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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Mitelman Database of Chromosome Aberrations in Cancer Resource Report Resource Website 100+ mentions |
Mitelman Database of Chromosome Aberrations in Cancer (RRID:SCR_012877) | database, data or information resource | The web site includes genomic data for humans and mice, including transcript sequence, gene expression patterns, single-nucleotide polymorphisms, clone resources, and cytogenetic information. Descriptions of the methods and reagents used in deriving the CGAP datasets are also provided. An extensive suite of informatics tools facilitates queries and analysis of the CGAP data by the community. One of the newest features of the CGAP web site is an electronic version of the Mitelman Database of Chromosome Aberrations in Cancer. The data in the Mitelman Database is manually culled from the literature and subsequently organized into three distinct sub-databases, as follows: -The sub-database of cases contains the data that relates chromosomal aberrations to specific tumor characteristics in individual patient cases. It can be searched using either the Cases Quick Searcher or the Cases Full Searcher. -The sub-database of molecular biology and clinical associations contains no data from individual patient cases. Instead, the data is pulled from studies with distinct information about: -Molecular biology associations that relate chromosomal aberrations and tumor histologies to genomic sequence data, typically genes rearranged as a consequence of structural chromosome changes. -Clinical associations that relate chromosomal aberrations and/or gene rearrangements and tumor histologies to clinical variables, such as prognosis, tumor grade, and patient characteristics. It can be searched using the Molecular Biology and Clinical (MBC) Associations Searcher -The reference sub-database contains all the references culled from the literature i.e., the sum of the references from the cases and the molecular biology and clinical associations. It can be searched using the Reference Searcher. CGAP has developed six web search tools to help you analyze the information within the Mitelman Database: -The Cases Quick Searcher allows you to query the individual patient cases using the four major fields: aberration, breakpoint, morphology, and topography. -The Cases Full Searcher permits a more detailed search of the same individual patient cases as above, by including more cytogenetic field choices and adding search fields for patient characteristics and references. -The Molecular Biology Associations Searcher does not search any of the individual patient cases. It searches studies pertaining to gene rearrangements as a consequence of cytogenetic aberrations. -The Clinical Associations Searcher does not search any of the individual patient cases. It searches studies pertaining to clinical associations of cytogenetic aberrations and/or gene rearrangements. -The Recurrent Chromosome Aberrations Searcher provides a way to search for structural and numerical abnormalities that are recurrent, i.e., present in two or more cases with the same morphology and topography. -The Reference Searcher queries only the references themselves, i.e., the references from the individual cases and the molecular biology and clinical associations. Sponsors: This database is sponsored by the University of Lund, Sweden and have support from the Swedish Cancer Society and the Swedish Children''s Cancer Foundation | expression, gene, aberration, abnormality, biology, breakpoint, cancer, cancer databases, characteristic, chromosomal, chromosome, clinical, clone, cytogenetic, genomic, grade, hisotology, human, mice, molecular, morphology, nucleotide, patient, pattern, polymorphism, prognosis, reagent, rearrangement, sequence, single, structural, topography, transcript, tumor, FASEB list | nif-0000-21268 | SCR_012877 | Mitelman Database | 2026-08-06 09:28:04 | 114 | ||||||||||
|
GARNET Resource Report Resource Website 10+ mentions |
