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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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XNAT Central Resource Report Resource Website 10+ mentions |
XNAT Central (RRID:SCR_006235) | XNAT Central | storage service resource, service resource, data repository, data or information resource, image repository, database | Online repository of open access images including MR Sessions, MRI, Freesurfer APARC, Freesurfer ASEGs, Clinical Assessments, Atlas Scaling Factors, and Fast Segmentations data. CENTRAL currently contains 374 Projects, 3808 Subjects, and 5174 Imaging Sessions (June 2014). Central is powered by XNAT (The Extensible Neuroimaging Archive Toolkit), an open source software platform designed to facilitate management and exploration of neuroimaging and related data. XNAT includes a secure database backend and a rich web-based user interface. | magnetic resonance, pet, computed tomography, neuroimaging, mri, computer axial tomography imaging protocol, freesurfer aparc, freesurfer aseg, clinical assessment, atlas scaling factor, fast segmentation, image collection, clinical |
is used by: NITRC-IR is used by: NIF Data Federation is used by: Integrated Datasets is listed by: re3data.org is related to: Morphometry BIRN is related to: XNAT - The Extensible Neuroimaging Archive Toolkit has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
Free, Freely available | nif-0000-04375, r3d100010874 | https://doi.org/10.17616/R3533H | SCR_006235 | Extensible Neuroimaging Archive Toolkit CENTRAL | 2026-08-06 09:26:32 | 40 | ||||||
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Amazon Web Services Public Data Sets Resource Report Resource Website 1+ mentions |
Amazon Web Services Public Data Sets (RRID:SCR_006318) | AWS Public Data Sets | storage service resource, data set, service resource, data repository, data or information resource | A multidisciplinary repository of public data sets such as the Human Genome and US Census data that can be seamlessly integrated into AWS cloud-based applications. AWS is hosting the public data sets at no charge for the community. Anyone can access these data sets from their Amazon Elastic Compute Cloud (Amazon EC2) instances and start computing on the data within minutes. Users can also leverage the entire AWS ecosystem and easily collaborate with other AWS users. If you have a public domain or non-proprietary data set that you think is useful and interesting to the AWS community, please submit a request and the AWS team will review your submission and get back to you. Typically the data sets in the repository are between 1 GB to 1 TB in size (based on the Amazon EBS volume limit), but they can work with you to host larger data sets as well. You must have the right to make the data freely available. | astronomy, biology, chemistry, climatology, economics, encyclopedia, dictionary, mathematics, data collection platform, data sharing, geography, data archive |
is listed by: re3data.org is listed by: DataCite has parent organization: Amazon Web Services |
Public, The community can contribute to this resource | nlx_152013, r3d100010855 | https://doi.org/10.17616/R3M91V | SCR_006318 | Public Data Sets on AWS | 2026-08-06 09:26:33 | 1 | ||||||
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ChemSpider Resource Report Resource Website 1000+ mentions |
ChemSpider (RRID:SCR_006360) | ChemSpider | software resource, data access protocol, service resource, mobile app, web service, data or information resource, software application, database | Collection of chemical structures. Provides access to structures, properties and associated information from hundreds of data sources to find compounds of interest and provides services to improve this data by curation and annotation and to integrate it with users applications. | collection, chemical, structure, property, data, compound, bio.tools, FASEB list |
is used by: Open PHACTS is used by: GEROprotectors is listed by: re3data.org is listed by: bio.tools is listed by: Debian has parent organization: Royal Society of Chemistry |
Waters ; GGA Software Services |
Free, Freely available, Registration required for some sites | nlx_152101, biotools:chemspider, r3d100010205 | https://bio.tools/chemspider, https://doi.org/10.17616/R38P4P | SCR_006360 | 2026-08-06 09:26:34 | 1759 | ||||||
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ResearchGate Resource Report Resource Website 100+ mentions |
ResearchGate (RRID:SCR_006505) | ResearchGate | portal, community building portal, database, data or information resource | A professional, social network and publication database geared to researchers where the latest field specific publications can be read, publications with other specialists can be discussed, and collaboration with colleagues is facilitated. They provide researchers with access to around 40 million abstracts and tens of thousands of Full texts, uploaded by the authors themselves. Researchers can search through 7 of the largest databases simultaneously, such as PubMed, IEEE & CiteSeer. | social network, biology, literature, publication, bibliographic, abstract, collaborate, statistics, citation, FASEB list |
