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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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NIF Registry Automated Crawl Data Resource Report Resource Website 1+ mentions |
NIF Registry Automated Crawl Data (RRID:SCR_012862) | NIF Registry Automated Crawl Data, RDP | data or information resource, data set | An automatic pipeline based on an algorithm that identifies new resources in publications every month to assist the efficiency of NIF curators. The pipeline is also able to find the last time the resource's webpage was updated and whether the URL is still valid. This can assist the curator in knowing which resources need attention. Additionally, the pipeline identifies publications that reference existing NIF Registry resources as this is also of interest. These mentions are available through the Data Federation version of the NIF Registry, http://neuinfo.org/nif/nifgwt.html?query=nlx_144509 The RDF is based on an algorithm on how related it is to neuroscience. (hits of neuroscience related terms). Each potential resource gets assigned a score (based on how related it is to neuroscience) and the resources are then ranked and a list is generated. | resource, mention, update |
is used by: NIF Data Federation is used by: Integrated Datasets is related to: PubMed Central is related to: Integrated Auto-Extracted Annotation is related to: Integrated Manually Extracted Annotation is related to: PubMed has parent organization: Neuroscience Information Framework |
U.S. Department of Health and Human Services ; NIH Blueprint for Neuroscience Research ; NIDA contract HHSN27120080035C |
PMID:22434839 | Individual resources within the data set are licensed by the respective owners. The data set of these resources is freely available for use and distribution by you subject to citation of NIF in accordance with the Creative Commons Attribution License. | nlx_144525 | http://lucene1.neuinfo.org/nif_resource/current/ | SCR_012862 | Resource Discovery Pipeline | 2026-09-03 05:08:00 | 2 | ||||
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NeuroVault Resource Report Resource Website 100+ mentions |
NeuroVault (RRID:SCR_003806) | data repository, service resource, storage service resource | Data repository where researchers can publicly store and share unthresholded statistical brain activation maps produced by MRI and PET studies. | neuroimaging, fmri, mri, functional mri assay, pet, brain activation map, brain, statistical map, neuroimaging repository |
uses: NeuroSynth is used by: NIF Data Federation is used by: Integrated Datasets is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Stanford Center for Reproducible Neuroscience |
International Neuroinformatics Coordinating Facility ; Max-Planck-Gesellschaft ; Max Planck Institute for Human Cognitive and Brain Sciences; Leipzig; Germany |
Creative Commons Zero License | nlx_158106, r3d100012842 | http://neurovault.org/api, https://doi.org/10.17616/R31NJMEI | SCR_003806 | NeuroVault - A public repository of unthresholded brain activation maps | 2026-09-03 04:46:37 | 363 | ||||||
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PubChem Resource Report Resource Website 10000+ mentions |
PubChem (RRID:SCR_004284) | data or information resource, data repository, database, service resource, storage service resource | Collection of information about chemical structures and biological properties of small molecules and siRNA reagents hosted by the National Center for Biotechnology Information (NCBI). | collection, information, data, chemical, structure, biological, property, small, molecule, siRNA reagent, bio.tools |
uses: ChEMBL is used by: NIF Data Federation is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: GEROprotectors is listed by: OMICtools is listed by: re3data.org is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is related to: NCBI Structure is related to: Molecular Libraries Program is related to: NIH Data Sharing Repositories is related to: PubChem BioAssay has parent organization: NCBI is parent organization of: PubChem Substance works with: MiMeDB |
NLM | PMID:21418625 PMID:21272340 PMID:20970519 PMID:20298522 PMID:19825798 |
Free, Freely Available | biotools:pubchem, nlx_42691, nlx_29861, r3d100010538, OMICS_01587 | https://bio.tools/pubchem, https://doi.org/10.17616/R3GW37 | SCR_004284 | 2026-09-03 04:47:03 | 15598 | ||||||
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NITRC-IR Resource Report Resource Website 1+ mentions |
NITRC-IR (RRID:SCR_004162) | NITRC IR | catalog, data or information resource, data repository, database, image database, image repository, service resource, storage service resource | 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 | NIBIB U24 EB023398; NINDS R44 NS074540 |
