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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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EndoMap Resource Report Resource Website 1+ mentions |
EndoMap (RRID:SCR_026690) | data or information resource, database | Structural interactome viewer. Interactive database of endosomal protein-protein interactions identified by cross-linking mass spectrometry and modeled by AlphaFold multimer. Structural protein interactome of human early endosomes. | Structural protein interactome, structural interactome viewer, endosomal protein-protein interactions, human early endosomes, | Aligning Science Across Parkinson ; NINDS R01NS110395; NIGMS RO1 GM132129; Michael J Fox Foundation |
DOI:10.1101/2025.02.07.636106 | Free, Freely available | SCR_026690 | EndoMAP.v1 | 2026-02-14 02:09:07 | 2 | ||||||||
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TEProf3 Resource Report Resource Website |
TEProf3 (RRID:SCR_027288) | software resource, source code, software toolkit | Software pipeline to detect Transposable Elements transcripts. Used to identify TE-derived promoters and transcripts using transcriptomic data from multiple sources, including short-read RNA-seq data, long-read RNA-seq data and single cell RNA-seq data. | Transposable Elements, Transposable Elements transcripts, detect TE transcripts, transcriptomic data, short-read RNA-seq data, long-read RNA-seq data, single cell RNA-seq data, | NHGRI R01HG007175; NIA R01AG078958; NINDS U24NS132103; NHGRI U01HG013227 |
PMID:40360186 | Free, Available for download, Freely available, | SCR_027288 | , TE-derived Promoter Finder 3 | 2026-02-14 02:09:54 | 0 | ||||||||
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hdWGCNA Resource Report Resource Website 1+ mentions |
hdWGCNA (RRID:SCR_027496) | software resource, source code, software toolkit | Software R package for performing weighted gene co-expression network analysis in high dimensional transcriptomics data such as single-cell RNA-seq or spatial transcriptomics. | weighted gene co-expression network, high dimensional transcriptomics data, single-cell RNA-seq, transcriptomics | NIA 1RF1AG071683; NINDS P01NS084974; NIDA 1U01DA053826; NIA U54 AG054349; NIA 3U19AG068054 |
PMID:37426759 | Free, Available for download, Freely available | SCR_027496 | hd Weighted Gene Co-expression Network Analysis | 2026-02-14 02:10:03 | 6 | ||||||||
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Reproducible Brain Charts Resource Report Resource Website |
Reproducible Brain Charts (RRID:SCR_027837) | data or information resource, data set | Open data resource for mapping brain development and its associations with mental health. Integrates data from 5 large studies of brain development in youth from three continents (N = 6,346). Bifactor models were used to create harmonized psychiatric phenotypes, capturing major dimensions of psychopathology. Neuroimaging data were carefully curated and processed using consistent pipelines in a reproducible manner. | Neuroimaging data, curated data, data resource, mapping brain development, mental health, | NIMH R01MH120482; NIMH R37MH125829; NIBIB R01EB022573; NIMH R01MH112847; NIMH R01MH113550; NIMH RF1MH121867; NIMH R01MH123550; NINDS U24NS130411; NIMH P50MH109429; NIMH R01MH123440; NIMH K08MH079364 |
PMID:40987284 | Free, Freely available | SCR_027837 | 2026-02-14 02:09:32 | 0 | |||||||||
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Baby Open Brains Resource Report Resource Website |
Baby Open Brains (RRID:SCR_027836) | data or information resource, data set | Open source resource of manually curated and expert reviewed infant brain segmentations hosted on OpenNeuro.org. and OSF.io. Anatomical MRI data was segmented from 71 infant imaging visits across 51 participants, using both T1w and T2w images per visit. Images showed dramatic differences in myelination and intensities across 1–9 months, emphasizing the need for densely sampled gold-standard segmentations across early life. This dataset provides a benchmark for evaluating and improving pipelines dependent upon segmentations in the youngest populations. As such, this dataset provides a vitally needed foundation for early-life large-scale studies such as HBCD. | MRI, image, dataset of infant brain segmentations, infant brain, brain segmentation, manually curated infant brain segmentations, | uses: OpenNeuro | Bill & Melinda Gates Foundation ; NIMH R01 MH104324; NIMH U01 MH110274; NINDS T32 NS109604; NIDA U01DA041148; NIDA U24DA055330; NIMH R01MH096773; NIMH R01MH125829; NIMH R37MH125829 |
