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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Textpresso Resource Report Resource Website 10+ mentions |
Textpresso (RRID:SCR_008737) | Textpresso | database, software application, text-mining software, data or information resource, software resource | An information extracting and processing package for biological literature that can be used online or installed locally via a downloadable software package, http://www.textpresso.org/downloads.html Textpresso's two major elements are (1) access to full text, so that entire articles can be searched, and (2) introduction of categories of biological concepts and classes that relate two objects (e.g., association, regulation, etc.) or describe one (e.g., methods, etc). A search engine enables the user to search for one or a combination of these categories and/or keywords within an entire literature. The Textpresso project serves the biological and biomedical research community by providing: * Full text literature searches of model organism research and subject-specific articles at individual sites. Major elements of these search engines are (1) access to full text, so that the entire content of articles can be searched, and (2) search capabilities using categories of biological concepts and classes that relate two objects (e.g., association, regulation, etc.) or identify one (e.g., cell, gene, allele, etc). The search engines are flexible, enabling users to query the entire literature using keywords, one or more categories or a combination of keywords and categories. * Text classification and mining of biomedical literature for database curation. They help database curators to identify and extract biological entities and facts from the full text of research articles. Examples of entity identification and extraction include new allele and gene names and human disease gene orthologs; examples of fact identification and extraction include sentence retrieval for curating gene-gene regulation, Gene Ontology (GO) cellular components and GO molecular function annotations. In addition they classify papers according to curation needs. They employ a variety of methods such as hidden Markov models, support vector machines, conditional random fields and pattern matches. Our collaborators include WormBase, FlyBase, SGD, TAIR, dictyBase and the Neuroscience Information Framework. They are looking forward to collaborating with more model organism databases and projects. * Linking biological entities in PDF and online journal articles to online databases. They have established a journal article mark-up pipeline that links select content of Genetics journal articles to model organism databases such as WormBase and SGD. The entity markup pipeline links over nine classes of objects including genes, proteins, alleles, phenotypes, and anatomical terms to the appropriate page at each database. The first article published with online and PDF-embedded hyperlinks to WormBase appeared in the September 2009 issue of Genetics. As of January 2011, we have processed around 70 articles, to be continued indefinitely. Extension of this pipeline to other journals and model organism databases is planned. Textpresso is useful as a search engine for researchers as well as a curation tool. It was developed as a part of WormBase and is used extensively by C. elegans curators. Textpresso has currently been implemented for 24 different literatures, among them Neuroscience, and can readily be extended to other corpora of text. | literature, extract, process, bibliographic resource, database application, linux, macos, pdf, perl, posix/unix-like, sh, bash, unix shell, web service, search engine, curation tool, dicty, neuroscience, regulon db, ecoliwiki, ecocyc, curation, text-mining |
is listed by: OMICtools is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: WormBase is related to: Dictyostelium discoideum genome database |
NHGRI HG004090 | PMID:18949581 PMID:15383839 |
Textpresso License | nlx_143812, OMICS_01199 | http://www.nitrc.org/projects/textpresso-2-0/ | SCR_008737 | Text presso, Textpresso - literature search engine | 2026-08-03 09:33:55 | 10 | ||||
|
Annmap Resource Report Resource Website 1+ mentions |
Annmap (RRID:SCR_011783) | Annmap | data or information resource, software resource, database | A genome browser that includes mappings between genomic features and Affymetrix microarrays. Associated with annmap is: * a Bioconductor package, annmap that provides programmatic access to the underlying MySQL database tables (which are freely available for download on this site) * xmapbridge, a Bioconductor package that outputs numeric data in a form suitable for presentation in the browser. This is supported by XMapBridge, a Java client that sits on the local desktop and performs the graph rendering for the browser. | is listed by: OMICtools | Cancer Research UK ; Cancer Research UK Manchester Institute |
