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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Randomized Controlled Trials Ontology Resource Report Resource Website |
Randomized Controlled Trials Ontology (RRID:SCR_005992) | RCTONT | data or information resource, controlled vocabulary, ontology | Ontology specifically for Randomized Controlled Trials in order to facilitate the production of systematic reviews and metaanalysis. | owl | is listed by: BioPortal | nlx_157568 | SCR_005992 | 2026-08-09 09:04:20 | 0 | |||||||||
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DataCite Ontology Resource Report Resource Website |
DataCite Ontology (RRID:SCR_006215) | DataCite Ontology | data or information resource, controlled vocabulary, ontology | An ontology written in OWL 2 DL to enable the metadata properties of the DataCite Metadata Kernel Specification version 2.2 (http://test.datacite.org/schema/meta/kernel-2.2/index.html) to be described in RDF. This version of the DataCite Ontology has been completely revised and significantly expanded to permit accurate mapping of this new version of the DataCite Metadata Kernel Specification to RDF. | annotation, alternate resource identifier, description type, funder identifier, funder identifier scheme, identifier, identifier scheme, personal identifier, personal identifier scheme, primary resource identifier, resource identifier, resource identifier scheme, owl, rdf, metadata |
is listed by: FORCE11 has parent organization: DataCite |
Creative Commons Attribution License | nlx_151759 | https://www.force11.org/node/4673 | SCR_006215 | 2026-08-09 09:04:24 | 0 | |||||||
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Read Codes Clinical Terms Version 3 Resource Report Resource Website 1+ mentions |
Read Codes Clinical Terms Version 3 (RRID:SCR_006055) | RCD | data or information resource, controlled vocabulary, ontology | Ontology of clinical terms Version 3 (CTV3) (Read Codes) (Q199): National Health Service National Coding and Classification Centre | umls | is listed by: BioPortal | nlx_157570 | SCR_006055 | Read Codes CTV3, Read Codes Clinical Terms Version 3 (CTV3) | 2026-08-09 09:04:20 | 1 | ||||||||
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Regulation of Transcription Ontology Resource Report Resource Website |
Regulation of Transcription Ontology (RRID:SCR_006238) | RETO | data or information resource, controlled vocabulary, ontology | An application ontology for the domain of gene transcription regulation. The ontology integrates fragments of GO and MI with data from GOA, IntAct, UniProt, NCBI, KEGG and orthology relations. | obo | is listed by: BioPortal | nlx_157573 | SCR_006238 | 2026-08-09 09:04:24 | 0 | |||||||||
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Ontology for Biomedical Investigations Resource Report Resource Website 10+ mentions |
Ontology for Biomedical Investigations (RRID:SCR_006266) | OBI | data or information resource, controlled vocabulary, ontology | An ontology for the description of biological and clinical investigations built with international, collaborative effort. The ontology represents the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. This includes a set of universal terms that are applicable across various biological and technological domains, and domain-specific terms relevant only to a given domain. Currently OBI is being built under the Basic Formal Ontology (BFO). This project was formerly titled the Functional Genomics Investigation Ontology (FuGO) project. | life-science, clinical, investigation, biomedical, protocol, instrumentation, experiment, biology, owl, molecular, cellular, organismal, multi-organismal |
is used by: Information Artifact Ontology is used by: Beta Cell Genomics Ontology is listed by: FORCE11 is listed by: BioPortal is listed by: OBO is related to: Information Artifact Ontology is related to: Chemical Methods Ontology is related to: Genomic Standards Consortium |
PMID:20626927 | Creative Commons Attribution License v3 | nif-0000-06698 | http://purl.obofoundry.org/obo/obi.owl, http://purl.obofoundry.org/obo/obi, https://www.force11.org/node/4700 | SCR_006266 | OBI Ontology | 2026-08-09 09:04:25 | 21 | |||||
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Stereotaxic MRI Brain Atlas of Monkey Resource Report Resource Website |
Stereotaxic MRI Brain Atlas of Monkey (RRID:SCR_007298) | data or information resource, atlas | Series of MRI slices from 3 male Japanese snow monkeys (Macaca fuscata). Images are provided of 2 mm MRI slices of male monkey brain in the coronal (N = 5), horizontal (N =1) and sagittal (N =1) planes. Slices are presented according to distance from interaural line. The slices are low resolution and no annotations are provided. Would be suitable for low resolution 3D reconstruction of monkey brain, however. Also, there are datasets provided for 5 monkeys total, 3 m.fuscata and 2 m. mulatta. | magnetic resonance imaging, stereotaxic brain atlas, monkey | has parent organization: Nihon University; Tokyo; Japan | nif-0000-00125 | SCR_007298 | Stereotaxic MRI Brain Atlas of Monkey | 2026-08-09 09:04:48 | 0 | |||||||||