PMID:40813378 | Free, Freely available, | SCR_027836 | , BOBs, Baby Open Brains (BOBs) Dataset | 2026-02-14 02:10:09 | 0 | |||||||
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NeuroJSON.io Resource Report Resource Website |
NeuroJSON.io (RRID:SCR_027793) | data or information resource, portal, project portal | Web application for human-readable, searchable neuroimaging datasets using universally accessible JSON format and URL-based RESTful APIs. NeuroJSON.io is built upon highly scalable document-store NoSQL database technologies, specifically, open-source Apache CouchDB engine, that can handle millions of datasets without major performance penalties. Provides fine-grained data search capabilities to allow users to find, preview and re-combine complex data records from public datasets before download. | neuroimaging datasets, JSON format, URL-based RESTful APIs, data search, public datasets, | NINDS U24 NS124027 | Free, Freely available | SCR_027793 | NeuroJSON | 2026-02-14 02:09:31 | 0 | |||||||||
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NITRC-IR Resource Report Resource Website 1+ mentions |
NITRC-IR (RRID:SCR_004162) | NITRC IR | data repository, storage service resource, image database, catalog, data or information resource, service resource, image repository, database | Data repository for neuroimaging data in DlCOM and NIFTI formats. It allows users to search for and freely download publicly available data sets relating to normal subjects and those with diagnoses such as: schizophrenia, ADHD, autism, and Parkinson's disease.XNAT-based image registry that supports both NIfTI and DICOM images to promote re-use and integration of NIH funded data. | database, neuroimaging, magnetic resonance, mri, image collection, nifti, dicom |
uses: XNAT Central is used by: NIF Data Federation lists: 1000 Functional Connectomes Project lists: studyforrest.org is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 1000 Functional Connectomes Project is related to: NITRC Enhanced Services has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Bipolar Disorder, Schizophrenia, Parkinson's disease, ADHD | NINDS R44 NS074540; NIBIB U24 EB023398 |
PMID:26044860 | Free, Available for download, Freely available | nlx_18447, SCR_015623 | SCR_004162 | NeuroImaging Tools and Resources Collaboratory Image Repository, NITRC Image Repository | 2026-02-14 02:00:56 | 8 | ||||
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NIMH Data Archive Resource Report Resource Website 100+ mentions |
NIMH Data Archive (RRID:SCR_004434) | NDA | data repository, storage service resource, data or information resource, service resource, database | The National Institute of Mental Health Data Archive (NDA) makes available human subjects data collected from hundreds of research projects across many scientific domains. Research data repository for data sharing and collaboration among investigators. Used to accelerate scientific discovery through data sharing across all of mental health and other research communities, data harmonization and reporting of research results. Infrastructure created by National Database for Autism Research (NDAR), Research Domain Criteria Database (RDoCdb), National Database for Clinical Trials related to Mental Illness (NDCT), and NIH Pediatric MRI Repository (PedsMRI). | afni brik, ascii, bshort, bfloat, connectome file format, cifti, clinical neuroinformatics, cor, dicom, imaging genomics, inc, minc2, nifti, os independent, philips par/rec, tex, vrml, phenotype, neuroimaging, genomic, gender, male, female, dti, fmri, mri, spectroscopy, eeg, microarray, snp, cnv, next-generation sequencing, gene regulation, gene expression, genotyping, pedigree, clinical assessment, FASEB list |
uses: HED Tags is used by: National Database for Clinical Trials related to Mental Illness is used by: RDoCdb is used by: NIH Heal Project is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: re3data.org is related to: National Database for Clinical Trials related to Mental Illness is related to: RDoCdb has parent organization: National Institute of Mental Health hosts: GUID Tool |
Autism, Autism spectrum disorder, Asperger Syndrome, Normal control, Sibling control, Parental control, Fragile X syndrome | NIMH ; NINDS ; NIEHS ; NICHD ; Center for Information Technology |