OMICS_00900 | SCR_011783 | 2026-08-03 09:35:00 | 6 | |||||||||
|
Biological General Repository for Interaction Datasets (BioGRID) Resource Report Resource Website 1000+ mentions |
Biological General Repository for Interaction Datasets (BioGRID) (RRID:SCR_007393) | BioGRID | data or information resource, database | 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 | 2026-08-03 09:33:22 | 2554 | ||||
|
Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) Resource Report Resource Website 5000+ mentions |
Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) (RRID:SCR_012820) | RCSB PDB | data repository, data or information resource, database, storage service resource, service resource | Collection of structural data of biological macromolecules. Database of information about 3D structures of large biological molecules, including proteins and nucleic acids. Users can perform queries on data and analyze and visualize results. | 3-dimensional, annotation, molecule, nucleic acid, protein, visualization, sequence, function, macromolecule, ligand, model, dna, x-ray crystallography, ribosome, structure, oncogene, nucleic acids, molecular structure, cryomicroscopy, gold standard, FASEB list |
is used by: Structural Genomics Consortium is used by: Ligand Expo is used by: DARC - Database for Aligned Ribosomal Complexes is used by: FireDB is used by: Protein Data Bank Bind Database is used by: Protein Data Bank Site is used by: NIF Data Federation is used by: ChannelPedia is used by: MobiDB is used by: BALBES is used by: Structural Antibody Database is used by: BioLiP 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: re3data.org is affiliated with: EMDataResource.org is affiliated with: ConSurf Database is related to: pdb-data is related to: PDB2MultiGif is related to: GlyProt is related to: pdb-care is related to: pdb2linucs is related to: GlyVicinity is related to: GlyTorsion is related to: GlySeq is related to: AffinDB is related to: StatAlign is related to: Community Structure-Activity Resource is related to: Binding MOAD is related to: ConSurf Database is related to: glycosciences.de is related to: DOMINE: Database of Protein Interactions is related to: Jenalib: Jena Library of Biological Macromolecules is related to: SynSysNet is related to: EMDataResource.org is related to: PDBe - Protein Data Bank in Europe is related to: TFinDIT is related to: HOLLOW is related to: ccPDB - Compilation and Creation of datasets from PDB is related to: DOMMINO - Database Of MacroMolecular INteractiOns is related to: InterEvol database is related to: Polbase is related to: PoSSuM is related to: ProtChemSI is related to: RNA CoSSMos is related to: PDBsum is related to: Worldwide Protein Data Bank (wwPDB) is related to: canSAR is related to: CAPS Database is related to: Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING is related to: Combinatorial Extension (CE) is related to: Metalloprotein Site Database is related to: PDBj - Protein Data Bank Japan is related to: Statistical Torsional Angles Potentials of NMR Refinement Database is related to: Metalloprotein Ligand Interaction Database is related to: CARP is related to: PDBTM is related to: RNA FRABASE - RNA FRAgments search engine and dataBASE is related to: AmiGO is related to: ConsensusPathDB is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: DNA DataBank of Japan (DDBJ) is related to: FlyMine is related to: NCBI Protein Database is related to: NCBI Nucleotide is related to: FunTree is related to: IndelFR - Indel Flanking Region Database is related to: NMR Restraints Grid is related to: Enzyme Structures Database is related to: Electron Microscopy Data Bank at PDBe (MSD-EBI) is related to: Worldwide Protein Data Bank (wwPDB) is related to: DNA DataBank of Japan (DDBJ) is related to: PDBe - Protein Data Bank in Europe is related to: MINAS - Metal Ions in Nucleic AcidS is related to: PDBj - Protein Data Bank Japan has parent organization: University of California at San Diego; California; USA has parent organization: Rutgers University; New Jersey; USA is parent organization of: RCSB PDB Software Tools is parent organization of: Protein Data Bank Markup Language is parent organization of: Ligand Expo works with: CellPhoneDB |
NIH ; DOE ; NSF DBI-1338415 |
PMID:12037327 | Public, Acknowledgement requested | nif-0000-00135, SCR_017379, r3d100010327 | http://www.rcsb.org, http://www.pdb.org, | http://www.rcsb.org/pdb/ | SCR_012820 | RCSB, Research Collaboratory for Structural Bioinformatics Protein Data Bank, The Protein Data Bank, PDB, Protein Databank, RCSB Protein Data Bank, Protein Data Bank | 2026-08-03 09:35:04 | 9870 | |||
|
Ensembl Variation Resource Report Resource Website 1+ mentions |