PMID:26044860 | Free, Available for download, Freely available | nlx_18447, SCR_015623 | SCR_004162 | NeuroImaging Tools and Resources Collaboratory Image Repository, NITRC Image Repository | 2026-09-03 04:47:02 | 8 | ||||
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BrainSpan: RNA-Seq exons Resource Report Resource Website |
BrainSpan: RNA-Seq exons (RRID:SCR_004344) | BrainSpan: RNA-Seq exons | data or information resource, atlas, expression atlas | BrainSpan, an atlas of the developing human brain, is designed as a foundational resource for studying transcriptional mechanisms involved in human brain development. One of the BrainSpan datasets, RNA-Seq exons, is presented. It is a downloadable archive of files containing normalized RNA-Seq expression values for analysis. | brain, development, brain development, exon, rna-seq, expression value, expression |
is used by: NIF Data Federation has parent organization: Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain) |
nlx_37081 | SCR_004344 | BrainSpan - RNA-Seq exons | 2026-09-03 04:47:10 | 0 | ||||||||
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NeuroPod Resource Report Resource Website |
NeuroPod (RRID:SCR_004329) | NeuroPod | data or information resource, narrative resource, podcast | NeuroPod is the neuroscience podcast from Nature, produced in association with the Dana Foundation. Each month, join us as we delve into the latest research on the brain, from its molecular makings to the mysteries of the mind. We''ll also be bringing you the latest news from neuroscience conferences around the globe, along with special reports on hot areas in neuroscience. |
is used by: NIF Data Federation is related to: Integrated Podcasts |
The Dana Foundation | nlx_34737 | SCR_004329 | NeuroPod Podcasts | 2026-09-03 04:47:06 | 0 | ||||||||
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Gray Matters Resource Report Resource Website |
Gray Matters (RRID:SCR_004433) | data or information resource, narrative resource, podcast | THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 06, 2013. Gray Matters is a radio series on brain topics that has been produced since 1994 by Public Radio International in association with the Dana Alliance. More than 25 programs have been created on topics ranging from stress, neuroethics, learning throughout life and sports, fitness and the Brain. Dana Alliance members serve as advisers to Gray Matters programming and are interviewed during the programs. The transcripts are also available. |
is used by: NIF Data Federation is related to: Integrated Podcasts |
The Dana Foundation | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_54435 | SCR_004433 | Gray Matters Radio Series | 2026-09-03 04:47:15 | 0 | ||||||||
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Health.Data.gov Resource Report Resource Website 10+ mentions |
Health.Data.gov (RRID:SCR_004386) | data or information resource, database, software resource | Public, high-value federal datasets, tools, and applications using data about health and health care gathered from agencies across the U.S. government. | health, medicare, medicaid, epidemiology, treatment, population statistics, biomedical research, safety, administrative, health care cost, quality measurement, health care provider, children's health, child, health care, data set |
is used by: NIF Data Federation is used by: Integrated Datasets has parent organization: Data.gov |
Public, Acknowledgement requested | r3d100010593, nlx_143714 | https://doi.org/10.17616/R3589H | http://www.data.gov/communities/node/81/data_tools | SCR_004386 | US HealthData Gov, Health Data and Tools, Health.Data.gov Data Tools, Health Data and Tools Available on Data.gov | 2026-09-03 04:47:09 | 20 | ||||||
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NIF Web Services Resource Report Resource Website |