GARNET (RRID:SCR_012033) | GARNET | data analysis service, production service resource, analysis service resource, service resource | An integrative platform for diverse types of gene set analysis with annotation network navigation. It includes tools for statistical analysis, visualization of annotation relationships, retrieval of genes from annotation database, and set operation for gene sets. In an effort to allow access to a full spectrum of amassed biological knowledge, they have integrated a variety of annotation data that include the GO, domain, disease, drug, chromosomal location, and custom-defined annotations. Diverse types of molecular networks (pathways, transcription and microRNA regulations, protein-protein interaction) are also included. The pair-wise relationship between annotation gene sets was calculated using kappa statistics. GARNET consists of three modules--gene set manager, gene set analysis and gene set retrieval, which are tightly integrated to provide virtually automatic analysis for gene sets. A dedicated viewer for annotation network has been developed to facilitate exploration of the related annotations. | statistical analysis, visualization, annotation, gene |
is listed by: OMICtools has parent organization: Ewha Womans University; Seoul; South Korea |
PMID:21342555 | OMICS_02224 | http://ercsb.ewha.ac.kr/garnet/ | http://ercsb.ewha.ac.kr:8080/GSEAWebApp/index.jsp, http://garnet.isysbio.org/ | SCR_012033 | Gene Annotation Relationship NEtwork Tools | 2026-08-06 09:27:51 | 18 | |||||
|
Mouse Genome Database Resource Report Resource Website 500+ mentions |
Mouse Genome Database (RRID:SCR_012953) | MGD | database, data or information resource | Community model organism database for laboratory mouse and authoritative source for phenotype and functional annotations of mouse genes. MGD includes complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information, all serving to further the use of the mouse as a model system for studying human biology and disease. MGD is a major component of the Mouse Genome Informatics.Contains standardized descriptions of mouse phenotypes, associations between mouse models and human genetic diseases, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information. Data are obtained and integrated via manual curation of the biomedical literature, direct contributions from individual investigators and downloads from major informatics resource centers. MGD collaborates with the bioinformatics community on the development and use of biomedical ontologies such as the Gene Ontology (GO) and the Mammalian Phenotype (MP) Ontology. | gene, genome, genetic, chromosome, clone, cytogenetic, dna, genomic, inbred, mammalian, mouse, mutant, ortholog, phenotype, primer, protein, reagent, sequence, strain, bio.tools |
is used by: DisGeNET is listed by: Debian is listed by: bio.tools is related to: Mouse Genome Informatics (MGI) has parent organization: Jackson Laboratory |
NHGRI HG000330 | PMID:21051359 | biotools:mgi, biotools:mgd, nif-0000-10301 | http://www.informatics.jax.org/mgihome/projects/overview.shtml, https://bio.tools/mgd, https://bio.tools/mgi | SCR_012953 | Mouse Genome Informatics: Mouse Genome Database, MGID, Mouse Genome Informatics Database | 2026-08-06 09:28:04 | 502 | |||||
|
Genetic Association Database Resource Report Resource Website 100+ mentions |
Genetic Association Database (RRID:SCR_013264) | database, data or information resource | The Genetic Association Database is an archive of human genetic association studies of complex diseases and disorders. The goal of this database is to allow the user to rapidly identify medically relevant polymorphism from the large volume of polymorphism and mutational data, in the context of standardized nomenclature. The data is from published scientific papers. Study data is recorded in the context of official human gene nomenclature with additional molecular reference numbers and links. It is gene centered. That is, each record is a record of a gene or marker. If a study investigated 6 genes for a particular disorder, there will be 6 records. Anyone may view this database and anyone may submit records. You do not have to be an author on the original study to submit a record. All submitted records will be reviewed before inclusion in the archive. Both genetic and environmental factors contribute to human diseases. Most common diseases are influenced by a large number of genetic and environmental factors, most of which individually have only a modest effect on the disease. Though genetic contributions are relatively well characterized for some monogenetic diseases, there has been no effort at curating the extensive list of environmental etiological factors. From a comprehensive search of the MeSH annotation of MEDLINE articles, they identified 3,342 environmental etiological factors associated with 3,159 diseases. They also identified 1,100 genes associated with 1,034 complex diseases from the NIH Genetic Association Database (GAD), a database of genetic association studies. 863 diseases have both genetic and environmental etiological factors available. Integrating genetic and environmental factors results in the etiome, which they define as the comprehensive compendium of disease etiology. | environmental, etiological, etiology, factor, gene, general human genetics databases, genetic, association, complex, disease, disorder, human, medically, molecular, monogenetic, mutational, nomenclature, polymorphism, scientific, FASEB list |