Ensembl Variation (RRID:SCR_001630) | Ensembl Variation | production service resource, data analysis service, service resource, database, analysis service resource, data or information resource | Public database that stores areas of genome that differ between individual genomes (variants) and, where available, associated disease and phenotype information. Different types of variants for several species: single nucleotide polymorphisms (SNPs), short nucleotide insertions and/or deletions, and longer variants classified as structural variants (including CNVs). Effects of variants on the Ensembl transcripts and regulatory features for each species are predicted. You can run same analysis on your own data using Variant Effect Predictor. These data are integrated with other data sources in Ensembl, and can be accessed using the API or website. For several different species in Ensembl, they import variation data (SNPs, CNVs, allele frequencies, genotypes, etc) from a variety of sources (e.g. dbSNP). Imported variants and alleles are subjected to quality control process to flag suspect data. In human, they calculate linkage disequilibrium for each variant, by population. | genome, disease, phenotype, genomic variant, single nucleotide polymorphism nucleotide, insertion, deletion, structural variant, copy number variation, inversion, translocation, somatic variant, allele frequency, genotype, disease phenotype, inherited disease |
is used by: MONARCH Initiative is related to: dbSNP is related to: Database of Genomic Variants Archive (DGVa) is related to: PubMed is related to: Animal QTLdb is related to: OMIA - Online Mendelian Inheritance in Animals has parent organization: Ensembl |
PMID:23203987 PMID:20562413 PMID:20459810 PMID:20459805 |
Free, Available for download, Freely available | nlx_153897 | SCR_001630 | ensembl variation | 2026-08-03 09:31:29 | 4 | ||||||
|
CYGD - Comprehensive Yeast Genome Database Resource Report Resource Website 10+ mentions |
CYGD - Comprehensive Yeast Genome Database (RRID:SCR_002289) | CYGD | production service resource, data analysis service, service resource, database, analysis service resource, data or information resource | The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition, the data of various projects on related yeasts are used for comparative analysis. | saccharomyces cerevisiae, yeast, yeast genome, genome | is related to: FunSpec | Federal Ministry of Education Science Research and Technology ; European Union ; Government of the Brussels Region - Belgium ; DFG |
PMID:15608217 | nif-0000-02713 | SCR_002289 | MIPS Saccharomyces cerevisiae genome database, MIPS Comprehensive Yeast Genome Database, Comprehensive Yeast Genome Database | 2026-08-03 09:31:45 | 14 | ||||||
|
Aging Genes and Interventions Database Resource Report Resource Website 1+ mentions |
Aging Genes and Interventions Database (RRID:SCR_002701) | AGEID | data repository, data or information resource, database, storage service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 17,2023. A database of genes and interventions connected with aging phenotypes including those with respect to their effects on life-span or age-related neurological diseases. Information includes: organism, aging phenotype, allele type, strain, gene function, phenotypes, mutant, and homologs. If you know of published data (or your own unpublished data that you'd like to share) not currently in the database, please use the Submit a Gene/Intervention link. | allele, strain, gene function, phenotype, mutant, homolog, mutation, degeneration, gene, intervention, life-span |
is used by: Aging Portal is used by: NIF Data Federation has parent organization: University of Washington; Seattle; USA |
Aging, Age-related neurological disease, Neurological disease | Ellison Medical Foundation | PMID:12044961 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-23326 | http://sageke.sciencemag.org/highlights/gidb/ | SCR_002701 | Aging Genes DB, Aging Genes Database, Genes/Interventions Database | 2026-08-03 09:32:06 | 2 | |||
|
Yeast Resource Center Resource Report Resource Website 1+ mentions |
Yeast Resource Center (RRID:SCR_007942) | YRC | training resource, biomedical technology research center | Biomedical technology research center that (1) exploits the budding yeast Saccharomyces cerevisiae to develop novel technologies for investigating and characterizing protein function and protein structure (2) facilitates research and extension of new technologies through collaboration, and (3) actively disseminates data and technology to the research community. Through collaboration, the YRC freely provides resources and expertise in six core technology areas: Protein Tandem Mass Spectrometry, Protein Sequence-Function Relationships, Quantitative Phenotyping, Protein Structure Prediction and Design, Fluorescence Microscopy, Computational Biology. | systems biology technology center, protein function, protein structure, mass spectrometry, protein, structure prediction, fluorescence microscopy, computational biology, sequence, function, phenotyping | has parent organization: University of Washington; Seattle; USA | NCRR ; NIGMS P41 GM103533 |
nif-0000-03650 | SCR_007942 | YRC | 2026-08-03 09:33:36 | 6 | |||||||