NIF Web Services (RRID:SCR_001631) | NIF Web Services | data access protocol, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Representational State Transfer (REST) model based service for accessing a set of Neuroscience Information Framework (NIF) data through a fixed set of operations. They are defined by a WADL file which allows clients to automatically generate code for these services. The services (AnnotateService, FederationService, LdaService, LexicalService, LiteratureService, QueryService, SummaryService, VocabularyService) include the ability to: * Retrieve a federation summary, e.g., http://nif-services.neuinfo.org/servicesv1/v1/summary?q=* * Retrieve data records from a NIF federation source for a search, e.g., http://nif-services.neuinfo.org/servicesv1/v1/federation/data/nif-0000-00007-1?q=purkinje * Retrieve registry data records from NIF, e.g., http://nif-services.neuinfo.org/servicesv1/v1/federation/data/nlx_144509-1?q=miame * Retrieve a complete search summary, e.g., http://nif-services.neuinfo.org/servicesv1/v1/federation/search?q=cortex * Retrieve NIF auto-complete suggestions, e.g., http://nif-services.neuinfo.org/servicesv1/v1/vocabulary?prefix=hippo * Use the NIF annotator for arbitrary text, e.g., http://nif-services.neuinfo.org/servicesv1/v1/annotate?content=The%20cerebellum%20is%20a%20wonderful%20thing These services are documented for developers in the WADL file (and client stubs should have the comments embedded in them). Visit, http://nif-services.neuinfo.org/servicesv1/ for more information | rest, data sharing, wadl |
is used by: NIF Data Federation is related to: SciCrunch Registry is related to: NIF Literature is related to: OntoQuest has parent organization: Neuroscience Information Framework |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153899 | SCR_001631 | Neuroscience Information Framework Web Services | 2026-09-03 04:44:58 | 0 | |||||||
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ASAP Resource Report Resource Website 50+ mentions |
ASAP (RRID:SCR_001849) | ASAP | data or information resource, data repository, database, service resource, storage service resource | Database and web interface developed to store, update and distribute genome sequence data and gene expression data. ASAP was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, and gene expression data from preliminary experiments. Use of some of this preliminary data is conditional, and it is the users responsibility to read the data release policy and to verify that any use of specific data obtained through ASAP is consistent with this policy. There are four main routes to viewing the information in ASAP: # a summary page, # a form to query the genome annotations, # a form to query strain collections, and # a form to query the experimental data. Navigational buttons appear on every page allowing users to jump to any of these four points., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene expression, genome, genome sequence, multiple genome sequence, post sequencing functional analysis, preliminary experiment, blast, annotation, data analysis service |
is used by: NIF Data Federation is listed by: SoftCite is related to: AmiGO has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
USDA 2001-52100-11316; NIGMS GM62994-02; NIGMS GM35682-15A1 |
PMID:12519969 | Free, Freely available | nif-0000-02571, r3d100010666 | https://omictools.com/asap-3-tool | SCR_001849 | A Systematic Annotation Package for Community Analysis of Genome, ASAP: a systematic annotation package for community analysis of genomes, A systematic annotation package for community analysis of genomes | 2026-09-03 04:45:04 | 53 | ||||
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Rafael Yustes Laboratory Resource Report Resource Website |
Rafael Yustes Laboratory (RRID:SCR_001845) | Yuste Lab | data or information resource, database, image collection, laboratory portal, organization portal, portal | Laboratory that aims to understand the function of the cortical microcircuit by reverse-engineering of the cortical microcircuit using the mouse neocortex in vitro and in vivo as their experimental preparations. The techniques applied are electrophysiology, anatomy, and a variety of optical methods, including infrared-DIC, voltage- and ion-sensitive dye imaging with confocal, two-photon and second harmonic microscopy. They also use laser uncaging, biolistics, electroporation, electron microscopy and numerical simulations, and make extensive use of genetically modified mouse strains. They focus is on two major questions: (1) What is the function of dendritic spines? (2) What are the multicellular patterns of activity under spontaneous or evoked activation of the circuit? Resources include: * Cell Reconstructions: Cell Database, PDF Images, .DAT Files * Circuit Diagrams: Full Circuit Diagram, Inhibitory Circuit Diagram, Excitatory Circuit Diagram, Simplified Circuit Diagram, Layer to Layer Simplified Circuit, Circuit diagram references | electron microscopy, electrophoration, electrophysiology, anatomy, biolistics, circuit, confocal, cortical, infrared-dic, ion sensitive dye imaging, voltage sensitive dye imaging, microcircuit, microscopy, mouse, multicellular, neocortex, optical method, second harmonic, two-photon, laser uncaging, cortical circuit, dendritic spine, cortical microcircuit, canonical microcircuit, cell reconstruction, cell, image, inhibitory circuit, excitatory circuit |
