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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Unified Human Interactome Resource Report Resource Website 10+ mentions |
Unified Human Interactome (RRID:SCR_005805) | UniHI | data or information resource, database | A database of human molecular interaction networks that integrates human protein-protein and transcriptional regulatory interactions from 15 distinct resources and aims to give direct and easy access to the integrated data set and to enable users to perform network-based investigations. The database includes tools (i) to search for molecular interaction partners of query genes or proteins in the integrated dataset, (ii) to inspect the origin, evidence and functional annotation of retrieved proteins and interactions, (iii) to visualize and adjust the resulting interaction network, (iv) to filter interactions based on method of derivation, evidence and type of experiment as well as based on gene expression data or gene lists and (v) to analyze the functional composition of interaction networks. | molecular interaction network, interactome, protein, protein interaction network, protein interaction, pathway, function, visualization, protein-protein interaction, transcriptional regulatory interaction, network |
is listed by: OMICtools has parent organization: University of Algarve; Faro; Portugal |
PMID:24214987 PMID:22218860 PMID:18984619 PMID:17158159 |
Public, Non-commercial | OMICS_01911, nif-0000-03609 | http://www.mdc-berlin.de/unihi | SCR_005805 | 2026-02-11 10:57:14 | 19 | ||||||
|
DroID - Drosophila Interactions Database Resource Report Resource Website 10+ mentions |
DroID - Drosophila Interactions Database (RRID:SCR_006634) | DroID | data or information resource, database | A gene and protein interactions database designed specifically for the model organism Drosophila including protein-protein, transcription factor-gene, microRNA-gene, and genetic interactions. For advanced searches and dynamic graphing capabilities the IM Browser and a DroID Cytoscape plugin are available. | interaction, gene, protein, protein interaction, annotation, transcription factor, rna, protein-protein interaction, interactome, gene expression, phenotype, interolog, ortholog |
is listed by: OMICtools is related to: Cytoscape has parent organization: Wayne State University School of Medicine; Michigan; USA |
PMID:21036869 PMID:18840285 |
Free, Public, Acknowledgement requested | nif-0000-02767, OMICS_01908 | SCR_006634 | DroID - The Drosophila Interactions Database | 2026-02-11 10:57:26 | 35 | ||||||
|
ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets Resource Report Resource Website 10+ mentions |
ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets (RRID:SCR_001774) | ReCount | data or information resource, data set | RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward. | rna-seq, gene count, gene, phenotype, r |
is listed by: OMICtools is related to: Myrna has parent organization: SourceForge has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA |
NIGMS T32GM074906 | PMID:22087737 | Free, Available for download, Freely available | OMICS_01953 | SCR_001774 | 2026-02-11 10:56:18 | 35 | ||||||
|
GenAge Resource Report Resource Website 100+ mentions |
GenAge (RRID:SCR_010223) | GenAge | data or information resource, database | Collection of annotated and manually curated data of genes related to aging divided into genes related to longevity and/or aging in model organisms (yeast, worms, flies, mice, etc.) and aging related human genes. | collection, curated, data, gene, aging, longevity |
is used by: GEROprotectors has parent organization: Human Ageing Genomic Resources |
Aging | HAGR''s lisense | nlx_156768 | SCR_010223 | GenAge, GenAge Database of Ageing-Related Genes, The Ageing Gene Database, Gene Database | 2026-02-11 10:58:14 | 138 | ||||||
|
GeneSeer Resource Report Resource Website |
GeneSeer (RRID:SCR_002626) | GeneSeer | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Database to access gene information through common names and allows identification of homologs and paralogs for a given gene. This publicly available tool leverages public sequence data, gene metadata information, and other publicly available data to calculate and display orthologous and paralogous gene relationships for all genes from several species, including yeasts, insects, worms, vertebrates, mammals, and primates such as humans. | gene, homolog, paralog, genome, search engine, ortholog | PMID:16176584 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156048 | http://katahdin.mssm.edu/geneseer/scripts/main.pl | http://geneseer.cshl.org/ | SCR_002626 | 2026-02-11 10:56:30 | 0 | ||||||