Restricted | nlx_143735, r3d100010717, r3d100012653 | http://www.nitrc.org/projects/ndarportal https://data-archive.nimh.nih.gov/ https://doi.org/10.17616/R37K63 https://doi.org/10.17616/R3XV5P |
http://ndar.nih.gov/ | SCR_004434 | NDAR, National Database for Autism Research, National Institute of Mental Health Data Archive, National Database for Autism Research (NDAR) | 2026-02-14 02:00:57 | 291 | |||
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Phenotypes and eXposures Toolkit Resource Report Resource Website 50+ mentions |
Phenotypes and eXposures Toolkit (RRID:SCR_006532) | PhenX Toolkit | catalog, data set, data or information resource, service resource, narrative resource, database, standard specification | Set of measures intended for use in large-scale genomic studies. Facilitate replication and validation across studies. Includes links to standards and resources in effort to facilitate data harmonization to legacy data. Measurement protocols that address wide range of research domains. Information about each protocol to ensure consistent data collection.Collections of protocols that add depth to Toolkit in specific areas.Tools to help investigators implement measurement protocols. | PhenX project, genome, phenotype, genome-wide association study, genetic variation, genomic study, substance abuse, addiction, substance use, environmental exposure, disease susceptibility, outcome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: RTI International has parent organization: Consensus Measures for Phenotype and Exposure has parent organization: Trans-Omics for Precision Medicine (TOPMed) Program has organization facet: PhenX Phenotypic Terms is organization facet of: Consensus Measures for Phenotype and Exposure |
NHGRI U01 HG004597; NHGRI U41HG007050; NIDA ; OBSSR ; NIMH ; NHLBI ; NIMHD ; TRSP ; NHGRI U24 HG012556; ODP ; NINDS ; NCI |
PMID:21749974 | Restricted | SCR_017475, biotools:PhenX_toolkit, nlx_144102 | https://bio.tools/PhenX_Toolkit | SCR_006532 | Phenotypes and eXposures Toolkit | 2026-02-14 02:01:18 | 61 | ||||
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Rat Genome Database: Neurological Disease Portal Resource Report Resource Website 10+ mentions |
Rat Genome Database: Neurological Disease Portal (RRID:SCR_008685) | data or information resource, portal, topical portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Portal that provides researchers with easy access to data on rat genes, QTLs, strain models, biological processes and pathways related to neurological diseases. This resource also includes dynamic data analysis tools. | gene, analysis, biological, data, database, disease, genome, model, neurological, neuroscience, pathway, phenotype, qtl, rat, research | has parent organization: Medical College of Wisconsin; Wisconsin; USA | Neurological disease | RGD ; NINDS |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33773 | http://rgd.mcw.edu | SCR_008685 | RGD Neurological Disease Portal | 2026-02-14 02:01:43 | 14 | |||||
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Brain Research Institute Biobank Resources Resource Report Resource Website |
Brain Research Institute Biobank Resources (RRID:SCR_008756) | biomaterial supply resource, material resource, tissue bank, brain bank | Brain bank resources which include postmortem human frozen brain tissue and matched cerebrospinal fluid (CSF) and blood available for scientists to search for etiopathogeneses of human disease. The National Neurological Research Specimen Bank and the Multiple Sclerosis Human Neurospecimen Bank maintains a collection of quick frozen and formalin fixed postmortem human brain tissue and frozen cerebrospinal fluid from patients with neurological diseases, including Alzheimer's Disease, amyotrophic lateral sclerosis, depressive disorder/suicide, and epilepsy, among others. Diagnoses are documented by clinical medical records and gross/microscopic neuropathology. The Neuropathology Laboratory at the UCLA Medical Center maintains a bank of frozen, formalin and paraformaldehyde-fixed and paraffin-embedded postmortem human brain tissues and frozen cerebrospinal fluid (CSF) from patients who die with Alzheimer's disease and other dementing and degenerative illnesses, as well as control materials removed in a similar fashion from patients who are neurologically normal. | postmortem, brain, coronal, brain tissue, cerebral spinal fluid, blood, cerebral spinal fluid cell, cell-free cerebral spinal fluid, serum, plasma, buffy coat, frozen, formalin fixed, paraformaldehyde-fixed, paraffin-embedded, neurological disease, alzheimer's disease, amyotrophic lateral sclerosis, depressive disorder, suicide, epilepsy, huntington's disease, multiple sclerosis, parkinson's disease, progressive supranuclear palsy, schizophrenia, stroke, cerebrovascular accident, fronto-temporal dementia, neurologically normal, coronal section, control, clinical data |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Brain Research Institute |