is used by: NIF Data Federation has parent organization: Columbia University; New York; USA |
Free, Freely available | nif-0000-10407 | SCR_001845 | Rafael Yuste''s Laboratory, Cortical Circuits and Dendritic Spines | 2026-09-03 04:45:09 | 0 | |||||||
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AutDB Resource Report Resource Website 50+ mentions |
AutDB (RRID:SCR_001872) | AutDB | data or information resource, data repository, database, service resource, storage service resource | Curated public database for autism research built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The genetic information includes data from linkage and association studies, cytogenetic abnormalities, and specific mutations associated with ASD. New gene submissions are welcome. Modules: * Human Gene: thoroughly annotated list of genes that have been studied in the context of autism, with information on the genes themselves, relevant references from the literature, and the nature of the evidence. Uniquely, SFARI Gene incorporates information on both common and rare variants. * Animal Model: information about lines of genetically modified mice that represent potential models of autism. This information includes the nature of the targeting construct, the background strain and, most importantly, a thorough summary of the phenotypic features of the mice that are most relevant to autism. * Protein Interaction (PIN): compilation of all known direct protein interactions for those gene products implicated in autism. It presents both graphical and tabular views of interactomes, highlighting connections between autism candidate genes. Each protein interaction is manually verified by consultation with the primary reference. * Copy Number Variant (CNV): a parallel resource providing genetic information about all known copy number variants linked to autism. * Gene Scoring: includes a "score" for each autism candidate gene, based on an assessment of the strength of human genetic evidence. | duplication, gene, genetic syndrome, genetic variation, allelic, autism, autism spectrum disorder, deletion, molecular function, molecular genetics, single-gene disruption, genetic association, genetic variation, allelic variant, copy number variant, cytogenetic, disruption, idiopathic asd, monogenic, mutation, polymorphism, human, animal model, mouse, protein interaction, sfari gene, phenotype, protein interaction, gene scoring, systems biology |
is listed by: NIF Data Federation is listed by: 3DVC is related to: Integrated Manually Extracted Annotation has parent organization: SFARI - Simons Foundation Autism Research Initiative |
Autism Spectrum Disorder, Autism | MindSpec: Informatics for Neurodevelopmental Conditions | PMID:19015121 | Free, Freely available | nif-0000-02587 | http://www.mindspec.org/products/autdb/, https://gene.sfari.org/autdb/ | http://autism.mindspec.org/autdb/ | SCR_001872 | AutDB - An Interface to Autism Research, Simons Foundation Autism Research Initiative Gene: Autism Database, SFARI Gene: AutDB, SFARI Gene, AutDB: a Genetic Database for Autism Spectrum Disorders | 2026-09-03 04:45:01 | 64 | ||
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NIH VideoCasting Resource Report Resource Website 1+ mentions |
NIH VideoCasting (RRID:SCR_001885) | VideoCast | data or information resource, narrative resource, podcast, video resource | VideoCasting of special NIH events, seminars, conferences, meetings and lectures available to viewers on the NIH network and the Internet from the VideoCast web site. VideoCasting is the method of electronically streaming digitally encoded video and audio data from a server to a client. VideoCast is often referred to as streaming video. Streaming files are not downloaded, but rather are broadcast in a manner similar to television broadcasts. The videos are processed by a compression program into a streaming format and delivered in a staggered fashion to minimize impact upon the network and maximize the experience of the content for the viewer. When users request a streaming file they will receive an initial burst of data after a short delay (file latency). While content is being viewed, the streaming server machine and software continues to stream data in such a manner that the viewer experiences no break in the content. CIT can broadcast your seminar, conference or meeting live to a world-wide audience over the Internet as a real-time streaming video. The event can be recorded and made available for viewers to watch at their convenience as an on-demand video or a downloadable podcast. CIT can also broadcast NIH-only or HHS-only content. | event, seminar, conference, meeting, lecture, multimedia |