|
PhenomeBLAST Ontology Resource Report Resource Website 1+ mentions |
PhenomeBLAST Ontology (RRID:SCR_005139) | PHENOMEBLAST | data or information resource, ontology, controlled vocabulary | A cross-species phenotype and anatomy ontology resulting from combining available anatomy and phenotype ontologies and their definitions. The ontology includes phenotype definitions for yeast, mouse, fish, worm, fly and human phenotypes and diseases. | owl | is listed by: BioPortal | nlx_157549 | SCR_005139 | 2026-02-12 09:44:01 | 1 | |||||||||
|
RIKEN BioResource Center Resource Report Resource Website 1000+ mentions |
RIKEN BioResource Center (RRID:SCR_003250) | BRC, RIKEN BRC | biomaterial supply resource, organism supplier, material resource | RIKEN BRC contributes to advancement of life science research by collecting, preserving and distributing biological resources such as experimental animals, experimental plants, cultured cell lines, genetic materials (DNA), and associated bioinformatics. The RIKEN BRC develops novel bioresources to promote scientific research and new technologies to increase the value of bioresources, and also to implement effective procedures for the preservation, quality control and usage of bioresources. The RIKEN BRC is working closely with institutions in Japan and abroad. | RIN, Resource Information Network, experimental animal, experimental plant, cultured cell line, dna, animal, plant, cell line, genetic material, virus, gene, cultured cell, embryo, sperm, tissue, organ, seed, cell, recombinant host, bioresource, FASEB list, RRID Community Authority |
is listed by: One Mind Biospecimen Bank Listing is listed by: Resource Information Network is related to: Federation of International Mouse Resources is related to: MGI strains has parent organization: RIKEN Tsukuba Institute; Kansai; Japan is parent organization of: JCM works with: Cellosaurus works with: International Mouse Strain Resource |
PMID:19448331 PMID:34532769 |
Free, Freely available | nif-0000-31407 | SCR_003250 | RIKEN Tsukuba Institute RIKEN BioResource Center | 2026-02-13 10:55:12 | 2208 | ||||||
|
Candida Genome Database Resource Report Resource Website 100+ mentions |
Candida Genome Database (RRID:SCR_002036) | CGD, CGD LOCUS, CGD REF | data repository, storage service resource, data or information resource, service resource, database | Database of genetic and molecular biological information about Candida albicans. Contains information about genes and proteins, descriptions and classifications of their biological roles, molecular functions, and subcellular localizations, gene, protein, and chromosome sequence information, tools for analysis and comparison of sequences and links to literature information. Each CGD gene or open reading frame has an individual Locus Page. Genetic loci that are not tied to DNA sequence also have Locus Pages. Provides Gene Ontology, GO, to all its users. Three ontologies that comprise GO (Molecular Function, Cellular Component, and Biological Process) are used by multiple databases to annotate gene products, so that this common vocabulary can be used to compare gene products across species. Development of ontologies is ongoing in order to incorporate new information. Data submissions are welcome. | protein, chromosome, classification, gene, genome, candidiasis, thrush, yeast, yeast gene, yeast genome, candida albicans, candida glabrata, data analysis service, biological role, molecular function, subcellular localization, chromosome sequence, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: ASPGD is related to: Gene Ontology has parent organization: Stanford University School of Medicine; California; USA |
NIDCR DE015873 | PMID:19808938 | Free, Available for download, Freely available | nif-0000-02634, biotools:cgd | https://bio.tools/cgd | SCR_002036 | 2026-02-13 10:54:58 | 472 | |||||
|
Genevestigator Resource Report Resource Website 100+ mentions |
