Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
GenBank Resource Report Resource Website 10000+ mentions |
GenBank (RRID:SCR_002760) | GB | data or information resource, data repository, database, service resource, storage service resource | 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 | 2026-08-29 11:21:31 | 64417 | ||||
|
SumsDB Resource Report Resource Website 10+ mentions |
SumsDB (RRID:SCR_002759) | SumsDB, WebCaret | analysis service resource, atlas, data analysis service, data or information resource, data repository, database, image repository, production service resource, service resource, storage service resource | 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 | 2026-08-29 11:21:13 | 14 | ||||
|
Genomes Online Database Resource Report Resource Website 100+ mentions |
Genomes Online Database (RRID:SCR_002817) | GOLD | data or information resource, data repository, database, service resource, storage service resource | 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 | 2026-08-29 11:21:32 | 161 | |||||
|
Human Proteinpedia Resource Report Resource Website 10+ mentions |
Human Proteinpedia (RRID:SCR_002948) | Human Proteinpedia | data or information resource, data repository, database, service resource, storage service resource | A community portal for sharing and integration of human protein data that allows research laboratories to contribute and maintain protein annotations. The Human Protein Reference Database (HPRD) integrates data that is deposited along with the existing literature curated information in the context of an individual protein. Data pertaining to post-translational modifications, protein-protein interactions, tissue expression, expression in cell lines, subcellular localization and enzyme substrate relationships can be submitted. | enzyme, protein expression, post-translational modification, protein-protein interaction, subcellular localization, enzyme substrate, tissue expression, protein, protein binding, peptide, mass spectrometry, mass spectrometry spectra, immunohistochemistry, western blotting, microarray, co-immunoprecipitation, fluorescence, annotation, cell line expression, disease tissue expression, FASEB list |
is listed by: re3data.org is related to: HPRD - Human Protein Reference Database has parent organization: Johns Hopkins University; Maryland; USA has parent organization: Institute of Bioinformatics; Bangalore; India |
PMID:18259167 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02999, r3d100010985 | https://doi.org/10.17616/R3V62C | SCR_002948 | 2026-08-29 11:21:18 | 32 | ||||||
|
ArrayExpress Resource Report Resource Website 5000+ mentions |
ArrayExpress (RRID:SCR_002964) | ArrayExpress | catalog, data or information resource, data repository, database, service resource, storage service resource | International functional genomics data collection generated from microarray or next-generation sequencing (NGS) platforms. Repository of functional genomics data supporting publications. Provides genes expression data for reuse to the research community where they can be queried and downloaded. Integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Contains a subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments. Data collected to MIAME and MINSEQE standards. Data are submitted by users or are imported directly from the NCBI Gene Expression Omnibus. | gold, standard, functional, genomics, data, collection, microarray, next, generation, sequencing, NGS, repository |
uses: MIAME uses: MINSEQE uses: Gene Expression Omnibus is used by: NIF Data Federation is used by: BioSample Database at EBI is used by: Integrated Datasets is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: DataCite is listed by: OMICtools is listed by: re3data.org is related to: DDBJ Omics Archive is related to: MIAME is related to: Gene Expression Atlas is related to: Experimental Factor Ontology is related to: Bgee: dataBase for Gene Expression Evolution is related to: ISA Infrastructure for Managing Experimental Metadata is related to: FlyMine is related to: MAGE-TAB is related to: Experimental Factor Ontology is related to: Magic is related to: ArrayExpress (R) is related to: CancerMIRNome has parent organization: European Bioinformatics Institute |
European Commission ; European Union ; Gen2Phen 200754; NHGRI P41 HG003619; SLING 226073 |
PMID:23193272 PMID:21071405 |
Available Public or Private, Free, Available for download, The community can contribute to this resource, Acknowledgement requested, to access private data registration required | OMICS_01023, nif-0000-30123, r3d100010222 | http://www.ebi.ac.uk/microarray-as/ae, https://doi.org/10.17616/R3302G | SCR_002964 | , ArrayExpress, ArrayExpress - functional genomics data, ArrayExpress Archive | 2026-08-29 11:21:38 | 7814 | ||||