is used by: NIF Data Federation is used by: Integrated Videos has parent organization: National Institutes of Health |
NIH | Public, The community can contribute to this resource | nif-0000-10454 | SCR_001885 | NIH VideoCasts, NIH VideoCasting and Podcasting, NIH VideoCasting Podcasting, NIH VideoCast, NIH Videos | 2026-09-03 04:45:06 | 2 | ||||||
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Brain Machine Interface Platform Resource Report Resource Website |
Brain Machine Interface Platform (RRID:SCR_001813) | BMI PF, BMI-PF | bibliography, data or information resource, data repository, database, service resource, software repository, software resource, storage service resource | Databases of accumulating BMI (Brain Machine Interfaces)-related experimental data, mathematical models, and tools generated in neuroscience, computational theory, and robotics. Databases include: # Database of BMI (Brain Machine Interfaces)-related papers: More than 3500 BMI-related papers are registered. Each paper has original tags, for example, recording method and subject, for easy searching. # Database of original contents: BMI-related materials (Movie, Picture, Data, Program) provided by scientists. # Database of BMI-related research sites: 185 BMI-related research sites in the world (university, institute and company) are registered. The research site can be searched either by the location using clickable map or by the field of interest. # Database of BMI-related materials: Links to BMI-related materials (Movie, Picture, Document, Data, Program) are listed. You can easily find materials of your interest since each material is classified into research field. # BMI-related column: The columns are written by researchers specialized in BMI. Original contents include: * Neuronal activity during performance of a memory-guided movement * Reconstructed visual images from human fMRI activity * fMRI data and program for visual image reconstruction * Brain sections of monkeys, stained for several gene markers * Cortical Box Method: The Cortical box method is an analytical method that standardizes the serial coronal sections of rodent cortex for quantitative analysis. * Multineuron activity in monkey prefrontal cortex * Monkey Atlas: **Brain sections of monkeys, stained for AChE, ER81 mRNA and Sema3E mRNA - These pictures are low-resolution photos of serial brain sections of monkeys, stained for AChE as well as for ER81 and Sema3E mRNAs. The compressed file contains JPEG photos and html files for web browser navigation. Other materials are available at our website BraInSitu dedicated for in situ hybridization resources for brains. BraInSitu http://www.nibb.ac.jp/brish/indexE.html ** MRI Brain Atlas of Japanese Snow Monkey (Macaca Fuscata) at different ages - MRI Brain Atlas of Japanese Snow Monkey (Macaca Fuscata) at different ages ** The Stereotaxic MRI Brain Atlas of Japanese Snow Monkey - The Stereotaxic MRI Brain Atlas of Japanese Snow Monkey * Monkey M1 BMI ** m-file for checking the results of wrist angle estimation- This program is m-file to train the relationship between joint angles and EMG signals using artificial neural network. The input signals are four EMG signals and the output signals are joint angles of wrist, such as flexion/extension, radial deviation/uln ** m-file for training of wrist angle estimation -This program is m-file to train the relationship between joint angles and EMG signals using artificial neural network. The input signals are four EMG signals and the output signals are joint angles of wrist, such as flexion/extension, radial deviation/ulnar deviation.ar deviation. ** M1 Neuronal Activity during monkey performing a motor task - video/x-ms-wmv ** Muscle tension - To estimate muscle tension from raw emg signal ** raw EMG signal - Raw EMG signal for 5 seconds ** training data of wrist angle and emg signal - This program is m-file to train the relationship between joint angles and EMG signals using artificial neural network. The input signals are four EMG signals and the output signals are joint angles of wrist, such as flexion/extension, radial deviation/ulnar deviation. ** Weight file of neural network - This program is m-file to train the relationship between joint angles and EMG signals using artificial neural network. The input signals are four EMG signals and the output signals are joint angles of wrist, such as flexion/extension, radial deviation/ulnar deviation. * Multineuron activity in monkey prefrontal cortex: Multineuron activity in monkey prefrontal cortex recorded by 3 tetrodes. Vertical 4 lines indicate one tetrode. Adjacent tetrodes are around 500 micron apart to each other. | experimental data, brain, collaboration, computational theory, cortex, mathematical model, model, monkey, motor, neuroscience, paper, physiology, robotics, rodent, sensor, signal processing, theory, tool, video, fmri, human, atlas |