Genevestigator (RRID:SCR_002358) | Genevestigator | commercial organization, data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | A high performance search engine for gene expression that integrates thousands of manually curated public microarray and RNAseq experiments and nicely visualizes gene expression across different biological contexts (diseases, drugs, tissues, cancers, genotypes, etc.). There are two basic analysis approaches: # for a gene of interest, identify which conditions affect its expression. # for condition(s) of interest, identify which genes are specifically expressed in this/these conditions. Genevestigator builds on the deep integration of data, both at the level of data normalization and on the level of sample annotations. This deep integration allows scientists to ask new types of questions that cannot be addressed using conventional tools. | gene, genetic, animal, development, disease, meta-analysis, regulation, stage, microarray, rnaseq, visualization, gene expression, disease, drug, tissue, cancer, genotype, pharma, biomedical, conditions, genotype, anatomy, neoplasm, chemical, hormone, infection, model organism, organ, cell type, cell line, target, biomarker, similarity, FASEB list | is parent organization of: RefGenes | 4 products:, Free, Free for academic use, Account required, Paid subscription, Local installation | nif-0000-21172, OMICS_00763 | SCR_002358 | 2026-02-13 10:55:01 | 396 | ||||||||
|
phenomeNET Resource Report Resource Website 10+ mentions |
phenomeNET (RRID:SCR_006165) | PhenomeNet | data analysis service, analysis service resource, data or information resource, production service resource, source code, service resource, software resource, database | PhenomeNet is a cross-species phenotype similarity network. It contains the experimentally observed phenotypes of multiple species as well as the phenotypes of human diseases. PhenomeNet provides a measure of phenotypic similarity between the phenotypes it contains. The latest release (from 22 June 2012) contains 124,730 complex phenotype nodes taken from the yeast, fish, worm, fly, rat, slime mold and mouse model organism databases as well as human disease phenotypes from OMIM and OrphaNet. The network is a complete graph in which edge weights represent the degree of phenotypic similarity. Phenotypic similarity can be used to identify and prioritize candidate disease genes, find genes participating in the same pathway and orthologous genes between species. To compute phenotypic similarity between two sets of phenotypes, we use a weighted Jaccard index. First, phenotype ontologies are used to infer all the implications of a phenotype observation using several phenotype ontologies. As a second step, the information content of each phenotype is computed and used as a weight in the Jaccard index. Phenotypic similarity is useful in several ways. Phenotypic similarity between a phenotype resulting from a genetic mutation and a disease can be used to suggest candidate genes for a disease. Phenotypic similarity can also identify genes in a same pathway or orthologous genes. PhenomeNet uses the axioms in multiple species-dependent phenotype ontologies to infer equivalent and related phenotypes across species. For this purpose, phenotype ontologies and phenotype annotations are integrated in a single ontology, and automated reasoning is used to infer equivalences. Specifically, for every phenotype, PhenomeNet infers the related mammalian phenotype and uses the Mammalian Phenotype Ontology for computing phenotypic similarity. Tools: * PhenomeBLAST - A tool for cross-species alignments of phenotypes * PhenomeDrug - method for drug-repurposing | phenotype, disease, gene, genotype, allele, model organism, human disease, candidate disease gene, pathway, orthologous gene, ortholog, ontology, semantic similarity, mutant phenotype, disease pathway, alignment, pharmacogenomics, drug |
is related to: OMIM is related to: Orphanet is related to: PharmGKB is related to: MPO has parent organization: University of Cambridge; Cambridge; United Kingdom |
European Union 7th FPRICORDO project 248502; NHGRI R01 HG004838-02; BBSRC BBG0043581 |
PMID:21737429 | The source code and all data are freely available on http://phenomeblast.googlecode.com | nlx_151667 | SCR_006165 | PhenomeNet - Cross Species Phenotype Network | 2026-02-13 10:55:46 | 13 | |||||
|
WebGestalt: WEB-based GEne SeT AnaLysis Toolkit Resource Report Resource Website 1000+ mentions |
WebGestalt: WEB-based GEne SeT AnaLysis Toolkit (RRID:SCR_006786) | WebGestalt | data access protocol, software resource, web service, web application | Web based gene set analysis toolkit designed for functional genomic, proteomic, and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources and provides a way for biologists to make sense out of gene lists. This version of WebGestalt supports eight organisms, including human, mouse, rat, worm, fly, yeast, dog, and zebrafish. | proteomic, gene expression, genome wide association study, statistical analysis, functional genomics, protein protein interaction, pathway, regulatory module, analysis toolkit, web application |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: Entrez Gene is related to: KEGG is related to: Pathway Commons is related to: WikiPathways is related to: PheWAS Catalog is related to: webgestaltr has parent organization: Vanderbilt University; Tennessee; USA |