Neurological disease, Alzheimer's disease, Amyotrophic Lateral Sclerosis, Depressive Disorder, Suicide, Epilepsy, Huntington's disease, Multiple Sclerosis, Parkinson's disease, Progressive Supranuclear Palsy, Schizophrenia, Stroke, Cerebrovascular Accident, Fronto-temporal dementia, Aging | NINDS ; NIMH ; National MS Society ; United States Department of Veterans Affairs ; Veterans Affairs West Los Angeles Healthcare Center ; NIA |
Public, Available to the research community | nlx_143996 | http://www.bri.ucla.edu/bri_research/research_resources.asp | SCR_008756 | Brain Research Institute Research Resources, Brain Research Institute Biobanks, BRI Research Resources, BRI Biobanks, BRI Biobank Resources | 2026-02-14 02:01:44 | 0 | |||||
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Mayo Clinic Jacksonville: Neuropathology and Microscopy Resource Report Resource Website 1+ mentions |
Mayo Clinic Jacksonville: Neuropathology and Microscopy (RRID:SCR_008753) | biomaterial supply resource, material resource, tissue bank, brain bank | A brain bank and laboratory focused on memory and motor disorders. Brains are sent to the laboratory for diagnosis and research for the State of Florida Alzheimer Disease Initiative and for the Society for Progressive Supranuclear Palsy. As part of this brain banking function, fixed and frozen brain samples are obtained at autopsy and sent to the laboratory for diagnostic evaluation and for various types of research studies. The major types of analyses performed on the brain samples include neuro-histology, immunohistochemistry, confocal microscopy, electron microscopy and image analysis, as well as immunoassays. The latter are based upon Western blotting and enzyme linked immunoassays. The laboratory has a specific interest in the interface between normal aging and Alzheimer's disease, as well as in non-Alzheimer's degenerative disorders such as Lewy body dementia, corticobasal degeneration, progressive supranuclear palsy and frontotemporal dementia. The primary focus of research on aging is neuropathologic characterization of brains of individuals who had been prospectively and longitudinally evaluated during life. These studies aim to determine differences in a range of biologic parameters in brains of people with normal cognitive, mild cognitive impairment and dementia. Their focus on Parkinson's disease is to identify preclinical Parkinson's disease in order to develop means for early diagnosis. | tissue, brain, fixed, frozen, alzheimer's disease, normal aging, memory disorder, motor disorder, parkinson's disease, progressive supranuclear palsy, lewy body disease, corticobasal degeneration, frontotemporal dementia, dementia, mild cognitive impairment, mouse, neurofibrillary degeneration, postmortem, normal control, autopsy |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Mayo Clinic Florida; Florida; USA has parent organization: Mayo Alzheimer's Disease Research Center has parent organization: Florida Alzheimer's Disease Research Center |
Alzheimer's disease, Aging, Memory disorder, Motor disorder, Parkinson's disease, Progressive Supranuclear Palsy, Lewy Body Disease, Corticobasal Degeneration, Frontotemporal dementia, Dementia, Mild Cognitive Impairment | NIA P50-AG16574; NIA P50-AG25711; NINDS P50-40256 |
nlx_143952 | SCR_008753 | Mayo Clinic Jacksonville: Neuropathology Microscopy, Mayo Clinic Florida: Neuropathology and Microscopy, Neuropathology and Microscopy - Dennis W. Dickson, Mayo Clinic Florida: Neuropathology and Microscopy - Dennis W. Dickson | 2026-02-14 02:01:47 | 1 | |||||||
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BMAP - Brain Molecular Anatomy Project Resource Report Resource Website 1+ mentions |