|
EUROpean Saccharomyces Cerevisiae ARchive for Functional Analysis Resource Report Resource Website 10+ mentions |
EUROpean Saccharomyces Cerevisiae ARchive for Functional Analysis (RRID:SCR_003093) | EUROSCARF | biomaterial supply resource, material resource, organism supplier | Archive of yeast strains and plasmids that were generated during various yeast functional analysis projects. | plasmid, strain, wild type, deletion, tap fusion, degron, orf, functional analysis, yeast |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Goethe University Frankfurt am Main; Hessen; Germany |
BMBF ; European UnionROFAN I and II ; European yeast industrial platform ; federal state of Hessen |
Free, Freely available | nif-0000-30504 | http://www.uni-frankfurt.de/fb15/mikro/EUROSCARF/indexhtml | SCR_003093 | 2026-08-03 09:32:11 | 40 | ||||||
|
I2D Resource Report Resource Website 10+ mentions |
I2D (RRID:SCR_002957) | I2D | production service resource, data analysis service, service resource, database, analysis service resource, data or information resource | Database of known and predicted mammalian and eukaryotic protein-protein interactions, it is designed to be both a resource for the laboratory scientist to explore known and predicted protein-protein interactions, and to facilitate bioinformatics initiatives exploring protein interaction networks. It has been built by mapping high-throughput (HTP) data between species. Thus, until experimentally verified, these interactions should be considered predictions. It remains one of the most comprehensive sources of known and predicted eukaryotic PPI. It contains 490,600 Source Interactions, 370,002 Predicted Interactions, for a total of 846,116 interactions, and continues to expand as new protein-protein interaction data becomes available. | interaction, prediction, protein-protein interaction, high-throughput, model organism, mammal, eukaryote, visualization, interolog, protein |
is related to: Interaction Reference Index is related to: IMEx - The International Molecular Exchange Consortium is related to: PSICQUIC Registry is related to: IntAct has parent organization: University of Toronto; Ontario; Canada |
National Science and Engineering Research Council RGPIN 203833-02; NIGMS P50-GM62413 |
PMID:17535438 PMID:15657099 |
Free, Available for download, Freely available | nif-0000-03005, r3d100010675 | https://doi.org/10.17616/R3BG8R | SCR_002957 | Interologous Interaction Database, OPHID, I2D - Interologous Interaction Database | 2026-08-03 09:31:54 | 23 | ||||
|
NLSdb: a database of nuclear localization signals Resource Report Resource Website 1+ mentions |
NLSdb: a database of nuclear localization signals (RRID:SCR_003273) | NLSdb | production service resource, data analysis service, service resource, database, analysis service resource, data or information resource | A database of nuclear localization signals (NLSs) and of nuclear proteins targeted to the nucleus by NLS motifs. NLSs are short stretches of residues mediating transport of nuclear proteins into the nucleus. The database contains 114 experimentally determined NLSs that were obtained through an extensive literature search. Using "in silico mutagenesis" this set was extended to 308 experimental and potential NLSs. This final set matched over 43% of all known nuclear proteins and matches no currently known non-nuclear protein. NLSdb contains over 6000 predicted nuclear proteins and their targeting signals from the PDB and SWISS-PROT/TrEMBL databases. The database also contains over 12 500 predicted nuclear proteins from six entirely sequenced eukaryotic proteomes (Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana and Saccharomyces cerevisiae). NLS motifs often co-localize with DNA-binding regions. This observation was used to also annotate over 1500 DNA-binding proteins. From this site you can: * Query NLSdb * Find out how to use NLSdb * Browse the entries in NLSdb * Find out if your protein has an NLS using PredictNLS * Predict subcellular localization of your protein using LOCtree | nuclear localization signal, nuclear protein, nucleus, motif, predict, protein | has parent organization: Columbia University; New York; USA | NIGMS 1-P50-GM62413-01; NSF DBI-0131168 |
PMID:12520032 | Free for academic use, Acknowledgement requested, All others should inquire about a commercial license | nif-0000-03191 | http://cubic.bioc.columbia.edu/db/NLSdb/ | SCR_003273 | NLSdb - a database of nuclear localization signals | 2026-08-03 09:32:02 | 4 | ||||
|
Reactome Resource Report Resource Website 1000+ mentions |