|
NCBI BioSystems Database Resource Report Resource Website 100+ mentions |
NCBI BioSystems Database (RRID:SCR_004690) | BioSystems | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | Database that provides access to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez. A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. BioSystem records list and categorize components, such as the genes, proteins, and small molecules involved in a biological system. The companion FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems. A number of databases provide diagrams showing the components and products of biological pathways along with corresponding annotations and links to literature. This database was developed as a complementary project to (1) serve as a centralized repository of data; (2) connect the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system; and (3) facilitate computation on biosystems data. The NCBI BioSystems Database currently contains records from several source databases: KEGG, BioCyc (including its Tier 1 EcoCyc and MetaCyc databases, and its Tier 2 databases), Reactome, the National Cancer Institute's Pathway Interaction Database, WikiPathways, and Gene Ontology (GO). It includes several types of records such as pathways, structural complexes, and functional sets, and is desiged to accomodate other record types, such as diseases, as data become available. Through these collaborations, the BioSystems database facilitates access to, and provides the ability to compute on, a wide range of biosystems data. If you are interested in depositing data into the BioSystems database, please contact them. | pathway, disease, gene, protein, small molecule, literature, computation, image, biomarker, drug, structural complex, functional set, biological system, molecule, gold standard, bio.tools |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: KEGG is related to: NCBI Structure is related to: BioCyc is related to: EcoCyc is related to: MetaCyc is related to: Reactome is related to: Pathway Interaction Database is related to: WikiPathways is related to: Gene Ontology has parent organization: NCBI |
NIH | PMID:19854944 | r3d100011033, biotools:biosystems, nlx_69646 | https://bio.tools/biosystems, https://doi.org/10.17616/R31K80 | SCR_004690 | BioSystems Database, NCBI BioSystems | 2026-08-29 11:21:58 | 118 | |||||
|
European Bioinformatics Institute Resource Report Resource Website 1000+ mentions |
European Bioinformatics Institute (RRID:SCR_004727) | EMBL-EBI | institution | Non-profit academic organization for research and services in bioinformatics. Provides freely available data from life science experiments, performs basic research in computational biology, and offers user training programme, manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. Part of EMBL. | organization, academic, bioinformatics, research, service, data, computational, biology, training, database, DNA, protein |
is used by: Blueprint Epigenome is listed by: re3data.org is related to: AgedBrainSYSBIO is related to: ProteomeXchange is related to: Open PHACTS is related to: RHEA is related to: TraCeR is related to: 3D-Beacons is related to: RNAcentral has parent organization: European Molecular Biology Laboratory is parent organization of: CoGenT++ is parent organization of: ENA Sequence Version Archive is parent organization of: Reaper - Demultiplexing trimming and filtering sequencing data is parent organization of: PeakAnalyzer is parent organization of: Tally is parent organization of: Clustal Omega is parent organization of: Biocatalogue - The Life Science Web Services Registry is parent organization of: Experimental Network for Functional Integration: A European Network of Excellence for Data Integration and Systems Biology is parent organization of: The Alternatve Splicing Database is parent organization of: BioModels is parent organization of: CHEBI is parent organization of: MAGE is parent organization of: Ensembl is parent organization of: MIAME is parent organization of: UniProt is parent organization of: Ligand-Gated Ion Channel Database is parent organization of: EBI Genomes is parent organization of: IMEx - The International Molecular Exchange Consortium is parent organization of: Toolbox at the European Bioinformatics Institute is parent organization of: Clustal W2 is parent organization of: ArrayExpress is parent organization of: IMGT/HLA is parent organization of: IntEnz- Integrated relational Enzyme database is parent organization of: IPD - Immuno Polymorphism Database is parent organization of: IPI is parent organization of: MicroArray and Gene Expression Markup Language is