NIAAA U01 AA016662; NIAAA U01 AA013512; NIDA P01 DA015027; NIMH P50 MH078028; NIMH P50 MH096972; NCI U24 CA159988; NIGMS R01 GM088822 |
PMID:24233776 PMID:15980575 PMID:14975175 |
Free, Freely available | OMICS_02222, nif-0000-30622 | http://bioinfo.vanderbilt.edu/webgestalt/ | SCR_006786 | GOTM, Gene Ontology Tree Machine, WebGestalt2, WEB-based GEne SeT AnaLysis Toolkit, WebGestalt | 2026-02-13 10:55:56 | 2760 | ||||
|
mAdb Resource Report Resource Website 10+ mentions |
mAdb (RRID:SCR_006677) | mAdb | data repository, storage service resource, data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | Microarray data management and analysis system for NCI / Center for Cancer Research scientists / collaborators. Data is secured and backed up on a regular basis, and investigators can authorize levels of access privileges to their projects, allowing data privacy while still enabling data sharing with collaborators. | microarray, bioinformatics, data management, analysis, gene expression, affymetrix, image, alignment, gene array list, cdna, oligonucleotide, gene discovery, prediction, comparison, cancer, FASEB list | has parent organization: Center for Cancer Research | Center for Information Technology | PMID:14728569 | Account required, Restricted to NIH users/collaborators, The community can contribute to this resource | nif-0000-00171 | http://nciarray.nci.nih.gov/ | SCR_006677 | Mad Bee, microArray database, Micro-array Database at the National Cancer Institute, NCI/CIT microArray database | 2026-02-13 10:55:54 | 38 | ||||
|
MARRVEL Resource Report Resource Website 10+ mentions |
MARRVEL (RRID:SCR_016871) | MARRVEL | data analysis service, analysis service resource, data or information resource, production service resource, service resource, database | Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research. | integration, database, model, genetic, resource, functional, annotation, genome, data, analysis, dataset, rare, variant, exploration, bio.tools |
uses: OMIM uses: ClinVar uses: DECIPHER uses: Geno2MP uses: Database of Genomic Variants is used by: Hypothesis Center is listed by: bio.tools is listed by: Debian |
NINDS 1U54NS093793; NIH Office of the Director R24 OD022005; The Robert and Janice McNair Foundation ; Baylor College of Medicine Medical Scientist Training Program ; NINDS U54 NS093793; NIGMS R01 GM067858; NIGMS R01 GM120033; NSF DMS 1263932; CPRIT RP170387; Houston Endowment ; Huffington Foundation ; Belfer Foundation ; T T Chao Family Foundation ; NIGMS R01 GM067761; NIGMS R01 GM084947; NCRR R24 RR032668; NIH Office of the Director R24 OD021997; NCI P30 CA06516; NHGRI U01 HG007709; Simons Foundation |
PMID:28502612 | Free, Public, Freely available | biotools:marrvel | https://bio.tools/marrvel | SCR_016871 | Model organism Aggregated Resources for Rare Variant ExpLoration | 2026-02-13 10:57:47 | 22 | ||||
|
BSA4Yeast Resource Report Resource Website 1+ mentions |
BSA4Yeast (RRID:SCR_017113) | web service, data analysis service, analysis service resource, production service resource, service resource, data access protocol, software resource | Web application for Quantitative Trait Loci mapping via bulk segregant analysis of yeast sequencing data. Application provides automated data processing, annotations, and web interface to explore identified QTLs. | quantitative, trait, loci, mapping, bulk, segregant, analysis, yeast, sequencing, data, processing, annotation, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Luxembourg; Luxembourg; Luxembourg |
Fonds Nationale de la Recherche (FNR) Luxembourg | Free, Freely available, Registration required | biotools:BSA4Yeast | https://bio.tools/BSA4Yeast | SCR_017113 | Bulk Segregant Analysis for Yeast | 2026-02-13 10:57:51 | 1 | ||||||
|
MOPED - Model Organism Protein Expression Database Resource Report Resource Website 1+ mentions |