is used by: DisGeNET is related to: KOBAS has parent organization: National Institute on Aging |
Aging | nif-0000-21163 | SCR_013264 | GAD | 2026-08-06 09:28:06 | 152 | ||||||||
|
Therapeutically Relevant Multiple Pathways Database Resource Report Resource Website 1+ mentions |
Therapeutically Relevant Multiple Pathways Database (RRID:SCR_013471) | database, data or information resource | The Therapeutically Relevant Multiple Pathways Database is designed to provide information about such multiple pathways and related therapeutic targets described in the literatures, the targeted disease conditions, and the corresponding drugs/ligands directed at each of these targets. This database currently contains 11 entries of multiple pathways, 97 entries of individual pathways, 120 targets covering 72 disease conditions along with 120 sets of drugs directed at each of these targets. Each entry can be retrieved through multiple methods including multiple pathway name, individual pathway name and disease name. Additional information provided include protein name, synonyms, Swissprot AC number, species, gene name and location, protein sequence (AASEQ) and gene sequence (NTSEQ) as well as potential therapeutic implications while applicable. Cross-links to other databases are provided which include Genecard, GDB, Locuslink, NCBI, KEGG, OMIM, SwissProt to facilitate the access of more detailed information about various aspects of the particular target or non-target protein. Queries can be submitted by entering or selecting the required information in any one or combination of the fields in the form. User can specify full name or any part of the name in a text field, or choose one item from an selection field. Sponsors: TRMP is supported by the National University of Singapore. | drug, gene, condition, disease, intermolecular interactions and signaling pathways databases, ligand, literature, location, pathway, protein, sequence, specie, target, therapeutic, therapy | nif-0000-21402 | SCR_013471 | TRMP | 2026-08-06 09:28:09 | 2 | ||||||||||
|
Heart and Calcium Functional Network Database Resource Report Resource Website |
Heart and Calcium Functional Network Database (RRID:SCR_013515) | HCNet | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A specialized database for mouse heart and calcium signaling toolkit genes. It contains the functional gene modules pre-calculated from the microarray data compendium using various algorithms for genetic network analyses. The Heart and Calcium functional Network (HCNet) database is a collection of functional gene clusters calculated from microarray data compendium obtained from the Korea Systems Biology Initiative and from the publicly available GEO database. It was designed to assist experimentalists especially in the field of cardiac and calcium signaling research to detect potential network motifs and gene clusters that are functionally related or co-regulated by common transcription factors. Genes of defined numbers are classified into two categories, 1) heart-specific genes and 2) heart-specific genes plus calcium signaling toolkit-genes. | gene, calcium, cardiac, heart, microarray data, mouse, network, research, signaling | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20851 | SCR_013515 | Heart and Calcium Functional Network, Heart and Calcium Functional Network Database | 2026-08-06 09:28:09 | 0 | ||||||||
|
RiceGE Resource Report Resource Website 50+ mentions |
RiceGE (RRID:SCR_015061) | database, data or information resource | Gene database for Japonica rice. RiceGE is associated with SIGnAL at the Salk Institute. | japonica rice, rice, gene, genome | has parent organization: SIGnAL Salk Institute Genomic Analysis Laboratory | Freely available | http://signal.salk.edu/cgi-bin/RiceGE5 | SCR_015061 | RiceGE: Genome Express Database, Rice Functional Genomic Express Database | 2026-08-06 09:28:31 | 73 | ||||||||
|
Danish Twin Registry Resource Report Resource Website |
Danish Twin Registry (RRID:SCR_017482) | DTR | database, data or information resource | Twin registry to studying causes of cancer, gene inheritance and environment. Contains information on twins born in Denmark. Comprises twins born through more than 125 years. | Twin, cancer, data, gene, environment | Restricted | SCR_017482 | 2026-08-06 09:29:05 | 0 | ||||||||||
|
EpiFactors Resource Report Resource Website 10+ mentions |