is listed by: FORCE11 is listed by: DataCite is listed by: re3data.org is related to: PubMed is parent organization of: ResearchGate: Research Jobs is parent organization of: ResearchGate: Research Conferences |
Free, Account required, The community can contribute to this resource | nlx_143849, DOI:10.1314, DOI:10.17616/R36H16, r3d100012227 | https://doi.org/10.17616/R36011, https://doi.org/10.17616/r36H16, https://doi.org/10.1314/, https://dx.doi.org/10.1314/, https://doi.org/10.17616/R36H16 | SCR_006505 | Research Gate, Research gate | 2026-08-06 09:26:36 | 346 | ||||||
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Electron Microscopy Data Bank at PDBe (MSD-EBI) Resource Report Resource Website 100+ mentions |
Electron Microscopy Data Bank at PDBe (MSD-EBI) (RRID:SCR_006506) | EMDB at PDBe | storage service resource, service resource, production service resource, data repository, data analysis service, data or information resource, analysis service resource, database | Repository for electron microscopy density maps of macromolecular complexes and subcellular structures at Protein Data Bank in Europe. Covers techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography. | electron microscopy, density map, macromolecule, complex, subcellular structure, single-particle analysis, electron tomography, electron crystallography, macromolecular complex, structure, protein, protein binding, electron, electron configuration, tomography, microscopy, gold standard |
is used by: DARC - Database for Aligned Ribosomal Complexes 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 related to: EMDataResource.org is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: PDBe - Protein Data Bank in Europe |
NIH | Public | r3d100010562, nlx_149453 | https://doi.org/10.17616/R3HP57 | SCR_006506 | MSD-EBI, Electron Microscopy Data Bank at Protein Data Bank in Europe, Electron Microscopy DataBank, Electron Microscopy Data Bank at PDBe (MSD-EBI), Electron Microscopy Data Bank at PDBe | 2026-08-06 09:26:37 | 144 | |||||
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Phytozome Resource Report Resource Website 1000+ mentions |
Phytozome (RRID:SCR_006507) | Phytozome | service resource, production service resource, data analysis service, data or information resource, analysis service resource, database | A comparative platform for green plant genomics. Families of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology / paralogy relationships as well as clade specific genes and gene expansions. As of release v9.1, Phytozome provides access to forty-one sequenced and annotated green plant genomes which have been clustered into gene families at 20 evolutionarily significant nodes. Where possible, each gene has been annotated with PFAM, KOG, KEGG, and PANTHER assignments, and publicly available annotations from RefSeq, UniProt, TAIR, JGI are hyper-linked and searchable., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | genome, genomics, plant, green plant, cluster sequence, alignment, gene, node, cluster, blast, blat, biomart, peptide homolog, gene ancestry, sequence, annotation, gene structure, gene family, genome organization, comparative genomics, physiology, comparative, bio.tools, FASEB list |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: Plant Co-expression Annotation Resource has parent organization: DOE Joint Genome Institute has parent organization: Lawrence Berkeley National Laboratory |
Gordon and Betty Moore Foundation ; DOE DE-AC02-05CH11231 |
PMID:22110026 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:phytozome, nlx_151490, r3d100010850 | https://bio.tools/phytozome, https://doi.org/10.17616/R38021 | SCR_006507 | 2026-08-06 09:26:36 | 3108 | |||||
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NIDDK Central Repository Resource Report Resource Website 50+ mentions |
NIDDK Central Repository (RRID:SCR_006542) | CDR, NIDDKCDR | storage service resource, biospecimen repository, service resource, data repository, data or information resource, material storage repository, database | NIDDK Central Repositories are two separate contract funded components that work together to store data and samples from significant, NIDDK funded studies. First component is Biorepository that gathers, stores, and distributes biological samples from studies. Biorepository works with investigators in new and ongoing studies as realtime storage facility for archival samples.Second component is Data Repository that gathers, stores and distributes incremental or finished datasets from NIDDK funded studies Data Repository helps active data coordinating centers prepare databases and incremental datasets for archiving and for carrying out restricted queries of stored databases. Data Repository serves as Data Coordinating Center and website manager for NIDDK Central Repositories website. | clinical supply resource, data, clinical, sample sharing, genotyping, genotype, phenotype, genetic analysis, data sharing, genetics, serum, plasma, stool, urine, dna, red blood cell, buffy coat, tissue, immortalized cell line, cell line, data set, digestive organ, kidney, diabetes, kidney disease, digestive disease, genome-wide association study, sequencing, FASEB list |
