, IITC Rotarod Treadmill, Rotarod Treadmill for mice and rats, IITC's Rotarod Test, Rotarod Test Rats and Mice, IITC Life Sciences Rotarod Treadmill | 2026-02-07 02:09:20 | 4 | ||||||||
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Multiple-Path Particle Dosimetry Model Resource Report Resource Website 10+ mentions |
Multiple-Path Particle Dosimetry Model (RRID:SCR_001486) | MPPD | software resource | Computational model that can be used for estimating human and rat airway particle dosimetry. The model is applicable to risk assessment, research, and education. The MPPD model calculates the deposition and clearance of monodisperse and polydisperse aerosols in the respiratory tracts of rats and human adults and children (deposition only) for particles ranging in size from ultrafine (0.01 micrometers) to coarse (20 micrometers). The models are based on single-path and multiple-path methods for tracking air flow and calculating aerosol deposition in the lung. The single-path method calculates deposition in a typical path per airway generation, while the multiple-path method calculates particle deposition in all airways of the lung and provides lobar-specific and airway-specific information. Within each airway, deposition is calculated using theoretically derived efficiencies for deposition by diffusion, sedimentation, and impaction within the airway or airway bifurcation. Filtration of aerosols by the nose and mouth is determined using empirical efficiency functions. The MPPD model includes calculations of particle clearance in the lung following deposition. | model, computational model, particle dosimetry, risk assessment, adult human, child, aerosol, deposition, clearance, lung | is related to: The Hamner Institute for Health Sciences: BMDExpress and The multiple-path particle dosimetry | PMID:8566482 | Free, Freely available | nlx_152744 | http://www.ara.com/products/mppd.htm | SCR_001486 | Multiple Path Particle Dosimetry Model | 2026-02-07 02:05:31 | 11 | |||||
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Model 1025 MR-compatible Small Animal Monitoring and Gating System Resource Report Resource Website 1+ mentions |
Model 1025 MR-compatible Small Animal Monitoring and Gating System (RRID:SCR_002090) | Model 1025 Monitoring & Gating System | instrument resource | Magnetic resonance compatible monitoring and gating system, including software, that enables monitoring rectal temperature, electrocardiogram and respiration rate during magnetic resonance imaging scan time. The PC displays multiple waveforms, measured values, trends and gating pulses. The data Acquisition modules are controlled by menu driven software from the PC. Data acquisition modules are available to measure the following parameters: ECG, respiration (three ways), temperature (two ways), pressure including invasive blood pressure (two ways), oxygen saturation and end-tidal CO2. | hardware, instrument, equipment, physiology, monitoring, gating, mr environment, respiration, temperature, blood pressure, oxygen saturation, end-tidal co2, magnetic resonance, electrocardiogram, magnetic resonance imaging, software resource | Free, Freely available | SciRes_000157 | https://wikihost.uib.no/mriwiki/images/4/4c/SAInstruments_1025.pdf | http://www.i4sa.com/web_app/main/defaultProduct.aspx?ID=82&PT=3 | SCR_002090 | Model 1025 Monitoring and Gating System, MR-Compatible Model 1025 Monitoring and Gating System, Small Animal Monitoring and Gating System | 2026-02-07 02:05:40 | 3 | ||||||
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Center for In Vivo Microscopy Resource Report Resource Website 10+ mentions |
Center for In Vivo Microscopy (RRID:SCR_001426) | CIVM | biomedical technology research center, training resource | Biomedical technology research center dedicated to the development of novel imaging methods for the basic scientist and the application of the methods to important biomedical questions. The CIVM has played a major role in the development of magnetic resonance microscopy with specialized MR imaging systems capable of imaging at more than 500,000x higher resolution than is common in the clinical domain. The CIVM was the first to demonstrate MR images using hyperpolarized 3He which has been moved from mouse to man with recent clinical trials performed at Duke in collaboration with GE. More recently the CIVM has developed the molecular imaging workbench---a system dedicated to multimodality cardiopulmonary imaging in the rodent. Their collaborators are employing these unique imaging systems in an extraordinary range of mouse and rat models of neurologic disease, cardiopulmonary disease and cancer to illuminate the underlying biology and explore new therapies. | imaging, magnetic resonance microscopy, magnetic resonance imaging, clinical, mri, ct, x-ray, ultrasound, confocal, optical, spect | has parent organization: Duke University; North Carolina; USA | Cardiopulmonary disease, Cancer, Neurological disease | NIBIB 4P41EB015897-27 | Free, Freely Available | nlx_152650 | SCR_001426 | Duke Center for In Vivo Microscopy | 2026-02-10 09:54:30 | 10 | |||||
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Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat Resource Report Resource Website 1+ mentions |
Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat (RRID:SCR_002816) | Temporal-lobe.com | data or information resource, data set | Interactive diagram containing existing knowledge of hippocampal-parahippocampal connections in which any connection can be turned on or off at the level of cortical layers. It includes references for each connection. | function, anatomical, connection, cortical, diagram, hippocampus, layer, neuroanatomy, neuroscience, parahippocampal, projection, subfield, temporal, lobe, topological, connectome, magnetic resonance, connectivity, formation, parahippocampal region, retrosplenial cortex, tract tracing |
is used by: NIF Data Federation is used by: Integrated Nervous System Connectivity is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Rat Hippocampus Atlas is related to: Integrated Manually Extracted Annotation has parent organization: Norwegian University of Science and Technology; Trondheim; Norway |
Research Council of Norway ; various independent donations |
PMID:21847380 PMID:19300446 |
Freely available, Account required | nif-0000-24805 | http://www.nitrc.org/projects/connectivity | SCR_002816 | Parahippocampal-hippocampal network, TEMPORAL-LOBE, Parahippocampal hippocampal connectivity | 2026-02-11 10:56:33 | 7 | ||||
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tfcheckpoint Resource Report Resource Website 1+ mentions |
tfcheckpoint (RRID:SCR_023880) | data or information resource, database | Collection of transcription factors annotated according to experimental and other evidence on their function as true DbTFs. Provides reference for both small scale experiments and genome scale studies. Curated compendium of specific DNA-binding RNA polymerase II transcription factors. | transcription factor, DNA-binding RNA polymerase II transcription factors, DNA-binding, RNA polymerase II transcription factors, | Norwegian Cancer Society ; Liaison Committee between the Central Norway Regional Health Authority ; Norwegian University of Science and Technology |
PMID:23933972 | Free, Freely available | SCR_023880 | 2026-02-11 11:00:39 | 3 | |||||||||
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APPRIS Resource Report Resource Website 50+ mentions |
APPRIS (RRID:SCR_012019) | APPRIS | data or information resource, database | A database that houses annotations of human splice isoforms. It adds reliable protein structural and functional data and information from cross-species conservation. A visual representation of the annotations for each gene allows users to easily identify functional changes brought about by splicing events. In addition to collecting, integrating and analyzing reliable predictions of the effect of splicing events, it also selects a single reference sequence for each gene, termed the principal isoform, based on the annotations of structure, function and conservation for each transcript. | isoform, function, annotation, splice, reference sequence, structure, conservation, transcript, FASEB list |
is listed by: OMICtools has parent organization: Spanish National Cancer Research Center |
PMID:23161672 | Free | OMICS_01881 | SCR_012019 | APPRIS - A system for annotating alternative splice isoforms | 2026-02-11 10:58:27 | 85 | ||||||
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COMPARTMENTS Subcellular localization database Resource Report Resource Website 1+ mentions |
COMPARTMENTS Subcellular localization database (RRID:SCR_015561) | data or information resource, database | Web resource that integrates evidence on protein subcellular localization from manually curated literature, high-throughput screens, automatic text mining, and sequence-based prediction methods. All evidence is mapped to common protein identifiers and Gene Ontology terms, and further unify it by assigning confidence scores that facilitate comparison of the different types and sources of evidence and visualize these scores on a schematic cell. | subcellular localization database | EMBL International PhD Programme 295–2012; Luxembourg Centre for Systems Biomedicine ; Novo Nordisk Foundation Center for Protein Research ; CSIRO Office of the Chief Executive ; CSIRO Computation and Simulation Sciences |
SCR_015561 | COMPARTMENTS, Compartments Database | 2026-02-11 10:59:11 | 7 | ||||||||||
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PolyA DB Resource Report Resource Website 100+ mentions |
PolyA DB (RRID:SCR_007867) | PolyA_DB | data or information resource, database | A database of mRNA polyadenylation sites. PolyA_DB version 1 contains human and mouse poly(A) sites that are mapped by cDNA/EST sequences. PolyA_DB version 2 contains poly(A) sites in human, mouse, rat, chicken and zebrafish that are mapped by cDNA/EST and Trace sequences. Sequence alignments between orthologous sites are available. PolyA_SVM predicts poly(A) sites using 15 cis elements identified for human poly(A) sites. | FASEB list | has parent organization: University of Medicine and Dentistry of New Jersey; New Jersey; USA | SCR_007867 | 2026-02-11 10:57:49 | 101 | ||||||||||
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Gemma Resource Report Resource Website 1000+ mentions |
