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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
PubSearch Resource Report Resource Website 1+ mentions |
PubSearch (RRID:SCR_005830) | PubSearch | service resource, data or information resource, software resource, database | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. PubSearch is a web-based literature curation tool, allowing curators to search and annotate genes to keywords from articles. It has a simple mySQL database backend and uses a set of Java Servlets and JSPs for querying, modifying, and adding gene, gene-annotation, and literature information. PubSearch can be downloaded from GMOD. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, annotate, editor, literature curation tool, literature, ontology or annotation editor |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: TAIR has parent organization: Stanford University; Stanford; California |
NHGRI R01HG02728 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149338 | SCR_005830 | 2026-08-03 09:32:56 | 1 | |||||||
|
EGAN: Exploratory Gene Association Networks Resource Report Resource Website 1+ mentions |
EGAN: Exploratory Gene Association Networks (RRID:SCR_008856) | EGAN | software resource, data processing software, software application, data analysis software | Exploratory Gene Association Networks (EGAN) is a software tool that allows a bench biologist to visualize and interpret the results of high-throughput exploratory assays in an interactive hypergraph of genes, relationships (protein-protein interactions, literature co-occurrence, etc.) and meta-data (annotation, signaling pathways, etc.). EGAN provides comprehensive, automated calculation of meta-data coincidence (over-representation, enrichment) for user- and assay-defined gene lists, and provides direct links to web resources and literature (NCBI Entrez Gene, PubMed, KEGG, Gene Ontology, iHOP, Google, etc.). EGAN functions as a module for exploratory investigation of analysis results from multiple high-throughput assay technologies, including but not limited to: * Transcriptomics via expression microarrays or RNA-Seq * Genomics via SNP GWAS or array CGH * Proteomics via MS/MS peptide identifications * Epigenomics via DNA methylation, ChIP-on-Chip or ChIP-Seq * In-silico analysis of sequences or literature EGAN has been built using Cytoscape libraries for graph visualization and layout, and is comparable to DAVID, GSEA, Ingenuity IPA and Ariadne Pathway Studio. There are pre-collated EGAN networks available for human (Homo sapiens), mouse (Mus musculus), rat (Rattus norvegicus), chicken (Gallus gallus), zebrafish (Danio rerio), fruit fly (Drosophila melanogaster), nematode (Caenorhabditis elegans), mouse-ear cress (Arabidopsis thaliana), rice (Oryza sativa) and brewer's yeast (Saccharomyces cerevisiae). There is now an EGAN module available for GenePattern (human-only). Platform: Windows compatible, Mac OS X compatible, Linux compatible | gene, gene association, network, protein-protein interaction, pathway, interaction, annotation, signaling pathway, enrichment, cytoscape, visualization |
is listed by: 3DVC is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: Cytoscape has parent organization: UCSF Helen Diller Family Comprehensive Cancer Center Biostatistics Core |
NCI P30 CA92103 | PMID:19933825 | Free for academic use | nlx_149222 | SCR_008856 | Exploratory Gene Association Networks, Exploratory Gene Association Networks (EGAN) | 2026-08-03 09:34:09 | 8 | |||||
|
GeneCodis Resource Report Resource Website 100+ mentions |
GeneCodis (RRID:SCR_006943) | GeneCodis | production service resource, data analysis service, web service, analysis service resource, data access protocol, service resource, software resource | Web-based tool for the ontological analysis of large lists of genes. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of genes under study with respect to a reference list. As well as single annotations, this tool allows users to simultaneously evaluate annotations from different sources, for example Biological Process and Cellular Component categories of Gene Ontology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | functional analysis, gene, annotation, statistical analysis, functional genomics, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: KEGG has parent organization: Spanish National Research Council; Madrid; Spain |
Juan de la Cierva research program ; Spanish Minister of Science and Innovation BIO2010-17527; Government of Madrid P2010/BMD-2305 |
PMID:22573175 PMID:19465387 PMID:17204154 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02221, biotools:genecodis3, nlx_149254 | https://bio.tools/genecodis3 | SCR_006943 | Gene annotations co-ocurrence discovery, GeneCodis - Gene annotations co-ocurrence discovery | 2026-08-03 09:33:18 | 348 | ||||
|
GeneMerge Resource Report Resource Website 10+ mentions |