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Sapienta Resource Report Resource Website 1+ mentions |
Sapienta (RRID:SCR_006993) | SAPIENTA | software application, source code, software resource | Software to help researchers process scientific papers faster and get the information they are interested in out of them. This is achieved by automating the recognition of core scientific concepts such as Motivation, Method, Result, Conclusion in papers and uses them to generate automatic summaries. This SAPIENTA tool adds additional functionality to the SAPIENT tool, an annotation tool implemented as a web application which enables experts to annotate scientific papers, sentence by sentence manually, according to the Core Scientific Concept (CSC) schema. | semantic mark up, semantic, annotation, annotation software | is listed by: FORCE11 | JISC | nlx_151311 | SCR_006993 | SAPIENTA - Automating the Semantic Annotation of Papers, Semantic Annotation of Papers: Interface & ENrichment Tool Automated | 2026-08-09 09:04:40 | 1 | |||||||
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POOLSCORE Resource Report Resource Website |
POOLSCORE (RRID:SCR_007514) | software application, software resource | Software program for analysis of case-control genetic association studies using allele frequency measurements on DNA pools (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | SCR_009373, nlx_154595, nlx_154087 | SCR_007514 | R/POOLSCORE | 2026-08-09 09:04:44 | 0 | |||||||||
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BrainNavigator Resource Report Resource Website 1+ mentions |
BrainNavigator (RRID:SCR_008289) | BrainNavigator | data or information resource, atlas | THIS RESOURCE IS NO LONGER IN SERVICE, documented December 31, 2013. An interactive atlas and 3D brain software for research, structure analysis, and education, it offers six atlases representing four species: the mouse, rat, monkey and human. The stereotaxic coordinates atlases are available for all four species and the rodent models have additional chemoarchitectonic atlases. BrainNavigator helps locate specific areas of the brain, making visualizing and experimental planning in the brain easier. *Plan: Browse 6 Atlases, Visualize with 3D models, Search Literature, Analyze gene expression, Identify connections *Publish: Access reference tools, Use and print images for publication, Search literature *Propose: Use and print images for proposals, Search literature, Locate gene expression in 2D and 3D, Identify connections *Produce: Simulate injections, Customize new coordinates, virtually slice sections, overlay atlas maps on your own images, create personal atlas maps With BrainNavigator, you''ll gain 24/7 access to their powerful 3D brain interactive software tool that helps further research in the neurosciences. In addition, their vast library of widely respected and referenced brain publications will provide a plethora of information on the most current brain research available. As publisher of the gold standard in brain atlas publications authored by the team around the leading brain cartographers George Paxinos and Charles Watson, they are pleased to bring an advanced tool to today''s neuroscientists and educators. Combining atlas content and 3D capabilities based on technologies from the Allen Institute for Brain Science, this online workflow solution brings brain research, analysis and education tools to your fingertips. | 3d, 2d, acetylcholinesterase, anatomy, brain, coronal, reconstruction, sagittal, sterotaxic, visualization, molecular neuroanatomy resource, training resource, connection, literature, gene expression, image | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-24037 | SCR_008289 | Brain Navigator | 2026-08-09 09:04:49 | 5 | ||||||||
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Digestive Diseases Statistics for the United States Resource Report Resource Website |
Digestive Diseases Statistics for the United States (RRID:SCR_006703) | Digestive Diseases Statistics for the United States | data or information resource, resource | A collection of statistics about specific digestive diseases, including prevalence, mortality, care delivery and cost. | epidemiology, prevalence, mortality, care delivery, cost, statistics, ambulatory care visit, hospitalization, inpatient procedure, surgical procedure |
is related to: NIDDK Information Network (dkNET) has parent organization: National Digestive Diseases Information Clearinghouse |
Digestive disease, Viral Hepatitis, Hepatitis B, Hepatitis A, Hepatitis C, Peptic Ulcer Disease, Pancreatitis, Liver disease, Irritable Bowel Syndrome, Ulcerative colitis, Hemorrhoid, Gastrointestinal infection, Gastroesophageal reflux disease, Gallstone, Diverticular disease, Chronic constipation, Abdominal wall hernia | NIDDK | nlx_152697 | SCR_006703 | Digestive Diseases in the United States: Epidemiology and Impact | 2026-08-09 09:04:27 | 0 | ||||||
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Allen Mouse Brain Connectivity Atlas Resource Report Resource Website 100+ mentions |