BMAP - Brain Molecular Anatomy Project (RRID:SCR_008852) | BMAP | data or information resource, funding resource, portal, topical portal | The Brain Molecular Anatomy Project is a trans-NIH project aimed at understanding gene expression and function in the nervous system. BMAP has two major scientific goals: # Gene discovery: to catalog of all the genes expressed in the nervous system, under both normal and abnormal conditions. # Gene expression analysis: to monitor gene expression patterns in the nervous system as a function of cell type, anatomical location, developmental stage, and physiological state, and thus gain insight into gene function. In pursuit of these goals, BMAP has launched several initiatives to provide resources and funding opportunities for the scientific community. These include several Requests for Applications and Requests for Proposals, descriptions of which can be found in this Web site. BMAP is also in the process of establishing physical and electronic resources for the community, including repositories of cDNA clones for nervous system genes, and databases of gene expression information for the nervous system. Most of the BMAP initiatives so far have focused on the mouse as a model species because of the ease of experimental and genetic manipulation of this organism, and because many models of human disease are available in the mouse. However, research in humans, other mammalian species, non-mammalian vertebrates, and invertebrates is also being funded through BMAP. For the convenience of interested investigators, we have established this Web site as a central information resource, focusing on major NIH-sponsored funding opportunities, initiatives, genomic resources available to the research community, courses and scientific meetings related to BMAP initiatives, and selected reports and publications. When appropriate, we will also post initiatives not directly sponsored by BMAP, but which are deemed relevant to its goals. Posting decisions are made by the Trans-NIH BMAP Committee |
has parent organization: National Institutes of Health is parent organization of: BMAP cDNA Resources |
Aging | NINDS ; NIMH ; NIDA ; NEI ; NIA ; NIAAA ; NICHD ; NIDCD ; NIEHS ; NHGRI ; NIGMS |
nlx_149083 | SCR_008852 | Brain Molecular Anatomy Project, Trans-NIH Brain Molecular Anatomy Project | 2026-02-14 02:01:48 | 6 | |||||||
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BRAINSDemonWarp Resource Report Resource Website 1+ mentions |
BRAINSDemonWarp (RRID:SCR_009524) | BRAINSDemonWarp | data processing software, software application, registration software, software resource, image analysis software | A command line program for image registration by using different methods including Thirion and diffeomorphic demons algorithms. The function takes in a template image and a target image along with other optional parameters and registers the template image onto the target image. The resultant deformation fields and metric values can be written to a file. The program uses the Insight Toolkit (www.ITK.org) for all the computations, and can operate on any of the image types supported by that library. This a an ITK based implementation of various forms of Thirion Demons based registration (including diffeomorphic demons registration originating from Tom Vercauteren at INRIA ). | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center has parent organization: University of Iowa; Iowa; USA |
NINDS NS050568; NINDS NS40068; NIMH MH31593; NIMH MH40856 |
nlx_155700 | http://www.nitrc.org/projects/brainsdemonwarp | SCR_009524 | 2026-02-14 02:01:51 | 1 | |||||||
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Olfactory Receptor DataBase Resource Report Resource Website 1+ mentions |
Olfactory Receptor DataBase (RRID:SCR_007830) | ORDB | data repository, storage service resource, data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | Database of vertebrate olfactory receptors genes and proteins. It supports sequencing and analysis of these receptors by providing a comprehensive archive with search tools for this expanding family. The database also incorporates a broad range of chemosensory genes and proteins, including the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfaction receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), and fungal pheromone receptors (FPRs). ORDB currently houses chemosensory receptors for more than 50 organisms. ORDB contains public and private sections which provide tools for investigators to analyze the functions