parent organization of: DaliLite Pairwise comparison of protein structures is parent organization of: Chemical Information Ontology is parent organization of: PANDIT : Protein and Associated Nucleotide Domains with Inferred Trees is parent organization of: Proteomics Identifications (PRIDE) is parent organization of: Software Ontology is parent organization of: FSSP - Families of Structurally Similar Proteins is parent organization of: Experimental Factor Ontology is parent organization of: Identifiers.org is parent organization of: HipSci is parent organization of: ProteomeXchange is parent organization of: Taxonomy is parent organization of: PDBe - Protein Data Bank in Europe is parent organization of: EBI Dbfetch is parent organization of: ProFunc is parent organization of: WSDbfetch (SOAP) is parent organization of: QuickGO is parent organization of: SAS - Sequence Annotated by Structure is parent organization of: UniProt DAS is parent organization of: UniParc at the EBI is parent organization of: Patent Abstracts is parent organization of: BioSample Database at EBI is parent organization of: Database of Genomic Variants Archive (DGVa) is parent organization of: European Genome phenome Archive is parent organization of: UniSave is parent organization of: ArchSchema is parent organization of: UniRef at the EBI is parent organization of: EBIMed is parent organization of: Kraken is parent organization of: SIMBioMS is parent organization of: Expression Profiler is parent organization of: Whatizit is parent organization of: InterProScan is parent organization of: VectorBase is parent organization of: DRCAT Resource Catalogue is parent organization of: FunTree is parent organization of: CREATE is parent organization of: BioMedBridges is parent organization of: PSICQUIC Registry is parent organization of: PDBsum is parent organization of: European Nucleotide Archive (ENA) is parent organization of: DrugPort is parent organization of: Ontology Lookup Service is parent organization of: EDAM Ontology is parent organization of: InterPro is parent organization of: MIRIAM Resources is parent organization of: EB-eye Search is parent organization of: SBO is parent organization of: Ensembl Genomes is parent organization of: NeuronVisio is parent organization of: IntAct is parent organization of: WSsas - Web Service for the SAS tool is parent organization of: Enzyme Structures Database is parent organization of: EMBOSS CpGPlot/CpGReport/Isochore is parent organization of: PaperMaker is parent organization of: CluSTr is parent organization of: Genome Reviews is parent organization of: GOA is parent organization of: Integr8 : Access to complete genomes and proteomes is parent organization of: IPD-ESTDAB- The European Searchable Tumour Line Database is parent organization of: IPD-HPA - Human Platelet Antigens is parent organization of: IPD-KIR - Killer-cell Immunoglobulin-like Receptors is parent organization of: IPD-MHC- Major Histocompatibility Complex is parent organization of: HilbertVis is parent organization of: Gene Expression Atlas is parent organization of: Parasite genome databases and genome research resources is parent organization of: Alternative Exon Database is parent organization of: AltExtron Database is parent organization of: Patent Data Resources is parent organization of: Pompep is parent organization of: Mouse finder is parent organization of: Gene Regulation Ontology is parent organization of: CiteXplore literature searching is parent organization of: MaxSprout is parent organization of: SRS is parent organization of: MicroCosm Targets is parent organization of: Kalign is parent organization of: MUSCLE is parent organization of: FASTA is parent organization of: WU-BLAST is parent organization of: Oases is parent organization of: HTS Mappers is parent organization of: CRAM is parent organization of: CSA - Catalytic Site Atlas is parent organization of: ArrayExpress (R) is parent organization of: WiggleTools is parent organization of: vsn is parent organization of: rlsim is parent organization of: ISA Infrastructure for Managing Experimental Metadata is parent organization of: BioMart Project is parent organization of: BioPerl is parent organization of: BioJS is parent organization of: EMDataResource.org is parent organization of: HTqPCR is parent organization of: Reactome is parent organization of: Europe PubMed Central is parent organization of: h5vc is parent organization of: LexGrid is parent organization of: Consensus CDS is parent organization of: 1000 Genomes: A Deep Catalog of Human Genetic Variation is parent organization of: OrChem is parent organization of: Orphanet Rare Disease Ontology is parent organization of: Reflect is parent organization of: BioLayout Express 3D is parent organization of: Virtual Fly Brain is parent organization of: GeneWise is parent organization of: PhenoMeNal is parent organization of: Ensembl Metazoa is parent organization of: Velvet |