Allen Mouse Brain Connectivity Atlas (RRID:SCR_008848) | ABA Mouse Connectivity | data or information resource, spatially referenced dataset, atlas | Map of neural connections in mouse brain, built on an array of transgenic mice genetically engineered to target specific cell types. In addition to the connectivity data, information about the transgenic mouse lines and genetic tracers is available. Consists of high resolution 2-D projectivity image data that can be viewed side-by-side with the associated reference atlas and other reference datasets. Enables 3-D visualization and spatial/ontological search of connectivity models through a combination of manual and informatics analyses. | brain, connectivity, atlas, neural, projection, mutant, mouse, strain, image, histology, neuroimaging, data |
is used by: NIF Data Federation is related to: Allen Mouse Brain Common Coordinate Framework has parent organization: Allen Institute for Brain Science has parent organization: Allen Brain Atlas |
Allen Institute for Brain Science | Free for academic use, Non-commercial, Acknowledgement required, Commercial use requires permission | nlx_146253 | http://connectivity.brain-map.org/static/brainexplorer | SCR_008848 | Allen Brain Atlas Connectivity Study, Allen Brain Mouse Connectivity, Allen Mouse Connectivity Atlas, Allen Brain Atlas Mouse Connectivity | 2026-08-09 09:05:02 | 210 | |||||
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GC/GCF Resource Report Resource Website 1+ mentions |
GC/GCF (RRID:SCR_009075) | software application, software resource | Software application where GC implements the genomic control models. GCF implements the basic Genomic Control approach, but adjusts the p-values for uncertainty in the estimated effect of substructure. This approach is preferable if a large number of tests will be evaluated because it provides a more accurrate assessment of the significance level for small p-values. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, linux | is listed by: Genetic Analysis Software | nlx_154072, SCR_000846, nlx_154584 | SCR_009075 | R/GCF, R/GC, Genomic Control | 2026-08-09 09:05:08 | 1 | |||||||||
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Functional ROI Atlas Resource Report Resource Website |
Functional ROI Atlas (RRID:SCR_009481) | Functional ROI Atlas | data or information resource, atlas | An effort to provide a set of quasi-probabilistic atlases for established functional ROIs in the human neuroimaging literature. Many atlases exist for various anatomical parcellation schemes, such as the Brodmann areas, the structural atlases, tissue segmentation atlases, etc. To date, however, there is no atlas for so-called functional ROIs. Such fROIs are typically associated with an anatomical label of some kind (e.g. the _fusiform_ face area), but these labels are only approximate and can be misleading inasmuch as fROIs are not constrained by anatomical landmarks, whether cytoarchitectonic or based on sulcal and gyral landmarks. The goal of this project is to provide quasi-probabilistic atlases for fROIs that are based on published coordinates in the neuroimaging literature. This is an open-ended enterprise and the atlas can grow as needed. Members of the neuroscience and neuroimaging community interested in contributing to the project are encouraged to do so. | magnetic resonance, nifti, functional roi, region of interest, neuroimaging | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License, The community can contribute to this resource | nlx_155628 | SCR_009481 | 2026-08-09 09:05:21 | 0 | ||||||||
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Atlasing of the basal ganglia Resource Report Resource Website 1+ mentions |
Atlasing of the basal ganglia (RRID:SCR_009431) | Atlasing of the basal ganglia | data or information resource, atlas | This atlas takes advantage of ultra-high resolution 7T MRI to provide unprecedented levels of detail on structures of the basal ganglia in-vivo. The atlas includes probability maps of the Subthalamic Nucleus (STh) using T2*-imaging. For now it has been created on 13 young healthy participants with a mean age of 24.38 (range: 22-28, SD: 2.36). We recently also created atlas STh probability maps from 8 middle-aged participants with a mean age of 50.67 (range: 40-59, SD: 6.63), and 9 elderly participants with a mean age of 72.33 (range: 67-77, SD: 2.87). You can find more details about the creation of these maps in the following papers: Young: http://www.ncbi.nlm.nih.gov/pubmed/22227131 Middle-aged & Elderly: http://www.ncbi.nlm.nih.gov/pubmed/23486960 Participating institutions are the Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany, and the Cognitive Science Center Amsterdam, University of Amsterdam, the Netherlands. | magnetic resonance, mri, late adult human, early adult human, middle adult human, basal ganglia |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: LEAD-DBS |
Aging | PMID:22227131 PMID:23486960 |
Creative Commons License | nlx_155581 | SCR_009431 | 2026-08-09 09:05:02 | 6 | ||||||