of these very large gene families of G protein-coupled receptors. It also provides links to a local cluster of databases of related information in SenseLab, and to other relevant databases worldwide. The database aims to house all of the known olfactory receptor and chemoreceptor sequences in both nucleotide and amino acid form and serves four main purposes: * It is a repository of olfactory receptor sequences. * It provides tools for sequence analysis. * It supports similarity searches (screens) which reduces duplicate work. * It provides links to other types of receptor information, e.g. 3D models. The database is accessible to two classes of users: * General public www users have full access to all the public sequences, models and resources in the database. * Source laboratories are the laboratories that clone olfactory receptors and submit sequences in the private or public database. They can search any sequence they deposited to the database against any private or public sequence in the database. This user level is suited for laboratories that are actively cloning olfactory receptors. | fungal, pheromone receptor, gene, chemosensory, chemosensory receptor, g protein-coupled receptor, olfaction receptor, protein, receptor, taste papilla receptor, vomeronasal organ receptor, olfactory receptor, nucleotide, amino acid, chemoreceptor sequence, olfactory receptor sequence, chemoreceptor, sequence |
is used by: NIF Data Federation is listed by: 3DVC is related to: Odor Molecules DataBase is related to: Integrated Manually Extracted Annotation has parent organization: Yale School of Medicine; Connecticut; USA |
Aging | Human Brain Project ; NIMH ; NIA ; NICD ; NINDS ; Multidisciplinary University Research Initiative ; National Aeronautics and Space Administration ; NIDCD RO1 DC 009977; NIDCD P01 DC 04732; NLM G08 LM05583 |
PMID:11752336 PMID:9847223 PMID:9218144 |
Public, Private, Acknowledgement requested, The community can contribute to this resource | nif-0000-03213 | SCR_007830 | Olfactory Receptors Database | 2026-02-14 02:01:26 | 4 | ||||
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Computational Neuroanatomy Group Resource Report Resource Website |
Computational Neuroanatomy Group (RRID:SCR_007150) | CNG | data or information resource, software resource, portal, topical portal | Multidisciplinary research team devoted to the study of basic neuroscience with a specific interest in the description and generation of dendritic morphology, and in its effect on neuronal electrophysiology. In the long term, they seek to create large-scale, anatomically plausible neural networks to model entire portions of a mammalian brain (such as a hippocampal slice, or a cortical column). Achievements by the CNG include the development of software for the quantitative analysis of dendritic morphology, the implementation of computational models to simulate neuronal structure, and the synthesis of anatomically accurate, large scale neuronal assemblies in virtual reality. Based on biologically plausible rules and biophysical determinants, they have designed stochastic models that can generate realistic virtual neurons. Quantitative morphological analysis indicates that virtual neurons are statistically compatible with the real data that the model parameters are measured from. Virtual neurons can be generated within an appropriate anatomical context if a system level description of the surrounding tissue is included in the model. In order to simulate anatomically realistic neural networks, axons must be grown as well as dendrites. They have developed a navigation strategy for virtual axons in a voxel substrate. | dendritic morphology, neuronal morphology, neuronal electrophysiology, mammalian brain, neural network, cell, model, morphology, network connectivity, basal ganglia, modeling software, hippocampus, hermissenda learning, caulescence, tree structure, neuron, virtual neural network, morphological class of neuron, virtual neuron, virtual brain, ca3 pyramidal cell, arborvitae, ca1 pyramidal cell, polymorphic cell, dg granule cell, axonal navigation, synaptic connectivity, neuroplasticity, neuroanatomy, neuroinformatics, computation, network model, neural circuit, cellular event, expression, ca3, ca1 pyramidal neuron, digital morphological reconstruction, digital reconstruction, dendrite, axon, neuronal tree, signaling pathway |