GeneMerge (RRID:SCR_005744) | GeneMerge | production service resource, data analysis service, software application, analysis service resource, service resource, software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Web-based and standalone application that returns a wide range of functional genomic data for a given set of study genes and provides rank scores for over-representation of particular functions or categories in the data. It uses the hypergeometric test statistic which returns statistically correct results for samples of all sizes and is the #2 fastest GO tool available (Khatri and Draghici, 2005). GeneMerge can be used with any discrete, locus-based annotation data, including, literature references, genetic interactions, mutant phenotypes as well as traditional Gene Ontology queries. GeneMerge is particularly useful for the analysis of microarray data and other large biological datasets. The big advantage of GeneMerge over other similar programs is that you are not limited to analyzing your data from the perspective of a pre-packaged set of gene-association data. You can download or create gene-association files to analyze your data from an unlimited number of perspectives. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, genomics, functional genomic data, analysis, post-genomic analysis, data mining, hypothesis testing, statistical analysis, slimmer-type tool, term enrichment, text mining, false discovery rate, bonferroni correction, false discovery rate and bonferroni correction, perl, microarray |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Harvard University; Cambridge; United States |
PMID:12724301 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149203 | http://genemerge.cbcb.umd.edu/ | SCR_005744 | 2026-08-03 09:32:46 | 26 | ||||||
|
MitoMiner Resource Report Resource Website 50+ mentions |
MitoMiner (RRID:SCR_001368) | data or information resource, database | A database of mitochondrial proteomics data. It includes two sets of proteins: the MitoMiner Reference Set, which has 10477 proteins from 12 species; and MitoCarta, which has 2909 proteins from mouse and human mitochondrial proteins. MitoMiner provides annotation from the Gene Ontology (GO) and UniProt databases. This reference set contains all proteins that are annotated by either of these resources as mitochondrial in any of the species included in MitoMiner. MitoMiner data via is available via Application Programming Interface (API). The client libraries are provided in Perl, Python, Ruby and Java. | mitochondrion, proteomics, function, homolog, proteome, protein expression, mass-spectrometry, protein, metabolism, green fluorescent protein tag, ortholog, FASEB list |
uses: HomoloGene uses: UniProt uses: KEGG uses: OMIM uses: The Human Protein Atlas uses: Gene Ontology |
MRC | PMID:22121219 PMID:19208617 |
Public, Acknowledgement requested, Code: | nlx_152504 | SCR_001368 | MitoMiner - A database of the mitochondrial proteome | 2026-08-03 09:31:18 | 76 | ||||||
|
Spliceosome Database Resource Report Resource Website 10+ mentions |
Spliceosome Database (RRID:SCR_002097) | Spliceosome Database | data or information resource, database | A database of proteins and RNAs that have been identified in various purified splicing complexes. Various names, orthologs and gene identifiers of spliceosome proteins have been cataloged to navigate the complex nomenclature of spliceosome proteins. Links to gene and protein records are also provided for the spliceosome components in other databases. To navigate spliceosome assembly dynamics, tools were created to compare the association of spliceosome proteins with complexes that form at specific stages of spliceosome assembly based on a compendium of mass spectrometry experiments that identified proteins in purified splicing complexes. | splicing, mass spectrometry, protein, rna, complex, spliceosome, small nuclear rna, structure, dynamics, ortholog, gene |
is listed by: OMICtools has parent organization: University of California at Santa Cruz; California; USA |
PMID:23118483 | Free, Freely available | OMICS_01891 | SCR_002097 | Spliceosome Database - A source of information for the SLPICEOSOME: The large ribonucleoprotein complex responsible for pre-mRNA splicing, Spliceosome Component Database | 2026-08-03 09:31:33 | 11 | ||||||
|
GermOnline Resource Report Resource Website 10+ mentions |
GermOnline (RRID:SCR_002807) | GermOnline | data or information resource, database | Cross-species microarray expression database focusing on high-throughput expression data relevant for germline development, meiosis and gametogenesis as well as the mitotic cell cycle. The database contains a unique combination of information: 1) High-throughput expression data obtained with whole-genome high-density oligonucleotide microarrays (GeneChips). 2) Sample annotation (mouse over the sample name and click on it) using the Multiomics Information Management and Annotation System (MIMAS 3.0). 3) In vivo protein-DNA binding data and protein-protein interaction data (available for selected species). 4) Genome annotation information from Ensembl version 50. 5) Orthologs are identified using data from Ensembl and OMA and linked to each other via a section in the report pages. The portal provides access to the Saccharomyces Genomics Viewer (SGV) which facilitates online interpretation of complex data from experiments with high-density oligonucleotide tiling microarrays that cover the entire yeast genome. The database displays only expression data obtained with high-density oligonucleotide microarrays (GeneChips)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026. | fertility, development, germline, microarray, annotation, in vivo, protein-dna binding, protein-protein interaction, genome, ortholog, high-density oligonucleotide microarray, gene expression, genome annotation, gene orthology, genechip, tiling array, development, meiosis, gametogenesis, mitotic cell cycle, data set, data repository, bio.tools |