BBSRC ; EMBL member states ; European Union ; Industry Programme partners ; NIH ; UK Research Councils ; Wellcome Trust |
grid.225360.0, Wikidata: Q1341845, ISNI: 0000 0000 9709 7726, nlx_72386 | https://ror.org/02catss52 | SCR_004727 | EBI, European Molecular Biology Laboratory - European Bioinformatics Institute | 2026-08-29 11:21:59 | 3760 | ||||||
|
NCBI Probe Resource Report Resource Website 10+ mentions |
NCBI Probe (RRID:SCR_004816) | NCBI Probe | data or information resource, data repository, database, service resource, storage service resource | Public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications including genotyping, gene expression studies, SNP discovery, genome mapping, and gene silencing. Probe records contain information on reagent distributors, probe effectiveness, and computed sequence similarities. The database is constantly updated, with over 11,000,000 probes available. Users may deposit their data into NCBI Probe Database. | reagent, probe, registry, nucleic acid, gene expression, gene mapping, gene silencing, dna data bank, nucleic acid probe, gold standard, bio.tools |
is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: UniSTS has parent organization: NCBI |
Public, The community can contribute to this resource | nlx_80513, r3d100010780, biotools:ncbi_dbprobe | http://www.ncbi.nlm.nih.gov/sites/entrez?db=probe, https://bio.tools/ncbi_dbprobe, https://doi.org/10.17616/R3D041 | SCR_004816 | NCBI Probe Database, Entrez Probe Database, ProbeDB, Probe Database, dbProbe | 2026-08-29 11:22:14 | 17 | ||||||
|
OpenNeuro Resource Report Resource Website 100+ mentions |
OpenNeuro (RRID:SCR_005031) | OpenNeuro, OpenfMRI | data or information resource, data repository, database, image repository, service resource, storage service resource | Open platform for analyzing and sharing neuroimaging data from human brain imaging research studies. Brain Imaging Data Structure ( BIDS) compliant database. Formerly known as OpenfMRI. Data archives to hold magnetic resonance imaging data. Platform for sharing MRI, MEG, EEG, iEEG, and ECoG data. | neuroinformatics, database, storing, dataset, neuroimaging, data, MRI, MEG, EEG, iEEG, ECoG, FASEB list |
uses: Brain Imaging Data Structure (BIDs) uses: HED Tags is used by: studyforrest.org is used by: DataLad is used by: NIF Data Federation is used by: Integrated Datasets is used by: NIH Heal Project is used by: Baby Open Brains is recommended by: National Library of Medicine is recommended by: BRAIN Initiative 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 listed by: DataCite is listed by: FAIRsharing is affiliated with: NEMAR is related to: Integrated Manually Extracted Annotation has parent organization: Stanford University; Stanford; California has parent organization: Stanford Center for Reproducible Neuroscience has parent organization: BRAIN Initiative is provided by: OpenNeuro |
BRAIN Initiative ; Laura and John Arnold Foundation ; NIDA ; NIMH ; NSF OCI1131441; Squishymedia ; Stanford |
Free, Freely available | DOI:10.25504/FAIRsharing.s1r9bw, r3d100010924, nlx_144048, DOI:10.17616/R33047, DOI:10.18112 | http://www.nitrc.org/projects/openfmri, https://github.com/OpenNeuroDatasets, https://doi.org/10.17616/R33047, https://doi.org/10.17616/r33047, https://doi.org/10.18112/, https://dx.doi.org/10.18112/, https://fairsharing.org/10.25504/FAIRsharing.s1r9bw, https://doi.org/10.17616/R33047 | http://openfmri.org | SCR_005031 | OpenfMRI, Open fMRI, OpenNeuro | 2026-08-29 11:22:05 | 310 | ||||
|
NCBI Popset Resource Report Resource Website 1+ mentions |
NCBI Popset (RRID:SCR_005049) | PopSet | data or information resource, data repository, database, service resource, storage service resource | Database containing a set of DNA sequences that have been collected to analyse the evolutionary relatedness of a population. The population could originate from different members of the same species, or from organisms from different species. Users may submit a Popset using Sequin. | nucleotide sequence, nucleotide, sequence, dna sequence, dna, evolution, population, genomics, eukaryotic cell, mutation, phylogenetic, ecosystem, gold standard |
is listed by: re3data.org has parent organization: NCBI |
nlx_99613, r3d100010777 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=popset, https://doi.org/10.17616/R3S901 | SCR_005049 | Entrez PopSet | 2026-08-29 11:22:14 | 9 | |||||||
|
ChemSpider Resource Report Resource Website 1000+ mentions |