EpiFactors (RRID:SCR_016956) | database, data or information resource | Manually curated collection of human epigenetic factors, their complexes, corresponding genes and products. | manually, curated, collection, human, epigenetic, factor, complex, corresponding, gene, target, product | is listed by: OMICtools | Russian Fund For Basic Research ; Ministerio de Economia Y Competividad ; Spain ; Åke Olsson’s foundation ; Swedish Cancer foundation ; Swedish Childhood cancer foundation ; Dynasty Foundation Fellowship ; Japanese Ministry of Education ; Culture ; Sports ; Science and Technology ; Norwegian University of Science and Technology |
PMID:26153137 | Free, Available for download, Freely available | SCR_016956 | 2026-08-06 09:28:59 | 16 | ||||||||
|
CoMeTa Website Resource Report Resource Website 1+ mentions |
CoMeTa Website (RRID:SCR_017357) | CoMeTa | service resource, database, data or information resource | Interactive database of miRNA targets and miRNA-regulated gene networks to integrate expression data from hundreds of cellular and tissue conditions. Website includes CoMeTa corank lists and additional targets for all of human miRNAs, their associated pathways resulting from COOL analysis, and miRNA communities with their corresponding enriched functional categories. Website is searchable by miRNA, target gene, or biological function of interest, and represents unique resource to gain insight into miRNA-controlled gene networks and functions. | Interactive, database, miRNA, target, gene, network, integrate, expression, condition, pathway, functional, data | Italian Telethon Foundation ; AIRC |
PMID:22345618 | Free, Freely available | SCR_017357 | Co-expression Meta-analysis of miRNA Target | 2026-08-06 09:29:05 | 3 | |||||||
|
HumanBase Resource Report Resource Website 50+ mentions |
HumanBase (RRID:SCR_016145) | database, data or information resource | Formerly known as GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), HumanBase applies machine learning algorithms to learn biological associations from massive genomic data collections. These integrative analyses reach beyond existing "biological knowledge" represented in the literature to identify novel, data-driven associations. | genome, analysis, tissue, network, gene, machine, learning, biology | NIGMS R01 GM071966; NHGRI R01 HG005998; NHLBI U54 HL117798; NIGMS P20 GM103534; NHGRI T32 HG003284; NCI T32 CA009528; NIGMS P50 GM071508; US Department Of Health And Human Services HHSN272201000054C |
PMID:25915600 | Free, Public | SCR_016145 | GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), GIANT | 2026-08-06 09:28:48 | 74 | ||||||||
|
ABA Mouse Brain: Atlas Resource Report Resource Website 100+ mentions |
ABA Mouse Brain: Atlas (RRID:SCR_017479) | service resource, database, data or information resource | Genome wide database of gene expression in mouse brain. Genome-wide atlas of gene expression in the adult mouse brain. | Genome, data, gene, expression, mouse, brain |
has parent organization: Allen Institute for Brain Science is provided by: Allen Brain Atlas |
PMID:17151600 | Free, Freely available | SCR_017479 | Allen Brain Atlas: Mouse Brain, , Allen Brain Atlas Mouse Brain: Atlas | 2026-08-06 09:29:05 | 328 | ||||||||
|
Jackson Laboratory Clinical Knowledgebase Resource Report Resource Website 10+ mentions |
Jackson Laboratory Clinical Knowledgebase (RRID:SCR_014965) | CKB | database, data or information resource | Semi-automated and manually curated database of gene/variant annotations, therapy knowledge, diagnostic/prognostic information, and oncology clinical trials. Users can search CKB via gene, gene variants, drug, drug class, indication, and clinical trials. | cancer, database, knowledgebase, clinical trial, clinical, gene, gene annotation, variant annotation, therapy, diagnosis | Cancer | PMID:26772741 | Available to the research community, For educational and research purposes only, Not intended to be used for medical advice/diagnosis or treatment | SCR_014965 | Jackson CKB | 2026-08-06 09:28:27 | 27 | |||||||
|
Attie Lab Diabetes Database Resource Report Resource Website 1+ mentions |
Attie Lab Diabetes Database (RRID:SCR_016639) | database, data or information resource | Interactive database of gene expression and diabetes related clinical phenotypes. Allows to search gene expression in tissues as a function of obesity, strain, and age, in a mouse. | interactive, database, gene, expression, diabetes, related, clinical, phenotype, mouse |
is listed by: OMICtools has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
diabetes | Free, Freely available | SCR_016639 | 2026-08-06 09:28:52 | 3 | |||||||||