is listed by: 3DVC is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Ensembl is related to: OMA Browser has parent organization: National Institute of Health and Medical Research; Rennes; France |
Swiss Institute of Bioinformatics ; bioinformatics platform of Biogenouest ; National Institute of Health and Medical Research; Rennes; France ; University of Rennes 1; Rennes; France |
PMID:21149299 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:germonline, nif-0000-02906, r3d100010248 | https://bio.tools/germonline, https://doi.org/10.17616/R37K5Q | SCR_002807 | 2026-08-03 09:32:09 | 17 | |||||
|
ADGO Resource Report Resource Website 1+ mentions |
ADGO (RRID:SCR_006343) | ADGO | data analysis service, service resource, analysis service resource, production service resource | A web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. It provides multiple gene set analysis methods for microarray inputs as well as enrichment analyses for lists of genes. It screens redundant composite annotations when generating and prioritizing them. It also incorporates union and subtracted sets as well as intersection sets. Users can upload their gene sets (e.g. predicted miRNA targets) to generate and analyze new composite sets. | microarray, gene, annotation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21624890 | Acknowledgement requested | OMICS_02229, biotools:adgo | https://bio.tools/adgo | SCR_006343 | 2026-08-03 09:32:59 | 3 | ||||||
|
BioGPS: The Gene Portal Hub Resource Report Resource Website 500+ mentions |
BioGPS: The Gene Portal Hub (RRID:SCR_006433) | BioGPS | data or information resource, database | An extensible and customizable gene annotation portal that emphasizes community extensibility and user customizability. It is a complete resource for learning about gene and protein function. Community extensibility reflects a belief that any BioGPS user should be able to add new content to BioGPS using the simple plugin interface, completely independently of the core developer team. User customizability recognizes that not all users are interested in the same set of gene annotation data, so the gene report layouts enable each user to define the information that is most relevant to them. Currently, BioGPS supports eight species: Human (Homo sapiens), Mouse (Mus musculus), Rat (Rattus norvegicus), Fruitfly (Drosophila melanogaster), Nematode (Caenorhabditis elegans), Zebrafish (Danio rerio), Thale-cress (Arabidopsis thaliana), Frog (Xenopus tropicalis), and Pig (Sus scrofa). BioGPS presents data in an ortholog-centric format, which allows users to display mouse plugins next to human ones. Our data for defining orthologs comes from NCBI's HomoloGene database. | gene, ortholog, plug-in, report, literature, genetics, expression, reagent, protein, pathway, snp, genomics, gene annotation, function, FASEB list |
is listed by: Biositemaps is related to: bioDBcore is related to: aGEM has parent organization: Scripps Research Institute |
Novartis Research Foundation ; NIGMS R01GM083924 |
PMID:19919682 | Free, The community can contribute to this resource | r3d100012402, nif-0000-10168 | http://biogps.gnf.org/, https://doi.org/10.17616/R33J20 | SCR_006433 | 2026-08-03 09:33:01 | 725 | |||||
|
Database of Arabidopsis Transcription Factors Resource Report Resource Website 10+ mentions |
Database of Arabidopsis Transcription Factors (RRID:SCR_007101) | DATF | data or information resource, database | Database that collects all arabidopsis transcription factors (totally 1922 Loci; 2290 Gene Models) and classifies them into 64 families. It uses not only locus (gene), but also gene model (transcript, protein) and the detail information is for each gene model not for locus. It adds multiple alignment of the DNA-binding domain of each family, Neighbor-Joining phylogenetic tree of each family, the GO annotation, homolog with the Database of Rice Transcription Factors (DRTF). It also keeps old information items such as the unique cloned and sequenced information of about 1200 transcription factors, protein domains, 3D structure information with BLAST hits against PDB, predicted Nuclear Location Signals, UniGene information, as well as links to literature reference. | gene, alignment, arabidopsis, binding, clone, dna, domain, locus, phylogenetic tree, transcription, chromosome, transcription factor, blast, family, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Peking University; Beijing; China |
State Key Laboratory of Protein and Plant Gene Research ; National Natural Science Foundation of China 31470330; China 863 Programs 2006AA02Z334; China Postdoctoral Science Foundation Grant 2014M560017 |
PMID:15731212 | Free | nif-0000-21112, OMICS_00551, biotools:datf | https://bio.tools/datf | SCR_007101 | 2026-08-03 09:33:16 | 36 | |||||
|
GlimmerHMM Resource Report Resource Website 500+ mentions |
GlimmerHMM (RRID:SCR_002654) | GlimmerHMM | software resource, source code | A gene finder based on a Generalized Hidden Markov Model (GHMM). Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single). | gene, hidden markov model |