uses: DataCite is used by: NIDDK Information Network (dkNET) is used by: NIF Data Federation 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 lists: HEALTHY study lists: Nonalcoholic Steatohepatitis Clinical Research Network lists: HALT-C Trial lists: Type 1 Diabetes Genetics Consortium lists: TEDDY lists: Type 1 Diabetes TrialNet lists: Rare and Atypical Diabetes Network lists: Diabetes Prevention Program lists: Diabetes Prevention Program Outcomes Study lists: Restoring Insulin Secretion Consortium (RISE) lists: Epidemiology of Diabetes Interventions and Complications lists: Diabetes Control and Complications Trial lists: Treatment Options for type 2 Diabetes in Adolescents and Youth is listed by: One Mind Biospecimen Bank Listing is listed by: re3data.org is listed by: Biospecimens/Biorepositories: Rare Disease-HUB (RD-HUB) is listed by: NIDDK Information Network (dkNET) is related to: NCBI database of Genotypes and Phenotypes (dbGap) is related to: Peginterferon and Ribavirin for Pediatric Patients with Chronic Hepatitis C is related to: Chronic Renal Insufficiency Cohort Study has parent organization: RTI International |
NIDDK | PMID:23396299 PMID:21959867 PMID:16595012 |
Restricted | nlx_152673, r3d100010377 | https://doi.org/10.17616/R3WP48 | https://www.niddkrepository.org, | SCR_006542 | NIDDK Central Repository, National Institute of Diabetes and Digestive and Kidney Diseases Central Repository, NIDDKCentral Repositories | 2026-08-06 09:26:36 | 85 | |||
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Influenza Research Database (IRD) Resource Report Resource Website 10+ mentions |
Influenza Research Database (IRD) (RRID:SCR_006641) | IRD | storage service resource, service resource, production service resource, data repository, data analysis service, data or information resource, analysis service resource, database | The Influenza Research Database (IRD) serves as a public repository and analysis platform for flu sequence, experiment, surveillance and related data. | avian, clinical, genomic, host, influenza, isolate, mammalian, nonhuman, phenotypic, preventive, proteomic, repository, strain, epitope, surveillance, treatment, virus, protein sequence, immune, 3d protein structure, align, blast, short peptide, flu protein, sequence variation, snp, phylogenetic tree, human, 3d spacial image, image, clinical data, clinical, genomic, proteomic, phenotype |
is recommended by: NIDDK Information Network (dkNET) is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing is related to: Los Alamos National Laboratory is related to: University of California at Davis; California; USA is related to: Sage Analytica is related to: J. Craig Venter Institute has parent organization: University of Texas Southwestern Medical Center; Texas; USA has parent organization: Los Alamos National Laboratory has parent organization: Sage Analytica |
Influenza virus, Influenza | NIAID | PMID:17965094 | Acknowledgement requested, The community can contribute to this resource | DOI:10.25504/FAIRsharing.ws7cgw, nif-0000-21222, DOI:10.35094, DOI:10.17616/R3S634, r3d100011558 | https://www.fludb.org/, https://doi.org/10.17616/R3S634, https://doi.org/10.17616/r3s634, https://doi.org/10.35094/, https://dx.doi.org/10.35094/, https://fairsharing.org/10.25504/FAIRsharing.ws7cgw, https://doi.org/10.17616/R3S634 | http://www.fludb.org/brc/home.do?decorator=influenza | SCR_006641 | , Influenza Research Database, IRD | 2026-08-06 09:26:39 | 28 | ||
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InnateDB Resource Report Resource Website 100+ mentions |
InnateDB (RRID:SCR_006714) | InnateDB | database, data or information resource | Publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralized resource. The database can be mined as a knowledgebase or used with the integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response. Although InnateDB curation focuses on innate immunity-relevant interactions and pathways, it also incorporates detailed annotation on the entire human, mouse and bovine interactomes by integrating data (178,000+ interactions & 3,900+ pathways) from several of the major public interaction and pathway databases. InnateDB also has integrated human, mouse and bovine orthology predictions generated using Ortholgue software. Ortholgue uses a phylogenetic distance-based method to identify possible paralogs in high-throughput orthology predictions. Integrated human and mouse conserved gene