is used by: NIF Data Federation is related to: Integrated Software has parent organization: RIKEN Brain Science Institute |
Free, Freely available | nif-0000-10378 | SCR_001813 | BMI (Brain Machine Interface) Platform, BMI platform, BMI-platform, Brain Machine Interface Platform (BMI PF) | 2026-09-03 04:44:59 | 0 | |||||||
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Addgene Resource Report Resource Website 10000+ mentions |
Addgene (RRID:SCR_002037) | data or information resource, material storage repository, organization portal, portal, service resource, storage service resource | Non-profit plasmid repository dedicated to helping scientists around the world share high-quality plasmids. Facilitates archiving and distributing DNA-based research reagents and associated data to scientists worldwide. Repository contains over 65,000 plasmids, including special collections on CRISPR, fluorescent proteins, and ready-to-use viral preparations. There is no cost for scientists to deposit plasmids, which saves time and money associated with shipping plasmids themselves. All plasmids are fully sequenced for validation and sequencing data is openly available. We handle the appropriate Material Transfer Agreements (MTA) with institutions, facilitating open exchange and offering intellectual property and liability protection for depositing scientists. Furthermore, we curate free educational resources for the scientific community including a blog, eBooks, video protocols, and detailed molecular biology resources. | RIN, Resource Information Network, plasmid, molecular biology, sequence alignment, repository, bio.tools, FASEB list, RRID Community Authority |
uses: GenomeCompiler is used by: NIF Data Federation is used by: NIDDK Information Network (dkNET) is used by: Structural Genomics Consortium is used by: ZCre is listed by: One Mind Biospecimen Bank Listing is listed by: DataCite is listed by: re3data.org is listed by: bio.tools is listed by: Debian is listed by: Resource Information Network is related to: zfishbook is related to: GenomeCompiler is related to: Phoenix is related to: Integrated Manually Extracted Annotation is related to: Genetic Tools Atlas is parent organization of: Vector Database |
Fees collected from plasmid sales support operation of the repository | DOI:10.1093/nar/gku893 | Free (deposit of plasmids), Limited (Some available to academic and non-profits, For-profit entities, Commercial license), Material Transfer Agreement, Non-commercial, Acknowledgement required, Copyrighted, For informational purposes only, Commercial with written consent, The community can contribute to this resource | ISNI: 0000 0004 5912 0787, Wikidata: Q4681063, grid.482682.2, biotools:Addgene, nif-0000-11872 | https://ror.org/01nn1pw54, https://bio.tools/Addgene | SCR_002037 | Addgene Repository, Addgene Plasmid Database | 2026-09-03 04:45:14 | 54912 | |||||
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Candida Genome Database Resource Report Resource Website 500+ mentions |
Candida Genome Database (RRID:SCR_002036) | CGD, CGD LOCUS, CGD REF | data or information resource, data repository, database, service resource, storage service resource | Database of genetic and molecular biological information about Candida albicans. Contains information about genes and proteins, descriptions and classifications of their biological roles, molecular functions, and subcellular localizations, gene, protein, and chromosome sequence information, tools for analysis and comparison of sequences and links to literature information. Each CGD gene or open reading frame has an individual Locus Page. Genetic loci that are not tied to DNA sequence also have Locus Pages. Provides Gene Ontology, GO, to all its users. Three ontologies that comprise GO (Molecular Function, Cellular Component, and Biological Process) are used by multiple databases to annotate gene products, so that this common vocabulary can be used to compare gene products across species. Development of ontologies is ongoing in order to incorporate new information. Data submissions are welcome. | protein, chromosome, classification, gene, genome, candidiasis, thrush, yeast, yeast gene, yeast genome, candida albicans, candida glabrata, data analysis service, biological role, molecular function, subcellular localization, chromosome sequence, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: ASPGD is related to: Gene Ontology has parent organization: Stanford University School of Medicine; California; USA |