Gemma (RRID:SCR_008007) | Gemma | data or information resource, database | Resource for reuse, sharing and meta-analysis of expression profiling data. Database and set of tools for meta analysis, reuse and sharing of genomics data. Targeted at analysis of gene expression profiles. Users can search, access and visualize coexpression and differential expression results. | chip, microarray, functional genomics, gene expression, coexpression, differential expression, FASEB list |
is used by: NIF Data Federation is used by: Integrated Data Annotation is listed by: Debian is listed by: SoftCite is related to: Gene Ontology is related to: Gene Expression Omnibus is related to: Phenocarta has parent organization: University of British Columbia; British Columbia; Canada is parent organization of: Neurocarta |
NIGMS GM076990; Canadian Foundation for Innovation ; Michael Smith Foundation for Health Research ; Canadian Institutes for Health Research |
PMID:22782548 | Free, Freely available | nif-0000-08127, r3d100012747 | https://sources.debian.org/src/gemma/ https://doi.org/10.17616/R36R54 https://doi.org/10.17616/R36R54 |
SCR_008007 | 2026-02-11 10:57:44 | 1112 | |||||
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EID: Exon-Intron Database Resource Report Resource Website 10+ mentions |
EID: Exon-Intron Database (RRID:SCR_002469) | EID | data or information resource, data set | Data sets of protein-coding intron-containing genes that contain gene information from humans, mice, rats, and other eukaryotes, as well as genes from species whose genomes have not been completely sequenced. This is a comprehensive and convenient dataset of sequences for computational biologists who study exon-intron gene structures and pre-mRNA splicing. The database is derived from GenBank release 112, and it contains protein-coding genes that harbor introns, along with extensive descriptions of each gene and its DNA and protein sequences, as well as splice motif information. They have created subdatabases of genes whose intron positions have been experimentally determined. The collection also contains data on untranslated regions of gene sequences and intron-less genes. For species with entirely sequenced genomes, species-specific databases have been generated. A novel Mammalian Orthologous Intron Database (MOID) has been introduced which includes the full set of introns that come from orthologous genes that have the same positions relative to the reading frames. | eukaryote genome, exon, exon-intro, gene structure, genome splicing, intron, ortholog, fasta, gene, protein-coding gene, splice, motif, gene prediction, structure, coding region |
is listed by: OMICtools has parent organization: University of Toledo; Ohio; USA |
PMID:16772261 PMID:10592221 |
Free, Available for download, Freely available | OMICS_01886, nif-0000-02793 | http://www.utoledo.edu/med/depts/bioinfo/database.html | http://www.meduohio.edu/bioinfo/eid/, http://mcb.harvard.edu/gilbert/EID | SCR_002469 | The Exon-Intron Database, Exon-Intron Database | 2026-02-11 10:56:28 | 11 | ||||
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Rat Gene Symbol Tracker Resource Report Resource Website 10+ mentions |
Rat Gene Symbol Tracker (RRID:SCR_003261) | RGST | data or information resource, database | 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 September 2, 2016. Database for defining official rat gene symbols. It includes rat gene symbols from three major sources: the Rat Genome Database (RGD), Ensembl, and NCBI-Gene. All rat symbols are compared with official symbols from orthologous human genes as specified by the Human Gene Nomenclature Committee (HGNC). Based on the outcome of the comparisons, a rat gene symbol may be selected. Rat symbols that do not match a human ortholog undergo a strict procedure of comparisons between the different rat gene sources as well as with the Mouse Genome Database (MGD). For each rat gene this procedure results in an unambiguous gene designation. The designation is presented as a status level that accompanies every rat gene symbol suggested in the database. The status level describes both how a rat symbol was selected, and its validity. Rat Gene Symbol Tracker approves rat gene symbols by an automatic procedure. The rat genes are presented with links to RGD, Ensembl, NCBI Gene, MGI and HGNC. RGST ensures that each acclaimed rat gene symbol is unique and follows the guidelines given by the RGNC. To each symbol a status level associated, describing the gene naming process. | gene, orthology, naming, gene symbol, nomenclature, human, mouse |
is related to: Rat Genome Database (RGD) is related to: Entrez Gene is related to: Ensembl is related to: Mouse Genome Informatics (MGI) is related to: HGNC has parent organization: RatMap |
Swedish MRC ; Nilsson-Ehle Foundation ; Sven and Lilly Lawski Foundation ; Erik Philip-Sorensen Foundation ; Wilhelm and Martina Lundgren Research Foundation ; SWEGENE Foundation |
PMID:18215257 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31426 | SCR_003261 | RGST (Rat Gene Symbol Tracker), RGST - Rat Gene Symbol Tracker | 2026-02-11 10:56:38 | 14 | |||||