has parent organization: George Mason University: Krasnow Institute for Advanced Study is parent organization of: L-Measure is parent organization of: Hippocampus 3D Model |
NINDS ; NIMH ; NSF ; Human Brain Project |
nif-0000-00503 | http://krasnow.gmu.edu/cn3/index3.html | SCR_007150 | Computational Neuroanatomy Group at the Krasnow Institute for Advanced Study | 2026-02-14 02:01:18 | 0 | ||||||
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BrainML Resource Report Resource Website |
BrainML (RRID:SCR_007087) | BrainML | data repository, storage service resource, data or information resource, service resource, narrative resource, database, standard specification |
Set of standards and practices for using XML to facilitate information exchange between user application software and neuroscience data repositories. It allows for common shared library routines to handle most of the data processing, but also supports use of structures specialized to the needs of particular neuroscience communities. This site also serves as a repository for BrainML models. (A BrainML model is an XML Schema and optional vocabulary files describing a data model for electronic representation of neuroscience data, including data types, formats, and controlled vocabulary. ) It focuses on layered definitions built over a common core in order to support community-driven extension. One such extension is provided by the new NIH-supported neuroinformatics initiative of the Society for Neuroscience, which supports the development of expert-derived terminology sets for several areas of neuroscience. Under a cooperative agreement, these term lists will be made available Open Source on this site. The repository function of this site includes the following features: * BrainML models are published in searchable, browsable form. * Registered users may submit new models or new versions of existing models to accommodate data of interest. * BrainML model schema and vocabulary files are made available at fixed URLs to allow software applications to reference them. * Users can check models and/or instance documents for correct format before submitting them using an online validation service. To complement the BrainML modeling language, a set of protocols have been developed for BrainML document exchange between repositories and clients, for indexing of repositories, and for data query. |
format, development, information, mechanism, metaformat, model, neuroinformatics, neuroscience, standard, terminology, validation, vocabulary, xml, data sharing, xml schema compact syntax, xml schema, interoperability, semantics |
is used by: Neurodatabase.org has parent organization: Weill Cornell Medical College; New York; USA |
Human Brain Project ; NIMH MH/NS57153; NINDS MH/NS57153 |
Public, The community can contribute to this resource | nif-0000-21070 | http://brainml.org | SCR_007087 | BrainML.org | 2026-02-14 02:01:26 | 0 | |||||
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ModelDB Resource Report Resource Website 100+ mentions |
ModelDB (RRID:SCR_007271) | ModelDB | data repository, storage service resource, data or information resource, service resource, database | Curated database of published models so that they can be openly accessed, downloaded, and tested to support computational neuroscience. Provides accessible location for storing and efficiently retrieving computational neuroscience models.Coupled with NeuronDB. Models can be coded in any language for any environment. Model code can be viewed before downloading and browsers can be set to auto-launch the models. The model source code has to be available from publicly accessible online repository or WWW site. Original source code is used to generate simulation results from which authors derived their published insights and conclusions. | repository, collection, network, neuron, computational, neuroscience, model, simulation, neural, data |
is used by: NIF Data Federation lists: ModelRun is listed by: 3DVC is listed by: Biositemaps is listed by: Integrated Models is related to: SimToolDB is related to: NeuronDB is related to: NeuronVisio is related to: Integrated Manually Extracted Annotation is related to: Allen Institute for Brain Science has parent organization: Yale University; Connecticut; USA works with: MicrocircuitDB |
NIMH ; NINDS ; NCI ; Human Brain Project ; NIDCD P01 DC004732; NIDCD R01 DC009977 |
PMID:15218350 PMID:15055399 PMID:8930855 |