NIDCR DE015873 | PMID:19808938 | Free, Available for download, Freely available | biotools:cgd, nif-0000-02634, r3d100010617 | https://bio.tools/cgd | SCR_002036 | 2026-09-03 04:45:19 | 506 | |||||
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NIDA Data Share Resource Report Resource Website 10+ mentions |
NIDA Data Share (RRID:SCR_002002) | catalog, data or information resource, data repository, database, service resource, storage service resource | Website which allows data from completed clinical trials to be distributed to investigators and public. Researchers can download de-identified data from completed NIDA clinical trial studies to conduct analyses that improve quality of drug abuse treatment. Incorporates data from Division of Therapeutics and Medical Consequences and Center for Clinical Trials Network. | drug of abuse, clinical, data, data sharing, human, clinical trial, experimental protocol, addiction, drug, addiction, data set, substance abuse |
is used by: NIF Data Federation is used by: Integrated Datasets is used by: NIH Heal Project is recommended by: National Library of Medicine is recommended by: BRAIN Initiative is listed by: re3data.org is related to: NIDA Networking Project: Facilitating information exchange and research collaboration is related to: Integrated Manually Extracted Annotation has parent organization: National Drug Abuse Treatment Clinical Trials Network |
NIDA | Restricted | nif-0000-21981 | http://www.ctndatashare.org/ | SCR_002002 | NIDA Clinical Trials Data Share, CTN database, CTN Data Share, NIDA CTN Data Share | 2026-09-03 04:45:09 | 25 | ||||||
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NeuroMorpho.Org Resource Report Resource Website 100+ mentions |
NeuroMorpho.Org (RRID:SCR_002145) | data or information resource, data repository, database, service resource, storage service resource | Centrally curated inventory of digitally reconstructed neurons associated with peer-reviewed publications that contains some of the most complete axonal arborizations digitally available in the community. Each neuron is represented by a unique identifier, general information (metadata), the original and standardized ASCII files of the digital morphological reconstruction, and a set of morphometric features. It contains contributions from over 100 laboratories worldwide and is continuously updated as new morphological reconstructions are collected, published, and shared. Users may browse by species, brain region, cell type or lab name. Users can also download morphological reconstructions for research and analysis. Deposition and distribution of reconstruction files ultimately prevents data loss. Centralized curation and annotation aims at minimizing the effort required by data owners while ensuring a unified format. It also provides a one-stop entry point for all available reconstructions, thus maximizing data visibility and impact. | neuron, morphological reconstruction, morphometry, axonal arborization, digital neuronal reconstruction, neuronal reconstruction, neuronal morphology, data sharing, annotation, brain region, neocortex, digital reconstruction, neurogenetics, neurochemistry, neuroscience, neurology, FASEB list |
is used by: NIF Data Federation is used by: BICCN 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: re3data.org is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: DONE: Detection of Outlier NEurons is related to: NIF Literature is related to: Computational Neurobiology and Imaging Center is related to: Integrated Manually Extracted Annotation is related to: xyz2swc is related to: Allen Institute for Brain Science has parent organization: George Mason University; Virginia; USA is parent organization of: NeuroMorpho.Org species ontology is parent organization of: NeuroMorpho.Org species ontology old |
MURI ONR N000141010198; NINDS R01 NS39600 |
PMID:17728438 PMID:16552417 PMID:18949582 |
Free, Available for download, Freely available | nif-0000-00006, r3d100010107 | http://www.nitrc.org/projects/neuromorpho_org, http://neuromorpho.org/, https://doi.org/10.17616/R3WW2K | SCR_002145 | Neuro Morpho, NeuroMorpho.org, NeuroMorpho | 2026-09-03 04:45:17 | 123 | |||||
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Cell Centered Database Resource Report Resource Website 10+ mentions |