order and synteny information has also been determined to provide further support for orthology predictions. InnateDB Capabilities: * View statistics for manually-curated innate immunity relevant molecular interactions. New manually curated interactions are submitted weekly. * Search for genes and proteins of interest. * Search for experimentally-verified molecular interactions by gene/protein name, interaction type, cell type, etc. * Search genes/interactions belonging to 3,900 pathways. * Visualize interactions using an intuitive subcellular localization-based layout in Cerebral. * Upload your own list of genes along with associated gene expression data (from up to 10 experimental conditions) to interactively analyze this data in a molecular interaction network context. Once you have uploaded your data, you will be able to interactively visualize interaction networks with expression data overlaid; carry out Pathway, Gene Ontology and Transcription Factor Binding Site over-representation analyses; construct orthologous interaction networks in other species; and much more. * Access curated interaction data via a dedicated PSICQUIC webservice. | gene, immune response, pathway, protein, signaling pathway, interaction, immune, signaling response, gene, orthology prediction, orthology, ortholg, annotation, interactome, gene expression, molecule, protein-protein interaction, molecular interaction, visualization, nucleic acid-protein, nucleic acid, network, web service, transcription factor binding site, software resource, FASEB list |
is listed by: re3data.org is related to: IMEx - The International Molecular Exchange Consortium is related to: Interaction Reference Index is related to: ConsensusPathDB is related to: IMEx - The International Molecular Exchange Consortium is related to: PSICQUIC Registry is related to: PSICQUIC Registry is related to: Gene Ontology is related to: IntAct has parent organization: Simon Fraser University; British Columbia; Canada has parent organization: University of British Columbia; British Columbia; Canada works with: IMEx - The International Molecular Exchange Consortium |
Microbial infection, Allergy, Asthma | Michael Smith Foundation for Health Research ; AllerGen 12ASI1; AllerGen 12B&B2; Teagasc RMIS6018; European Union PSIMEx project contract FP7-HEALTH-2007-223411 |
PMID:23180781 PMID:18766178 |
Free, Freely available | nif-0000-20808, r3d100010676 | https://doi.org/10.17616/R36S43 | SCR_006714 | A Knowledge Resource for Innate Immunity Interactions and Pathways, InnateDB: Systems Biology of the Innate Immune Response, InnateDB - A Knowledge Resource for Innate Immunity Interactions and Pathways | 2026-08-06 09:26:40 | 496 | |||
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Surveillance Epidemiology and End Results Resource Report Resource Website 5000+ mentions |
Surveillance Epidemiology and End Results (RRID:SCR_006902) | SEER | data set, report, data or information resource, narrative resource, database | SEER collects cancer incidence data from population-based cancer registries covering approximately 47.9 percent of the U.S. population. The SEER registries collect data on patient demographics, primary tumor site, tumor morphology, stage at diagnosis, and first course of treatment, and they follow up with patients for vital status.There are two data products available: SEER Research and SEER Research Plus. This was motivated because of concerns about the increasing risk of re-identifiability of individuals. The Research Plus databases require more rigorous process for access that includes user authentication through Institutional Account or multiple-step request process for Non-Institutional users. | cancer, statistics, epidemiology, registry, mortality, cancer mortality, african-american, hispanic, american-indian, alaska native, asian, hawaiian, pacific islander, demographic, tumor site, tumor morphology, stage, treatment, follow-up, vital status, FASEB list |
is listed by: re3data.org is related to: SEER*Stat is related to: NCI SEER Cancer Stage Variable Documentation is related to: SEER Datasets and Software is related to: NCI Division of Cancer Control and Population Sciences SEER-Medicare Comorbidity SAS Macros is related to: NCI Division of Cancer Control and Population Sciences SEER-Medicare Linked Data Resource has parent organization: National Cancer Institute |
Cancer, Leukemia | NCI | nif-0000-21366, r3d100010884 | SCR_006902 | Surveillance Epidemiology and End Results (SEER) Program, Surveillance Epidemiology End Results, Surveillance Epidemiology End Results (SEER) Program | 2026-08-06 09:26:42 | 6023 | ||||||
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PeptideAtlas Resource Report Resource Website 100+ mentions |