Reactome (RRID:SCR_003485) | production service resource, data analysis service, service resource, database, analysis service resource, data or information resource | Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets. | pathway, interaction, reaction, nucleic acid, protein, complex, small molecule, signaling pathway, immune function, transcriptional regulation, translation, apoptosis, metabolism, ortholog, visualization, protein-protein interaction, web service, book, biomart, gold standard, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: DisGeNET is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: WikiPathways is related to: Pathway Commons is related to: ConsensusPathDB is related to: FlyMine is related to: AmiGO is related to: PSICQUIC Registry is related to: Integrated Molecular Interaction Database is related to: NCBI BioSystems Database is related to: MOPED - Model Organism Protein Expression Database is related to: KOBAS is related to: PSICQUIC Registry is related to: Pathway Interaction Database is related to: hiPathDB - human integrated Pathway DB with facile visualization is related to: Algal Functional Annotation Tool has parent organization: Ontario Institute for Cancer Research has parent organization: Cold Spring Harbor Laboratory has parent organization: European Bioinformatics Institute has parent organization: New York University School of Medicine; New York; USA works with: PathwayMatcher |
Ontario Research Fund ; European Molecular Biology Laboratory ; NHGRI P41 HG003751; European Union FP6 ENFIN LSHG-CT-2005-518254; NIGMS GM080223; NIGMS R01 GM100039 |
PMID:21082427 PMID:21067998 |
Open source, Public, Freely available | r3d100010285, nif-0000-03390, biotools:reactome | https://bio.tools/reactome, https://doi.org/10.17616/R3V59P | SCR_003485 | Reactome Functional Interaction Network | 2026-08-03 09:32:16 | 4282 | |||||
|
DNAtraffic Resource Report Resource Website |
DNAtraffic (RRID:SCR_008886) | DNAtraffic | data or information resource, database | DNAtraffic database is dedicated to be an unique comprehensive and richly annotated database of genome dynamics during the cell life. DNAtraffic contains extensive data on the nomenclature, ontology, structure and function of proteins related to control of the DNA integrity mechanisms such as chromatin remodeling, DNA repair and damage response pathways from eight model organisms commonly used in the DNA-related study: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Escherichia coli and Arabidopsis thaliana. DNAtraffic contains comprehensive information on diseases related to the assembled human proteins. Database is richly annotated in the systemic information on the nomenclature, chemistry and structure of the DNA damage and drugs targeting nucleic acids and/or proteins involved in the maintenance of genome stability. One of the DNAtraffic database aim is to create the first platform of the combinatorial complexity of DNA metabolism pathway analysis. Database includes illustrations of pathway, damage, protein and drug. Since DNAtraffic is designed to cover a broad spectrum of scientific disciplines it has to be extensively linked to numerous external data sources. Database represents the result of the manual annotation work aimed at making the DNAtraffic database much more useful for a wide range of systems biology applications. DNAtraffic database is freely available and can be queried by the name of DNA network process, DNA damage, protein, disease, and drug. | dna, cell cycle, genome, nomenclature, ontology, structure, function, protein, chromatin remodeling, dna repair, damage response pathway, pathway, damage, drug, annotation, disease, dna network process, dna damage, gene sequence, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Polish Academy of Sciences Warsaw; Warsaw; Poland |
Norwegian Financial Mechanism PNRF-143-AI-1/07; Polish Ministry of Science and Higher Education N N301 165835 |
PMID:22110027 | Free | biotools:dnatraffic, nlx_151312 | https://bio.tools/dnatraffic | SCR_008886 | DNAtraffic database | 2026-08-03 09:34:09 | 0 | ||||
|
Pittsburgh Center for Kidney Research Model Organisms Resource Report Resource Website |
Pittsburgh Center for Kidney Research Model Organisms (RRID:SCR_015288) | resource, service resource, access service resource, core facility | Core that uses the yeast S. cerevisiae and the zebrafish D. rerio to dissect fundamental aspects of kidney development and protein structure and function. | renal disease, protein disorders, kidney disease, zebrafish |
is listed by: NIDDK Information Network (dkNET) has parent organization: Pittsburgh Center for Kidney Research is organization facet of: Pittsburgh Center for Kidney Research |
NIDDK P30DK079307; University of Pittsburgh School of Medicine; Pennsylvania; USA ; Icahn School of Medicine at Mount Sinai; New York; USA |
Available to the research community | SCR_015288 | 2026-08-03 09:36:09 | 0 | |||||||||
|
GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool Resource Report Resource Website 100+ mentions |
GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool (RRID:SCR_006848) | GOrilla | data analysis service, service resource, analysis service resource, production service resource | A tool for identifying and visualizing enriched GO terms in ranked lists of genes. It can be run in one of two modes: * Searching for enriched GO terms that appear densely at the top of a ranked list of genes or * Searching for enriched GO terms in a target list of genes compared to a background list of genes. | gene, genetic, ontology, ontology or annotation visualization, statistical analysis, term enrichment, visualization, analysis, protein |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology |
European Union FP6 ; Yeshaya Horowitz Association |
PMID:19192299 | Acknowledgement requested, Free, Public | nlx_80425, OMICS_02282 | SCR_006848 | Gene Ontology enRIchment anaLysis and visuaLizAtion tool, GOrilla: Gene Ontology Enrichment Analysis Visualization Tool | 2026-08-03 09:33:11 | 492 | |||||
|
PhenoM - Phenomics of yeast Mutants Resource Report Resource Website |
PhenoM - Phenomics of yeast Mutants (RRID:SCR_006970) | PhenoM | image collection, production service resource, data analysis service, service resource, database, analysis service resource, data or information resource | Database of morphological phenotypes caused by mutation of essential genes in Saccharomyces cerevisiae, it allows storing, retrieving, visualizing and data mining the quantitative single-cell measurements extracted from micrographs of the temperature-sensitive (ts) mutant cells. PhenoM allows users to rapidly search and retrieve raw images and their quantified morphological data for genes of interest. The database also provides several data-mining tools, including a PhenoBlast module for phenotypic comparison between mutant strains and a Gene Ontology module for functional enrichment analysis of gene sets showing similar morphological alterations. About one-fifth of the genes in the budding yeast are essential for haploid viability and cannot be functionally assessed using standard genetic approaches such as gene deletion. To facilitate genetic analysis of essential genes, we and others have assembled collections of yeast strains expressing temperature-sensitive (ts) alleles of essential genes. To explore the phenotypes caused by essential gene mutation we used a panel of genetically engineered fluorescent markers to explore the morphology of cells in the ts strain collection using high-throughput microscopy. The database contains quantitative measurements of 1,909,914 cells and 78,194 morphological images for 775 temperature-sensitive mutants spanning 491 different essential genes in permissive temperature (26* C) and restrictive temperature (32* C). The morphological images were generated by high-content screening (HCS) technology. | phenomics, phenotype, yeast, mutant, cell, morphology, essential gene, gene, high-content screening, microscopy, micrograph, mutant cell, temperature-sensitive allele, allele, genetic analysis, blast, mutation, orf, actin, dna damage, nucleus, mitochondria, plasma membrane, mitotic spindle, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada |
Ontario Research Fund ; Fudan University - University of Toronto Exchange Scholarship ; Canadian Institutes of Health Research GMX-201237; Canadian Institutes of Health Research GMX-211012; Canadian Foundation for Innovation LEF-21475 |
PMID:22009677 | Free | nlx_151489, biotools:phenom, r3d100012722 | https://bio.tools/phenom, https://doi.org/10.17616/R3GJ5J | SCR_006970 | Phenomics of yeast Mutants, Phenomics of yeast Mutants (PhenoM) | 2026-08-03 09:33:13 | 0 | ||||
|
YeTFaSCo Resource Report Resource Website 10+ mentions |
YeTFaSCo (RRID:SCR_006893) | YeTFaSCo | data repository, production service resource, data analysis service, service resource, database, storage service resource, analysis service resource, data or information resource | Collection of all available transcription factor (TF) specificities for the yeast Saccharomyces cerevisiae in Position Frequency Matrix (PFM) or Position Weight Matrix (PWM) formats. The specificities are evaluated for quality using several metrics. With this website, you can scan sequences with the motifs to find where potential binding sites lie, inspect precomputed genome-wide binding sites, find which TFs have similar motifs to one you have found, and download the collection of motifs. Submissions are welcome. | transcription factor, binding site, sequence, yeast, motif, gene, genome, protein, protein complex |
is listed by: OMICtools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada |
Ontario Graduate Scholarship awards ; Canadian Institutes of Health Research Operating Grant MOP-490425; Canadian Institutes of Health Research Operating Grant MOP-86705 |
PMID:22102575 | Acknowledgement requested | nlx_151611, OMICS_01861 | SCR_006893 | Yeast Transcription Factor Specificity Compendium, YeTFaSCo: The Yeast Transcription Factor Specificity Compendium | 2026-08-03 09:33:12 | 34 | |||||
|
Organelle DB Resource Report Resource Website 1+ mentions |