Cell Centered Database (RRID:SCR_002168) | CCDB | data or information resource, data repository, database, image repository, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented June 5, 2017. It has been merged with Cell Image Library. Database for sharing and mining cellular and subcellular high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated imaging that makes unique and valuable datasets available to the scientific community for visualization, reuse and reanalysis. Techniques range from wide field mosaics taken with multiphoton microscopy to 3D reconstructions of cellular ultrastructure using electron tomography. Contributions from the community are welcome. The CCDB was designed around the process of reconstruction from 2D micrographs, capturing key steps in the process from experiment to analysis. The CCDB refers to the set of images taken from microscope the as the Microscopy Product. The microscopy product refers to a set of related 2D images taken by light (epifluorescence, transmitted light, confocal or multiphoton) or electron microscopy (conventional or high voltage transmission electron microscopy). These image sets may comprise a tilt series, optical section series, through focus series, serial sections, mosaics, time series or a set of survey sections taken in a single microscopy session that are not related in any systematic way. A given set of data may be more than one product, for example, it is possible for a set of images to be both a mosaic and a tilt series. The Microscopy Product ID serves as the accession number for the CCDB. All microscopy products must belong to a project and be stored along with key specimen preparation details. Each project receives a unique Project ID that groups together related microscopy products. Many of the datasets come from published literature, but publication is not a prerequisite for inclusion in the CCDB. Any datasets that are of high quality and interest to the scientific community can be included in the CCDB. | electron microscope, light microscopy, electron tomography, electron microscopy, image, cell, microscopy, tomography |
is used by: NIF Data Federation is used by: Integrated Datasets is listed by: re3data.org is related to: Cell Image Library (CIL) is related to: Cell Image Library (CIL) is related to: Whole Brain Catalog is related to: Integrated Manually Extracted Annotation has parent organization: University of California at San Diego; California; USA has parent organization: University of California; San Diego;National Center for Microscopy and Imaging Research - NCMIR is parent organization of: Subcellular Anatomy Ontology is parent organization of: CCDB Image Converter is parent organization of: Jinx is parent organization of: WebImageBrowser is parent organization of: Image Workflow is parent organization of: Animal Imaging Database |
PMID:18054501 PMID:12160711 |
Free, Freely available | nif-0000-00007, r3d100000018 | SCR_002168 | CCDB, Cell-Centered Database | 2026-09-03 04:45:15 | 31 | ||||||
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Community Structure-Activity Resource Resource Report Resource Website 10+ mentions |
Community Structure-Activity Resource (RRID:SCR_002206) | CSAR | data or information resource, data repository, data set, service resource, storage service resource | Experimental datasets of crystal structures and binding affinities for diverse protein-ligand complexes. Some datasets are generated in house while others are collected from the literature or deposited by academic labs, national centers, and the pharmaceutical industry. For the community to improve their approaches, they need exceptional datasets to train scoring functions and develop new docking algorithms. They aim to provide the highest quality data for a diverse collection of proteins and small molecule ligands. They need input from the community in developing target priorities. Ideal targets will have many high-quality crystal structures (apo and 10-20 bound to diverse ligands) and affinity data for 25 compounds that range in size, scaffold, and logP. It is best if the ligand set has several congeneric series that span a broad range of affinity, with low nanomolar to mid-micromolar being most desirable. They prefer Kd data over Ki data over IC50 data (no % activity data). They will determine solubility, pKa, logP/logD data for the ligands whenever possible. They have augmented some donated IC50 data by determining Kon/Koff and ITC data. | crystal structure, binding affinity, protein-ligand complex, protein, small molecule, ligand, compound |
is used by: NIF Data Federation is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: University of Michigan; Ann Arbor; USA |
NIGMS | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154720 | SCR_002206 | 2026-09-03 04:45:13 | 16 |
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