Free, Freely available, Acknowledgement requested | nif-0000-00004, r3d100011330 | https://doi.org/10.17616/R3P61F | SCR_007271 | Model_DB, Model Database, Model DB, Model-DB | 2026-02-14 02:01:23 | 304 | ||||
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Cognitive and Emotional Health Project: The Healthy Brain Resource Report Resource Website |
Cognitive and Emotional Health Project: The Healthy Brain (RRID:SCR_007390) | CEHP | data or information resource, portal, database, topical portal | Trans-NIH project to assess the state of longitudinal and epidemiological research on demographic, social and biologic determinants of cognitive and emotional health in aging adults and the pathways by which cognitive and emotional health may reciprocally influence each other. A database of large scale longitudinal study relevant to healthy aging in 4 domains was created based on responses of investigators conducting these studies and is available for query. The four domains are: * Cognitive Health * Emotional Health * Demographic and Social Factors * Biomedical and Physiologic Factors | healthy aging, cognitive health, demographics, longitudinal study, aging study, late adult human, cognition, emotion, adult human, longitudinal, epidemiology, psychosocial, questionnaire, social factor, physiologic factor | has parent organization: National Institutes of Health | Cognitive impairment, Emotional disorder, Aging | NIA ; NIMH ; NINDS |
nif-0000-00421 | SCR_007390 | Cognitive and Emotional Health Project (CEHP), Cognitive Emotional Health Project: The Healthy Brain, Cognitive Emotional Health Project, Cognitive and Emotional Health Project | 2026-02-14 02:01:31 | 0 | ||||||
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National NeuroAIDS Tissue Consortium Resource Report Resource Website 10+ mentions |
National NeuroAIDS Tissue Consortium (RRID:SCR_007323) | NNTC | biomaterial supply resource, material resource, tissue bank, brain bank | Collects, stores, and distributes samples of nervous tissue, cerebrospinal fluid, blood, and other tissue from HIV-infected individuals. The NNTC mission is to bolster research on the effects of HIV infection on human brain by providing high-quality, well-characterized tissue samples from patients who died with HIV, and for whom comprehensive neuromedical and neuropsychiatric data were gathered antemortem. Researchers can request tissues from patients who have been characterized by: * degree of neurobehavioral impairment * neurological and other clinical diagnoses * history of drug use * antiretroviral treatments * blood and CSF viral load * neuropathological diagnosis The NNTC encourages external researchers to submit tissue requests for ancillary studies. The Specimen Query Tool is a web-based utility that allows researchers to quickly sort and identify appropriate NNTC specimens to support their research projects. The results generated by the tool reflect the inventory at a previous time. Actual availability at the local repositories may vary as specimens are added or distributed to other investigators. | human immunodeficiency virus, nervous tissue, cerebral spinal fluid, blood, tissue, brain, neuromedical data, neuropsychiatric data, tissue, plasma, peripheral blood mononuclear cell, serum, urine, spinal cord, nervous tissue, pituitary gland, trigeminal ganglia, dorsal root ganglion, peripheral nerve, lymph node, liver, spleen, adipose tissue, bone marrow, muscle, hair, heart, thymus, kidney, lung, eye, brain, ante-mortem, post-mortem, normal, subsyndromic, minor cognitive motor disorder, hiv - associated dementia, cytomegalovirus encephalitis, neurological impairment, traumatic brain injury, neurocognitive disease, frozen, fixed, aids, one mind tbi, asymptomatic neurocognitive impairment, minor cognitive disorder, gene array, snp |
is listed by: One Mind Biospecimen Bank Listing is related to: Manhattan HIV Brain Bank is related to: CHARTER - CNS HIV Antiretroviral Therapy Effects Research |
Human immunodeficiency virus, Neurocognitive disease, Normal, Subsyndromic, Minor Cognitive Motor Disorder, HIV - Associated Dementia, Cytomegalovirus Encephalitis, Neurological impairment, Infectious disease | NIMH ; NINDS ; NIH Blueprint for Neuroscience Research |
Public: The NNTC encourages external researchers to submit tissue requests for ancillary studies. | nif-0000-00193 | SCR_007323 | nntc.org, nntc | 2026-02-14 02:01:21 | 11 |
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