PeptideAtlas (RRID:SCR_006783) | PeptideAtlas | storage service resource, service resource, data repository, data or information resource, database | Multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences. All results of sequence and spectral library searching are subsequently processed through the Trans Proteomic Pipeline to derive a probability of correct identification for all results in a uniform manner to insure a high quality database, along with false discovery rates at the whole atlas level. The raw data, search results, and full builds can be downloaded for other uses. All results of sequence searching are processed through PeptideProphet to derive a probability of correct identification for all results in a uniform manner ensuring a high quality database. All peptides are mapped to Ensembl and can be viewed as custom tracks on the Ensembl genome browser. The long term goal of the project is full annotation of eukaryotic genomes through a thorough validation of expressed proteins. The PeptideAtlas provides a method and a framework to accommodate proteome information coming from high-throughput proteomics technologies. The online database administers experimental data in the public domain. You are encouraged to contribute to the database. | proteomics, peptide, mass spectrometry, annotation, eukaryotic, genome, peptide sequence, high-throughput mass spectrometry, ensembl, peptideprophet, protein sequence, blood plasma, protein, eukaryotic cell, dna, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: ProteomeXchange is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: Biositemaps is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Ensembl is related to: ProteomeXchange is related to: NIH Data Sharing Repositories is related to: Integrated Manually Extracted Annotation has parent organization: Institute for Systems Biology; Washington; USA |
NCI ; NHGRI ; NIGMS |
PMID:20013378 PMID:23215161 PMID:16381952 PMID:15642101 |
Public, The community can contribute to this resource, Acknowledgement requested | nif-0000-03266, r3d100010889, biotools:peptideatlas | https://bio.tools/peptideatlas, https://doi.org/10.17616/R3BK61 | SCR_006783 | Peptide Atlas, PeptideAtlas | 2026-08-06 09:26:41 | 479 | ||||
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fMRI Data Center Resource Report Resource Website 10+ mentions |
fMRI Data Center (RRID:SCR_007278) | fMRIDC | storage service resource, service resource, data repository, data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 25, 2013 Public curated repository of peer reviewed fMRI studies and their underlying data. This Web-accessible database has data mining capabilities and the means to deliver requested data to the user (via Web, CD, or digital tape). Datasets available: 107 NOTE: The fMRIDC is down temporarily while it moves to a new home at UCLA. Check back again in late Jan 2013! The goal of the Center is to help speed the progress and the understanding of cognitive processes and the neural substrates that underlie them by: * Providing a publicly accessible repository of peer-reviewed fMRI studies. * Providing all data necessary to interpret, analyze, and replicate these fMRI studies. * Provide training for both the academic and professional communities. The Center will accept data from those researchers who are publishing fMRI imaging articles in peer-reviewed journals. The goal is to serve the entire fMRI community. | fmri, cognitive, cortex, mri, talairach, neuroimaging, cognitive neuroscience, brain, structure, function, magnetic resonance, intellect, image collection, data set |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: re3data.org has parent organization: University of California at Santa Barbara; California; USA |
NSF ; W. M. Keck Foundation ; NIMH ; Sun Microsystems Center of Excellence |
PMID:11545705 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00025 | http://www.fmridc.org/ | SCR_007278 | The fMRI Data Center | 2026-08-06 09:26:48 | 16 | ||||
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Cambridge Structural Data Base Resource Report Resource Website 100+ mentions |
Cambridge Structural Data Base (RRID:SCR_007310) | CSD | database, data or information resource, software resource |
It records bibliographic, chemical and crystallographic information for organic molecules and metal-organic compounds whose 3D structures have been determined using X-ray diffraction and neutron diffraction. The CSD records results of single crystal studies and powder diffraction studies which yield 3D atomic coordinate data for at least all non-H atoms. In some cases the CCDC is unable to obtain coordinates, and incomplete entries are archived to the CSD. The CSD includes crystal structure data arising from: * publications in the open literature * Private Communications to the CSD (via direct data deposition) The Cambridge Structural Database System (CSDS) is a single product that comprises the following components: The Cambridge Structural Database (CSD); CSDS Software: search and information retrieval (ConQuest), structure visualization (Mercury), statistical analysis of retrieved data (VISTA), and software for database creation (PreQuest); Knowledge bases derived from the CSD: Mogul (intramolecular geometry) and IsoStar (intermolecular interactions, including data from the PDB). Cambridge Structural Database (CSD) is the world repository of small-molecule crystal structures. For example, the crystal structures supported by the National Institute on Drug Abuse are deposited here. |