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Neurofly Resource Report Resource Website 1+ mentions |
Neurofly (RRID:SCR_013833) | data or information resource, atlas | An on-going atlas project of the Virtual Insect Brain Project with the goal of reconstructing and standardizing Gal4 expression patterns in Drosophila brains. Neurofly will be a web-based tool that will enable the online comparison of mutations and Gal4 expression patterns in the Drosophila brain. To this end, a database of reconstructed and standardized Gal4 expression patterns - on the basis of the existing Drosophila StandardBrain - was developed along with tools for 3D image data set processing. Users will be able to evaluate the expression patterns intersections of various Gal4 driver lines and/or mutations. | atlas, database, Drosophila, Gal4, tool, Virtual Insect Brain Project |
is listed by: Educational Resources in Neuroscience is related to: Educational Resources in Neuroscience has parent organization: University of Wurzburg; Bavaria; Germany |
Free, Public | SCR_013833 | Virtual Insect Brain Lab | 2026-08-09 09:06:14 | 1 | |||||||||
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499 fROI atlas Resource Report Resource Website 50+ mentions |
499 fROI atlas (RRID:SCR_014756) | data or information resource, atlas | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Atlas of functional ROIs (fROIs) containing 499 regions, with extensive gray matter coverage. Atlases are available for download directly from the website. | roi, dmn, fmri, atlas, functional roi, gray matter, grey matter, brain | is related to: 90 fROI atlas | PMID:26068849 | THIS RESOURCE IS NO LONGER IN SERVICE. | SCR_014756 | Willard atlas | 2026-08-09 09:06:31 | 77 | ||||||||
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Striatal Subregional VOImap Resource Report Resource Website |
Striatal Subregional VOImap (RRID:SCR_014173) | data or information resource, atlas | An atlas intended to provide accurate data in terms of specific uptake location to make the BP quantitation. The VOIs were manually drawn with software Analyze 9.0 (Mayo Clinic) in 18F-DOPA brain image after spatial normalization with a 18F-DOPA Template. Each striatum was divided into 6 sub-regions: ventral caudate, anterior dorsal caudate, posterior dorsal caudate, ventral putamen, anterior dorsal putamen and posterior dorsal putamen. | atlas, map, bp quantitation, striatum, uptake location | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Available to the research community, Free, Acknowledgement requested | SCR_014173 | 2026-08-09 09:06:21 | 0 | ||||||||||
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Brain Coactivation Map Resource Report Resource Website |
Brain Coactivation Map (RRID:SCR_014172) | data or information resource, atlas | The Brain Coactivation Map describes all the coactivation networks in the human brain based on the meta-analysis of more than 5,400 neuroimaging articles (from NeuroSynth) containing more than 16,000 individual experiments. The map can be browsed interactively (CoactivationMap.app on GitHub) or queried from a shell using a command line tool (cmtool on GitHub). | atlas, map, coactivation network, human brain, interactive, command line |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Pasteur Institute |
Available to the research community | https://github.com/r03ert0/CoactivationMap.app, https://github.com/r03ert0/cmtool | SCR_014172 | 2026-08-09 09:06:03 | 0 | |||||||||
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WormGUIDES Resource Report Resource Website 1+ mentions |
WormGUIDES (RRID:SCR_013733) | data or information resource, atlas | A worm atlas that provides an interactive 4D atlas of nuclear positions, from zygote until hatching which can be used to guide cell identification. The tools enable examination of the connectome during development from integrate knowledge of C. elegans embryogenesis to widely used resources, such as WormAtlas and WormBase. | embryogenesis, development, neural connectivity, diSPIM, 4d atlas, c elegans | has parent organization: Yale University; Connecticut; USA | NIH Office of the Director R24 OD016474 | Free, Public, Requires Java | SCR_014203 | https://orip.nih.gov/comparative-medicine/programs/invertebrate-models, http://www.wormguides.org/wormguides | SCR_013733 | Global Understanding in Dynamic Embryonic Systems | 2026-08-09 09:06:01 | 4 | ||||||
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Adult Zebrafish Brain Atlas Resource Report Resource Website 1+ mentions |
Adult Zebrafish Brain Atlas (RRID:SCR_021732) | AZBA | data or information resource, atlas | Software tool as 3D adult zebrafish brain atlas for digital age. Built by combining tissue clearing, light-sheet fluorescence microscopy, and three-dimensional image registration of nuclear and antibody stains. | 3D adult zebrafish brain atlas, zebrafish brain, adult zebrafish brain, 3D brain | DOI:10.1101/2021.05.04.442625 | Free, Freely available | SCR_021732 | 2026-08-09 09:07:41 | 2 |
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