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Peptide Sequence Database Resource Report Resource Website |
Peptide Sequence Database (RRID:SCR_005764) | PepSeqDB | data or information resource, database | The Peptide Sequence Database contains putative peptide sequences from human, mouse, rat, and zebrafish. Compressed to eliminate redundancy, these are about 40 fold smaller than a brute force enumeration. Current and old releases are available for download. Each species'' peptide sequence database comprises peptide sequence data from releveant species specific UniGene and IPI clusters, plus all sequences from their consituent EST, mRNA and protein sequence databases, namely RefSeq proteins and mRNAs, UniProt''s SwissProt and TrEMBL, GenBank mRNA, ESTs, and high-throughput cDNAs, HInv-DB, VEGA, EMBL, IPI protein sequences, plus the enumeration of all combinations of UniProt sequence variants, Met loss PTM, and signal peptide cleavages. The README file contains some information about the non amino-acid symbols O (digest site corresponding to a protein N- or C-terminus) and J (no digest sequence join) used in these peptide sequence databases and information about how to configure various search engines to use them. Some search engines handle (very) long sequences badly and in some cases must be patched to use these peptide sequence databases. All search engines supported by the PepArML meta-search engine can (or can be patched to) successfully search these peptide sequence databases. | peptide, sequence | has parent organization: Edwards Lab | nlx_149230 | SCR_005764 | 2026-02-11 10:57:13 | 0 | |||||||||
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DisGeNET Resource Report Resource Website 1000+ mentions |
DisGeNET (RRID:SCR_006178) | DisGeNET | data or information resource, database | Database and discovery platform containing publicly available collections of genes and variants associated to human diseases. Integrates data from curated repositories, GWAS catalogues, animal models and scientific literature. | gene, disease, gene-disease association, gene-disease ontology, gene-disease text mining, text mining, genotype-phenotype, rdf, genotype, phenotype, gene-disease, variant-disease, FASEB list |
uses: Comparative Toxicogenomics Database (CTD) uses: Genetic Association Database uses: UniProt uses: Mouse Genome Database uses: Reactome uses: Unified Medical Language System uses: Entrez Gene uses: MEDLINE uses: National Center for Biomedical Ontology uses: National Cancer Institute Thesaurus uses: Human Phenotype Ontology uses: Semanticscience Integrated Ontology uses: Cytoscape uses: Literature-derived human gene-disease network uses: Rat Genome Database (RGD) uses: National Library of Medicine uses: PsyGeNET is used by: HmtPhenome is listed by: 3DVC is affiliated with: Gene-Disease Association Type Ontology has parent organization: Pompeu Fabra University; Barcelona; Spain |
EFPIA ; Instituto de Salud Carlos III-Fondo Europeo de Desarrollo Regional ; Elixir-Excelerate ; Innovative Medicines Initiative Joint Undertaking ; European Union Seventh Framework Programme ; European Union Horizon 2020 |
PMID:27924018 PMID:25877637 PMID:21695124 PMID:20861032 |
Restricted | nlx_151710, r3d100013301 | https://doi.org/10.17616/R31NJMR9 | SCR_006178 | database of gene disease associations | 2026-02-11 10:57:15 | 2210 | ||||
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PEpiD Resource Report Resource Website 1+ mentions |
PEpiD (RRID:SCR_000235) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A database to store the curated epigenetic data from studies of prostate cancer retrieved by literature mining. The Prostate Epigenetic Database (PEpiD) is meant as a resource for finding previous studies of prostate cancer in humans, mice and rats. Searches can be targeted through the categories of DNA methylation, histone modification, and microRNA. | epigenetic, prostate cancer, dna methylation, histone modification, micro rna, mrna |
is listed by: OMICtools has parent organization: Tongji University; Shanghai; China |
Prostate Cancer | PMID:23696878 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01845 | SCR_000235 | Prostate Epigenetic Database | 2026-02-11 10:56:00 | 2 | ||||||
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BAMS Connectivity Resource Report Resource Website 1+ mentions |
BAMS Connectivity (RRID:SCR_000561) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9,2022. Database of information about brain region circuitry, it collates data from the literature on tract tracing studies and provides tools for analysis and visualization of connectivity between brain regions., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | brain, neural circuitry, connectivity, brain region, neuroanatomy, neuronal tract tracing, connectome |
is used by: NIF Data Federation is related to: Integrated Manually Extracted Annotation has parent organization: Brain Architecture Management System |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_144138 | http://brancusi.usc.edu/bkms/, http://brancusi.usc.edu/ | SCR_000561 | Brain Architecture Management System Connectivity Data | 2026-02-11 10:56:04 | 1 |
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