Organelle DB (RRID:SCR_007837) | Organelle DB | image collection, data repository, d spatial image, data or information resource, database, storage service resource, service resource | Database of organelle proteins, and subcellular structures / complexes from compiled protein localization data from organisms spanning the eukaryotic kingdom. All data may be downloaded as a tab-delimited text file and new localization data (and localization images, etc) for any organism relevant to the data sets currently contained in Organelle DB is welcomed. The data sets in Organelle DB encompass 138 organisms with emphasis on the major model systems: S. cerevisiae, A. thaliana, D. melanogaster, C. elegans, M. musculus, and human proteins as well. In particular, Organelle DB is a central repository of yeast protein localization data, incorporating results from both previous and current (ongoing) large-scale studies of protein localization in Saccharomyces cerevisiae. In addition, we have manually curated several recent subcellular proteomic studies for incorporation in Organelle DB. In total, Organelle DB is a singular resource consolidating our knowledge of the protein composition of eukaryotic organelles and subcellular structures. When available, we have included terms from the Gene Ontologies: the cellular component, molecular function, and biological process fields are discussed more fully in GO. Additionally, when available, we have included fluorescent micrographs (principally of yeast cells) visualizing the described protein localization. Organelle View is a visualization tool for yeast protein localization. It is a visually engaging way for high school and undergraduate students to learn about genetics or for visually-inclined researchers to explore Organelle DB. By revealing the data through a colorful, dimensional model, we believe that different kinds of information will come to light. | gene, fly, vertebrate, human, mouse, plant, worm, yeast, protein, k-12, organelle, protein localization, function, subcellular structure, protein complex, sequence, annotation, micrograph, visualization, data analysis service |
is related to: Gene Ontology has parent organization: University of Michigan; Ann Arbor; USA |
American Cancer Society Research Scholar Grant RSG-06-179-01-MBC; March of Dimes Basil O'Connor Starter Scholar Research award 5-FY05-1224; NSF DBI-0543017 |
PMID:17130152 PMID:15608270 |
Free, Acknowledgement requested | nif-0000-03226 | SCR_007837 | Organelle DB: A Database of Organelles and Protein Complexes | 2026-08-03 09:33:33 | 7 | |||||
|
Yeast snoRNA Database Resource Report Resource Website 1+ mentions |
Yeast snoRNA Database (RRID:SCR_007980) | production service resource, data analysis service, service resource, database, analysis service resource, data or information resource | A database of S. cerevisiae H/ACA and C/D box snoRNAs, useful for research on rRNA nucleotide modifications in the ribosome, especially those created by small nucleolar RNA:protein complexes (snoRNPs). The interactive service enables a user to visualize the positions of pseudouridines, 2'-O-methylations, and base methylations in three-dimensional space in the ribosome and also in linear and secondary structure formats of ribosomal RNA. The tools provide additional perspective on where the modifications occur relative to functional regions within the rRNA and relative to other nearby modifications. This package of tools is presented as a major enhancement of an existing but significantly upgraded yeast snoRNA database. The other key features of the enhanced database include details of the base pairing of snoRNAs with target RNAs, genomic organization of the yeast snoRNA genes, and information on corresponding snoRNAs and modifications in other model organisms. | saccharomyces cerevisiae |
is related to: 3D Ribosomal Modification Maps Database has parent organization: University of Massachusetts Amherst; Massachusetts; USA |
U.S. Public Health Service ; NIGMS GM19351 |
PMID:17283215 | nif-0000-03651 | http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html | SCR_007980 | Yeast snoRNA Database at UMass-Amherst | 2026-08-03 09:33:37 | 1 | ||||||
|
Saccharomyces Genome Deletion Project Resource Report Resource Website 10+ mentions |
Saccharomyces Genome Deletion Project (RRID:SCR_014961) | data or information resource, database, portal, project portal | Database and project to reveal open reading frames (ORFs) in the yeast genome in order to discover their functions. A PCR-based gene deletion strategy is used to assign functions through phenotypic analysis of mutants. | yeast, open reading frames, ORF, genome, deletion, Saccharomyces cerevisiae | Free | SCR_014961 | 2026-08-03 09:35:41 | 18 |
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 RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID 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 RRID then you can log in from here to get additional features in RRID 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 RRID 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.