|
Molecular Signatures Database Resource Report Resource Website 500+ mentions |
Molecular Signatures Database (RRID:SCR_016863) | MSigDB | database, data or information resource | Collection of annotated gene sets for use with Gene Set Enrichment Analysis (GSEA) software. | collection, annotated, gene, set, GSEA, enrichment, analysis, genome, RNA, expression, data, FASEB list, DRKB |
uses: GSEA uses: Gene Set Enrichment Analysis has parent organization: Broad Institute |
NIH ; NIGMS ; NCI CA295532 |
Free, Freely available, Registration required to download GSEA software | https://www.gsea-msigdb.org/gsea/msigdb/ | SCR_016863 | Molecular Signatures Database, The Molecular Signatures Database, MSigDB, MSigDB database v6.2 | 2026-08-06 09:28:58 | 762 | ||||||
|
Human Mouse Disease Connection Resource Report Resource Website 1+ mentions |
Human Mouse Disease Connection (RRID:SCR_017522) | HMDC | service resource, database, data or information resource | Collection of published and potential mouse models of human disease, discovery of candidate genes and investigation of phenotypic similarity between mouse models and human patients. Mouse mutation, and phenotype and disease model data from Mouse Genome Informatics database are integrated with human gene to disease relationships from the National Center for Biotechnology Information and Online Mendelian Inheritance in Man and human disease to phenotype relationships from the Human Phenotype Ontology. | Collection, mouse, model, human, disease, discovery, candidate, gene, phenotypic, similarity, patient |
has parent organization: Mouse Genome Informatics (MGI) works with: Human Phenotype Ontology works with: OMIM works with: NCBI |
Free, Freely available | SCR_017522 | Human - Mouse: Disease Connection | 2026-08-06 09:29:05 | 1 | ||||||||
|
GCBI database Resource Report Resource Website 10+ mentions |
GCBI database (RRID:SCR_018971) | database, data or information resource | Database provides information on research status of gene related diseases, gene expression in different tissues, regulatory relationship among genes, information of diseases, mRNA, Transcription Fctor, miRNA and other information shared among genes. | Gene, gene related disease, gene expression, tissue, regulatory gene relationship, mRNA data, transcription factor data, miRNA data, gene data | Restricted | SCR_018971 | Gene radar | 2026-08-06 09:29:25 | 26 | ||||||||||
|
Codon and Codon-Pair Usage Tables Resource Report Resource Website 1+ mentions |
Codon and Codon-Pair Usage Tables (RRID:SCR_018504) | CoCoPUTs | database, data or information resource | Database includes genomic codon-pair and dinucleotide statistics of all organisms with sequenced genome. Facilitates genetic variation analyses and recombinant gene design. Derived from all available GenBank and RefSeq data. | Codon-pair, codon, nucleotide, gene, genomic codon pair, dinucleotide statistic, sequence, genetic variation, recombinant gene design, data |
is related to: GenBank is related to: RefSeq |
PMID:31029701 | Free, Freely available | SCR_018504 | 2026-08-06 09:29:26 | 5 | ||||||||
|
MitoCarta Resource Report Resource Website 100+ mentions |
MitoCarta (RRID:SCR_018165) | database, data or information resource | Collection of genes encoding proteins with strong support of mitochondrial localization. Inventory of genes encoding mitochondrial-localized proteins and their expression across 14 mouse tissues. Database is based on human and mouse RefSeq proteins that are mapped to NCBI Gene loci. MitoCarta 2.0 inventory provides molecular framework for system-level analysis of mammalian mitochondria. | Gene, protein, mitochondrial protein, protein expression, data, human, mouse, RefSeq protein, analysis, mammalian mitochondra, FASEB list | NIGMS GM0077465; NIDDK DK43351; NIDDK DK57521; Australian NHMRC ; Burroughs Wellcome Fund Career Award in the Biomedical Sciences ; Howard Hughes Medical Institute ; Charles E. Culpeper Scholarship in Medical Science |
PMID:26450961 PMID:18614015 |
Free, Freely available | SCR_018165 | MitoCarta2.0 | 2026-08-06 09:29:15 | 183 | ||||||||
|
ResistomeDB Resource Report Resource Website 1+ mentions |
ResistomeDB (RRID:SCR_018305) | service resource, database, data or information resource | Web tool to explore and visualize Antibiotic Resistance Genes found on Tara Oceans samples. Can be explored by individual ARG or grouped by antibiotic class. | Antibiotic Resistance Gene, Tara Oceans, data, antibiotic resistance, antibiotic, gene | DOI:10.1101/765446 | Free, Freely available | SCR_018305 | 2026-08-06 09:29:17 | 1 |
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.