3d structure, crystal, crystal studies, csd, metal-organic compounds, neutron diffraction, organic molecules, powder diffraction, x-ray diffraction |
is listed by: DataCite is listed by: re3data.org is listed by: FAIRsharing has parent organization: University of Cambridge; Cambridge; United Kingdom |
DOI:10.25504/FAIRsharing.vs7865, r3d100010197, nif-0000-00174, DOI:10.5517, DOI:10.25505, DOI:10.17616/R36011 | http://www.ccdc.cam.ac.uk/products/csd/, https://doi.org/10.17616/R30P93, https://doi.org/10.17616/r36011, https://doi.org/10.5517/, &&https://doi.org/10.25505/, , https://dx.doi.org/10.5517/, https://dx.doi.org/10.25505/, https://fairsharing.org/10.25504/FAIRsharing.vs7865, https://doi.org/10.17616/R36011 | SCR_007310 | Cambridge Structural Database | 2026-08-06 09:26:49 | 132 | |||||||
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Biological General Repository for Interaction Datasets (BioGRID) Resource Report Resource Website 1000+ mentions |
Biological General Repository for Interaction Datasets (BioGRID) (RRID:SCR_007393) | BioGRID | database, data or information resource | Curated protein-protein and genetic interaction repository of raw protein and genetic interactions from major model organism species, with data compiled through comprehensive curation efforts. | budding yeast, fission yeast, protein, gene, protein interaction, genetic interaction, model organism, interaction, dataset, gene annotation, phenotype, orthologous interaction, yeast, cellular interaction network, physical interaction, protein-peptide, protein-rna, protein-protein interaction, genetics, publication, raw protein, genetic interaction, web service, pathway, network, biology, gene mapping, statistics, bio.tools, FASEB list |
is used by: NIF Data Federation 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: OMICtools is listed by: DataCite is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is related to: TissueNet - The Database of Human Tissue Protein-Protein Interactions is related to: Pathway Commons is related to: Cytoscape is related to: Interaction Reference Index is related to: ConsensusPathDB is related to: FlyMine is related to: IMEx - The International Molecular Exchange Consortium is related to: Integrated Molecular Interaction Database is related to: PSICQUIC Registry is related to: PSI-MI is related to: NIH Data Sharing Repositories is related to: Agile Protein Interactomes DataServer is related to: Integrated Manually Extracted Annotation has parent organization: Princeton University; New Jersey; USA has parent organization: University of Edinburgh; Scotland; United Kingdom has parent organization: University of Montreal; Quebec; Canada works with: IMEx - The International Molecular Exchange Consortium |
NCRR R01 RR024031; NHGRI HG02223; Canadian Institutes of Health Research ; BBSRC ; NIH Office of the Director R24 OD011194 |
PMID:23203989 PMID:21071413 PMID:16381927 PMID:12620108 |
Free, Freely available | nif-0000-00432, r3d100010350, OMICS_01901, biotools:the_grid | https://orip.nih.gov/comparative-medicine/programs/genetic-biological-and-information-resources, https://bio.tools/the_grid, https://doi.org/10.17616/R34C7G | SCR_007393 | , BioGRID, Biological General Repository for Interaction Datasets | 2026-08-06 09:26:50 | 2554 | ||||
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INFEVERS Resource Report Resource Website 10+ mentions |
INFEVERS (RRID:SCR_007738) | Infevers | storage service resource, data set, service resource, data repository, data or information resource | Registry for Familial Mediterranean Fever (FMF) and hereditary inflammatory disorders mutations. As of 2014, it includes twenty genes including: MEFV, MVK, TNFRSF1A, NLRP3, NOD2, PSTPIP1, LPIN2 and NLRP7, and contains over 1338 sequence variants. Confidential data, simple and complex alleles are accepted. For each gene, a menu offers: 1) a tabular list of the variants that can be sorted by several parameters; 2) a gene graph providing a schematic representation of the variants along the gene; 3) statistical analysis of the data according to the phenotype, alteration type, and location of the mutation in the gene; 4) the cDNA and gDNA sequences of each gene, showing the nucleotide changes along the sequence, with a color-based code highlighting the gene domains, the first ATG, and the termination codon; and 5) a download menu making all tables and figures available for the users, which, except for the gene graphs, are all automatically generated and updated upon submission of the variants. The entire database was curated to comply with the HUGO Gene Nomenclature Committee (HGNC) and HGVS nomenclature guidelines, and wherever necessary, an informative note was provided. | sequence variant, mutation, allele, genetics, dna, rna, protein, disease, heredity, inflammation, gene, function, phenotype, complex allele, simple allele, exon, intron, cdna sequence, genomic sequence, gdna, FASEB list |