MOPED - Model Organism Protein Expression Database (RRID:SCR_006065) | MOPED | data analysis service, analysis service resource, resource, data or information resource, production service resource, service resource, database | An expanding multi-omics resource that enables rapid browsing of gene and protein expression information from publicly available studies on humans and model organisms. MOPED also serves the greater research community by enabling users to visualize their own expression data, compare it with existing studies, and share it with others via private accounts. MOPED uniquely provides gene and protein level expression data, meta-analysis capabilities and quantitative data from standardized analysis utilizing SPIRE (Systematic Protein Investigative Research Environment). Data can be queried for specific genes and proteins; browsed based on organism, tissue, localization and condition; and sorted by false discovery rate and expression. MOPED links to various gene, protein, and pathway databases, including GeneCards, Entrez, UniProt, KEGG and Reactome. The current version of MOPED (MOPED 2.5) The current version of MOPED (MOPED 2.5, 2014) contains approximately 5 million total records including ~260 experiments and ~390 conditions. | protein expression, gene expression, model organism, gene, protein, pathway, proteomics, transcriptomics, data visualization, overlap plot, heatmap, dot plot, data sharing, protein localization, gene localization |
is related to: GeneCards is related to: UniProt is related to: KEGG is related to: Reactome |
Robert B McMillen Foundation ; NSF DBI0544757; NIGMS 5R01GM076680; NIDDK UO1DK072473; NIDDK 1U01DK089571 |
PMID:24350770 PMID:22139914 |
nlx_151470 | SCR_006065 | Multi-Omics Profiling Expression Database | 2026-02-13 10:55:45 | 2 | ||||||
|
Information Hyperlinked Over Proteins Resource Report Resource Website 10+ mentions |
Information Hyperlinked Over Proteins (RRID:SCR_004829) | iHOP | data or information resource, service resource, database | Information system that provides a network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. It provides this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research. Moreover, this literature network can be superimposed on experimental interaction data (e.g., yeast-two hybrid data from Drosophila melanogaster and Caenorhabditis elegans) to make possible a simultaneous analysis of new and existing knowledge. The network contains half a million sentences and 30,000 different genes from humans, mice, D. melanogaster, C. elegans, zebrafish, Arabidopsis thaliana, yeast and Escherichia coli. | phenotype, gene, protein, interaction, pathology, physiology, gene network, network, literature, gene function, text-mining, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: PubMed has parent organization: Autonomous University of Madrid; Madrid; Spain |
European Union IST-2001- 32688; European Union QLRT-2001-00015 |
PMID:15226743 | Creative Commons Attribution-NoDerivs License, Works v3 | biotools:ihop, nif-0000-00232, OMICS_01185 | https://bio.tools/ihop | SCR_004829 | iHOP - Information Hyperlinked over Proteins | 2026-02-13 10:55:31 | 24 | ||||
|
Arabidopsis Nucleolar Protein Database Resource Report Resource Website 1+ mentions |
Arabidopsis Nucleolar Protein Database (RRID:SCR_001793) | AtNoPDB | data or information resource, database, image | Database of proteins found in the nucleoli of Arabidopsis, identified through proteomic analysis. The Arabidopsis Nucleolar Protein database (AtNoPDB) provides information on the plant proteins in comparison to human and yeast proteins, and images of cellular localizations for over a third of the proteins. A proteomic analysis was carried out of nucleoli purified from Arabidopsis cell cultures and to date 217 proteins have been identified. Many proteins were known nucleolar proteins or proteins involved in ribosome biogenesis. Some proteins, such as spliceosomal and snRNP proteins, and translation factors, were unexpected. In addition, proteins of unknown function which were either plant-specific or conserved between human and plant, and proteins with differential localizations were identified. | image, plant protein, plant, protein, homologue, blast, human proteome, orthologue, human, yeast, cell culture, blast, nucleolar protein | has parent organization: James Hutton Institute; Scotland; United Kingdom | Scottish Executive Environment and Rural Affairs Department ; BBSRC |
PMID:15608277 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02562 | SCR_001793 | AtNoPDB Database | 2026-02-13 10:54:55 | 7 |
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 nidm-terms Resources search. From here you can search through a compilation of resources used by nidm-terms and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that nidm-terms 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 nidm-terms then you can log in from here to get additional features in nidm-terms 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 nidm-terms 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.