ChemSpider (RRID:SCR_006360) | ChemSpider | data access protocol, data or information resource, database, mobile app, service resource, software application, software resource, web service | 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 |
GGA Software Services ; Waters |
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 | 2026-08-29 11:22:37 | 2112 | ||||||
|
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 | data or information resource, data repository, data set, service resource, storage service 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 | 2026-08-29 11:22:36 | 1 | ||||||
|
ResearchGate Resource Report Resource Website 100+ mentions |
ResearchGate (RRID:SCR_006505) | ResearchGate | community building portal, data or information resource, database, portal | 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 | 2026-08-29 11:22:42 | 432 | ||||||
|
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 | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | 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 | 2026-08-29 11:22:38 | 153 | |||||
|
Phytozome Resource Report Resource Website 1000+ mentions |
Phytozome (RRID:SCR_006507) | Phytozome | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | 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 | 2026-08-29 11:22:38 | 3189 | |||||
|
NIDDK Central Repository Resource Report Resource Website 50+ mentions |
NIDDK Central Repository (RRID:SCR_006542) | CDR, NIDDKCDR | biospecimen repository, data or information resource, data repository, database, material storage repository, service resource, storage service resource | 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 | 2026-08-29 11:22:38 | 92 | |||
|
Influenza Research Database (IRD) Resource Report Resource Website 50+ mentions |
Influenza Research Database (IRD) (RRID:SCR_006641) | IRD | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | 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:10.17616/R3S634, DOI:10.35094, 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 | 2026-08-29 11:22:40 | 55 | ||
|
InnateDB Resource Report Resource Website 500+ mentions |
InnateDB (RRID:SCR_006714) | InnateDB | data or information resource, database | 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 | 2026-08-29 11:22:42 | 571 | |||
|
PeptideAtlas Resource Report Resource Website 500+ mentions |
PeptideAtlas (RRID:SCR_006783) | PeptideAtlas | data or information resource, data repository, database, service resource, storage service resource | 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 | 2026-08-29 11:22:42 | 511 | ||||
|
Animal QTLdb Resource Report Resource Website 50+ mentions |
Animal QTLdb (RRID:SCR_001748) | Animal QTLdb | data or information resource, data repository, database, service resource, storage service resource | Database of trait mapping data, i.e. QTL (phenotype / expression, eQTL), candidate gene and association data (GWAS) and copy number variations (CNV) mapped to livestock animal genomes, to facilitate locating and comparing discoveries within and between species. New data and database tools are continually developed to align various trait mapping data to map-based genome features, such as annotated genes. QTLdb is open to house QTL/association date from other animal species where feasible. Most scientific journals require that any original QTL/association data be deposited into public databases before paper may be accepted for publication. User curator accounts are provided for direct data deposit. Users can download QTLdb data from each species or individual chromosome. | chromosome, comparative genomics, dna sequence, genome, livestock, quantitative trait locus, non-human animal, structural genomics, single-nucleotide polymorphism, gene association, genomics, trait, copy number variation, trait, phenotype, expression, eqtl, genome wide association study, candidate gene, genotype |
uses: Entrez Gene uses: Ensembl is used by: NIF Data Federation is used by: MONARCH Initiative is listed by: re3data.org is related to: Ensembl Variation is related to: Vertebrate Trait Ontology has parent organization: Iowa State University; Iowa; USA has parent organization: NAGRP Bioinformatics Coordination Program |
USDA 2007-04187; USDA NRSP-8 |
PMID:23180796 PMID:17245610 |
Free, Freely available | nif-0000-02550, r3d100010744 | http://www.animalgenome.org/QTLdb/ | SCR_001748 | Animal QTL database, Animal Quantitative Trait Loci database, AnimalQTLdb, Animal Quantitative Trait Loci (QTL) database | 2026-08-29 11:21:06 | 56 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on NIF then you can log in from here to get additional features in NIF such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into NIF you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