is listed by: re3data.org is related to: Human Genome Variation Society is related to: HGNC |
Familial Mediterranean Fever, Auto-inflammatory Disorder, Hereditary Auto-inflammatory Disorder | European Union | PMID:18409191 PMID:15300846 PMID:12520003 |
Acknowledgement required, Free, Public | nif-0000-03022, r3d100010548 | http://fmf.igh.cnrs.fr/infevers, https://doi.org/10.17616/R3B61B | SCR_007738 | Internet Fevers | 2026-08-06 09:26:57 | 37 | |||
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Reciprocal Net Resource Report Resource Website 1+ mentions |
Reciprocal Net (RRID:SCR_008238) | Reciprocal Net | database, data or information resource | Database of crystallographic information. Its membership includes crystallographic service facilities (that analyze crystals submitted by research chemists) located at major universities. These labs analyze anywhere from a few dozen to several hundred molecular structures each year and post the data online for the public to access. A distributed database engine takes care of shuttling this data across the Internet so that every structure can be located by the search engine. There may be a delay of a year or more between the time a structure is first analyzed and the time it finally becomes available for the public to see. This is due to intellectual property issues - the intervening time allows the chemists who first discovered the structure to publish it in a trade journal. | 3d molecular structure, chemistry, digital, molecular, structure, molecular structure, crystallography, chemical process |
is listed by: re3data.org has parent organization: Indiana University; Indiana; USA |
NSF | Free, Freely available, | nif-0000-21353, r3d100010767 | https://doi.org/10.17616/R3T90B | SCR_008238 | Reciprocal Net - a distributed crystallography network for researchers students and the general public | 2026-08-06 09:27:07 | 2 | |||||
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Genomes Online Database Resource Report Resource Website 100+ mentions |
Genomes Online Database (RRID:SCR_002817) | GOLD | storage service resource, service resource, data repository, data or information resource, database | Database of information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. It also provides information related to organism properties such as phenotype, ecotype and disease. Both complete and ongoing projects, along with their associated metadata, can be accessed. Users can also register, annotate and publish genome and metagenome data. | genome, genetics, metagenome, biosample, phenotype, ecotype, disease, sequencing, FASEB list |
is listed by: re3data.org has parent organization: DOE Joint Genome Institute |
PMID:22135293 PMID:19914934 PMID:17981842 PMID:16381880 PMID:11125068 PMID:10498782 |
Free, Freely available, Available for download | r3d100010808, nif-0000-02918 | https://doi.org/10.17616/R39310 | SCR_002817 | Genomes On Line Database (GOLD), GOLD:Genomes Online Database | 2026-08-06 09:25:43 | 159 | |||||
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NCBI database of Genotypes and Phenotypes (dbGap) Resource Report Resource Website 500+ mentions |
NCBI database of Genotypes and Phenotypes (dbGap) (RRID:SCR_002709) | dbGaP | storage service resource, service resource, data repository, data or information resource, database | Database developed to archive and distribute clinical data and results from studies that have investigated interaction of genotype and phenotype in humans. Database to archive and distribute results of studies including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits. | clinical, trial, genotype, interaction, homology, cell, morphology, interaction, phenotype, molecular diagnosis, genetic recombination, gold standard, bio.tools |
is used by: International Genomics of Alzheimers Project is used by: NIDDK Inflammatory Bowel Disease Genetics Consortium is used by: NIH Heal Project is used by: Genomic Data Commons Data Portal (GDC Data Portal) 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: OMICtools is listed by: re3data.org is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: NIDDK Central Repository is related to: eMERGE Network: electronic Medical Records and Genomics is related to: Framingham Heart Study is related to: PhenoExplorer is related to: Chronic Renal Insufficiency Cohort Study is related to: DbGaP Cleaner is related to: Psychiatric Genomics Consortium is related to: ISCA Consortium is related to: Allen Institute for Brain Science has parent organization: NCBI is parent organization of: Resource for Genetic Epidemiology Research on Adult Health and Aging |