is related to: Glimmer has parent organization: Johns Hopkins University; Maryland; USA |
NIH ; NLM R01-LM06845; NLM R01-LM007938 |
PMID:15145805 | Free, Available for download, Freely available | nlx_156092 | SCR_002654 | GlimmerHMM - Eukaryotic Gene-Finding System | 2026-08-03 09:32:04 | 576 | |||||
|
HINT Resource Report Resource Website 100+ mentions |
HINT (RRID:SCR_002762) | HINT | data or information resource, database | A database of high-quality protein-protein interactions in different organisms. | protein-protein interaction, bio.tools, FASEB list |
is used by: Mutation Annotation and Genomic Interpretation is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Cornell University; New York; USA |
PMID:22846459 | Free, Freely available, Available for download | OMICS_02898, biotools:hint | https://bio.tools/hint | SCR_002762 | High-quality INTeractomes | 2026-08-03 09:32:00 | 306 | |||||
|
HomoloGene Resource Report Resource Website 100+ mentions |
HomoloGene (RRID:SCR_002924) | HomoloGene | service resource, data or information resource, database | Automated system for constructing putative homology groups from complete gene sets of wide range of eukaryotic species. Databse that provides system for automatic detection of homologs, including paralogs and orthologs, among annotated genes of sequenced eukaryotic genomes. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences. Reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man, Mouse Genome Informatics, Zebrafish Information Network, Saccharomyces Genome Database and FlyBase. | homolog, paralog, ortholog, genome, gene, protein, protein alignment, phenotype, conserved domain, homology, amino acid sequence, cell, dna, gold standard |
is used by: NIF Data Federation is used by: Nowomics is used by: MitoMiner is listed by: OMICtools is listed by: re3data.org is related to: OMIM is related to: Mouse Genome Informatics (MGI) is related to: Zebrafish Information Network (ZFIN) is related to: SGD is related to: FlyBase is related to: ProbeMatchDB 2.0 is related to: Biomine is related to: Consensus CDS has parent organization: NCBI |
PMID:23193264 | Free, Freely availalbe | nif-0000-02975, r3d100010781, OMICS_01544 | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene, https://doi.org/10.17616/R3889F | SCR_002924 | NCBI HomoloGene | 2026-08-03 09:32:05 | 437 | |||||
|
MIPS Arabidopsis thaliana Database Resource Report Resource Website 1+ mentions |
MIPS Arabidopsis thaliana Database (RRID:SCR_003088) | data or information resource, database | Repository for genome sequence data in the European Scientists Sequencing Arabidopsis (ESSA) project, part of the Arabidopsis Genome Initiative. It is moving towards becoming an integrated biological knowledge resource by integrating diverse data, tools, query and visualization capabilities. The aim is to create a comprehensive resource for Arabidopsis as a model that can then be used to transfer knowledge onto sequences from other species, including crop plants. | plant genome, plant database, plant genome database | PMID:11752263 | Free, Available for download, Freely available | nif-0000-03104 | https://pmc.ncbi.nlm.nih.gov/articles/PMC99069/ | SCR_003088 | MAtDB | 2026-08-03 09:32:10 | 1 | |||||||
|
PPDB: Plant Promoter Database Resource Report Resource Website |
PPDB: Plant Promoter Database (RRID:SCR_003395) | PPDB | data or information resource, database | A plant promoter database that provides information on transcription start sites (TSSs), core promoter structure and regulatory element groups (REGs) as putative and comprehensive transcriptional regulatory elements. Microarray data-based predictions have been appended as REG annotations which inform their putative physiological roles. | gene, transcription start site, promoter structure, promoter, regulatory element group, homolog |
is listed by: OMICtools has parent organization: Gifu University; Gifu; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:24194597 PMID:17947329 |
Free, Available for download, Freely available | nif-0000-03329, OMICS_01874 | http://ppdb.gene.nagoya-u.ac.jp/cgi-bin/index.cgi | SCR_003395 | Plant Promoter Database | 2026-08-03 09:32:15 | 0 | ||||
|
Information Hyperlinked Over Proteins Resource Report Resource Website 10+ mentions |
Information Hyperlinked Over Proteins (RRID:SCR_004829) | iHOP | service resource, data or information 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 | 2026-08-03 09:32:44 | 24 | ||||
|
BaCelLo Resource Report Resource Website 10+ mentions |
BaCelLo (RRID:SCR_011965) | BaCelLo | data analysis service, service resource, analysis service resource, production service resource | A predictor for the subcellular localization of proteins in eukaryotes that is based on a decision tree of several support vector machines (SVMs). It classifies up to four localizations for Fungi and Metazoan proteins and five localizations for Plant ones. BaCelLo's predictions are balanced among different classes and all the localizations are considered as equiprobable. | protein, data set, proteome |
is listed by: OMICtools is listed by: SoftCite has parent organization: University of Bologna; Bologna; Italy |
PMID:16873501 | OMICS_01616 | SCR_011965 | 2026-08-03 09:35:01 | 45 |
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.