NLM | PMID:24297256 PMID:17898773 |
Restricted | nif-0000-23342, OMICS_00263, biotools:dbgap, r3d100010788 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=gap, https://bio.tools/dbgap, https://doi.org/10.17616/R3GS4K | SCR_002709 | database of Genotypes and Phenotypes (dbGaP), dbGaP, NCBI, Database of Genotypes and Phenotypes | 2026-08-06 09:25:42 | 683 | ||||
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GenBank Resource Report Resource Website 10000+ mentions |
GenBank (RRID:SCR_002760) | GB | storage service resource, service resource, data repository, data or information resource, database | NIH genetic sequence database that provides annotated collection of all publicly available DNA sequences for almost 280 000 formally described species (Jan 2014) .These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. It is part of International Nucleotide Sequence Database Collaboration and daily data exchange with European Nucleotide Archive (ENA) and DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through NCBI Entrez retrieval system, which integrates data from major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of GenBank database are available by FTP. | genetic sequence, dna sequence, human genetics, human genome, nucleotide sequence, nucleotide, dna, dna data bank, gene mapping, genetics, gold standard |
is used by: Structural Genomics Consortium is used by: xFITOM is used by: Transcriptional Regulatory Element Database 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: OMICtools is listed by: re3data.org is listed by: CINERGI is related to: High Throughput Genomic Sequences Division is related to: DNA DataBank of Japan (DDBJ) is related to: HS3D - Homo Sapiens Splice Sites Dataset is related to: Influenza Virus Resource is related to: TPA is related to: Anopheles gambiae (African malaria mosquito) genome view is related to: Nucleotide database is related to: NCBI BioSample is related to: NCBI Nucleotide is related to: SpliceDB is related to: MaizeGDB is related to: NCBI Assembly Archive Viewer is related to: DNA DataBank of Japan (DDBJ) is related to: European Molecular Biology Laboratory is related to: INSDC is related to: NCBI Protein Database is related to: TrED is related to: Xenopus Gene Collection is related to: Mammalian Gene Collection is related to: Zebrafish Gene Collection is related to: INSDC is related to: NCBI Virus is related to: Codon and Codon-Pair Usage Tables has parent organization: NCBI is parent organization of: NCBI Genome Survey Sequences Database is parent organization of: NCBI Genome Survey Sequences Database works with: OGDraw works with: A plasmid Editor works with: Webcutter works with: merge-gbk-records works with: PremierBiosoft Proteo IQ Software works with: SARS-CoV-2-Sequences works with: rentrez works with: MiMeDB |
NLM | PMID:24217914 PMID:23193287 PMID:21071399 |
Free, Freely available | nif-0000-02873, r3d100010528, OMICS_01650 | https://doi.org/10.17616/R3D31X | SCR_002760 | , Gen Bank, GenBank | 2026-08-06 09:25:42 | 61478 | ||||
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SumsDB Resource Report Resource Website 10+ mentions |
SumsDB (RRID:SCR_002759) | SumsDB, WebCaret | storage service resource, atlas, service resource, production service resource, data repository, data analysis service, data or information resource, analysis service resource, image repository, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figures | segmentation, volume, neuroimaging, brain, fmri, stereotaxic foci, stereotaxic coordinate, brain-mapping, foci, structural mri, mri, cerebral cortex, cerebellar cortex, afni brik, analyze, atlas, nifti, registration, rendering, spatial transformation, surface analysis, surface rendering, visualization, volume rendering, brain mapping, neuroanatomy |
is used by: NIF Data Federation is listed by: Biositemaps is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: re3data.org is related to: Computerized Anatomical Reconstruction and Editing Toolkit is related to: Integrated Manually Extracted Annotation has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
Mental disease, Neurological disorder, Normal | Human Brain Project ; NSF ; NCI ; NLM ; NASA ; National Partnership for Advanced Computational Infrastructure ; NIMH R01 MH60974-06 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00016, r3d100010169 | http://brainvis.wustl.edu/wiki/index.php/Sums:About http://www.nitrc.org/projects/sumsdb, https://doi.org/10.17616/R3JC76 | SCR_002759 | SumsDB WebCaret, SumsDB Database, Web Caret, WebCaret Online Visualization, Surface Management System Database and WebCaret Online Visualization, SumsDB and WebCaret, Sums database, SumsDB (Surface Management System Database) and WebCaret Online Visualization, Sums DB, SumsDB (Surface Management System Database) WebCaret Online Visualization, Surface Management System Database | 2026-08-06 09:25:42 | 13 |
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