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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Comparative Fungal Genomics Platform Resource Report Resource Website 10+ mentions |
Comparative Fungal Genomics Platform (RRID:SCR_012910) | data or information resource, database |
The CFGP (Comparative Fungal Genomics Platform) was designed for comparative genomics projects with diverse fungal genomes. The CFGP provides important bioinformatic tools, such as BLAST search, ClustalW analysis, InterPro Scan, SignalP, and PSORT2, which are very common tools for the researchers in the field of genomics. Many of them have been executed in the unix environment, so some specific computing knowledge is required. In the CFGP, users can use these tools simply by clicking their mouse button. In addition, all of the results of the analysis will be stored in the CFGP, so you can easily share those results with other members. |
fungal genome, comparative genomics, genomics | has parent organization: Seoul National University; Seoul; South Korea | nif-0000-02653 | http://cfgp.snu.ac.kr | SCR_012910 | CFGP | 2026-08-10 09:34:39 | 23 | ||||||||
|
Blue Collar Bioinformatics Resource Report Resource Website 1+ mentions |
Blue Collar Bioinformatics (RRID:SCR_012913) | Blue Collar Bioinformatics | data or information resource, blog, narrative resource | This blog will appeal to those dealing with the practical day to day work of biological data analysis and presentation. | is listed by: OMICtools | OMICS_01712 | SCR_012913 | 2026-08-10 09:34:47 | 1 | ||||||||||
|
NHLBI Exome Sequencing Project (ESP) Resource Report Resource Website 1000+ mentions |
NHLBI Exome Sequencing Project (ESP) (RRID:SCR_012761) | EVS | data or information resource, database | The goal of the project is to discover novel genes and mechanisms contributing to heart, lung and blood disorders by pioneering the application of next-generation sequencing of the protein coding regions of the human genome across diverse, richly-phenotyped populations and to share these datasets and findings with the scientific community to extend and enrich the diagnosis, management and treatment of heart, lung and blood disorders. The groups participating and collaborating in the NHLBI GO ESP include: Seattle GO - University of Washington, Seattle, WA Broad GO - Broad Institute of MIT and Harvard, Cambridge, MA WHISP GO - Ohio State University Medical Center, Columbus, OH Lung GO - University of Washington, Seattle, WA WashU GO - Washington University, St. Louis, MO Heart GO - University of Virginia Health System, Charlottesville, VA ChargeS GO - University of Texas Health Sciences Center at Houston | bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA |
NHLBI | nlx_156901, biotools:esp, biotools:exome_variant_server | https://bio.tools/esp, https://bio.tools/exome_variant_server | SCR_012761 | Exome Variant Server, NHLBI GO Exome Sequencing Project (ESP) | 2026-08-10 09:34:37 | 2231 | ||||||
|
ENA Sequence Search Resource Report Resource Website 1+ mentions |
ENA Sequence Search (RRID:SCR_013170) | ENA Sequence Search | production service resource, data analysis service, analysis service resource, service resource | A nucleotide sequence similiary search tool which is far faster than BLAST for large datasets, with only a marginal loss in search sensitivity. | nucleotide sequencing |
is listed by: OMICtools has parent organization: European Nucleotide Archive (ENA) |
OMICS_00993 | SCR_013170 | 2026-08-10 09:34:49 | 7 | |||||||||
|
PhenomicDB Resource Report Resource Website 10+ mentions |
PhenomicDB (RRID:SCR_013051) | PhenomicDB | data or information resource, database | PhenomicDB is a multi-organism phenotype-genotype database including human, mouse, fruit fly, C.elegans, and other model organisms. The inclusion of gene indices (NCBI Gene) and orthologs (same gene in different organisms) from HomoloGene allows to compare phenotypes of a given gene over many organisms simultaneously. PhenomicDB contains data from publicly available primary databases: FlyBase, Flyrnai.org, WormBase, Phenobank, CYGD, MatDB, OMIM, MGI, ZFIN, SGD, DictyBase, NCBI Gene, and HomoloGene. We brought this wealth of data into a single integrated resource by coarse-grained semantic mapping of the phenotypic data fields, by including common gene indexes (NCBI Gene), and by the use of associated orthology relationships (HomoloGene). PhenomicDB is thought as a first step towards comparative phenomics and will improve the understanding of the gene functions by combining the knowledge about phenotypes from several organisms. It is not intended to compete with the much more dedicated primary source databases but tries to compensate its partial loss of depth by linking back to the primary sources. The basic functional concept of PhenomicDB is an integrated meta-search-engine for phenotypes. Users should be aware that comparison of genotypes or even phenotypes between organisms as different as yeast and man can have serious scientific hurdles. Nevertheless finding that the phenotype of a given mouse gene is described as ��similar to psoriasis�� and at the same time that the human ortholog has been described as a gene causing skin defects can lead to novelty and interesting hypotheses. Similarly, a gene involved in cancer in mammalian organisms could show a proliferation phenotype in a lower organism such as yeast and thus, give further insights to a researcher. | phenotype, human, mouse, drosophila, caenorhabditis elegans, dictyostelium discoideum, yeast, zebrafish | PMID:20562418 | nif-0000-03274 | SCR_013051 | 2026-08-10 09:34:48 | 10 | |||||||||
|
LIGand Attachment SITE Database Resource Report Resource Website 1+ mentions |
LIGand Attachment SITE Database (RRID:SCR_013172) | data or information resource, database | A gold-standard dataset of biologically relevant binding sites in protein structures. It consists of proteins with one unbound structure and at least one structure of the protein-ligand complex. Both a redundant and a non-redundant (sequence identity lower than 25) version is available. Quaternary structures proposed by PQS (2) are used for all structures in the dataset. The availability of both unbound and bound structures for each protein guarantees that our dataset can be used to benchmark binding site prediction methods, in conditions that mimic cases where the binding site is truly unknown. In cases where several different bound structures are available for a given protein, all are used to define the binding sites. |
has parent organization: University of Toronto; Ontario; Canada has parent organization: King's College London; London; United Kingdom |
nif-0000-03083 | SCR_013172 | LigASite | 2026-08-10 09:34:43 | 2 | ||||||||||
|
ComiR Resource Report Resource Website 10+ mentions |
ComiR (RRID:SCR_013023) | ComiR | production service resource, data analysis service, analysis service resource, service resource | Data analysis service that predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression to improve and combine multiple miRNA targets for each of the four prediction algorithms: miRanda, PITA, TargetScan and mirSVR. The composite scores of the four algorithms are then combined using a support vector machine trained on Drosophila Ago1 IP data. | mirna, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Pittsburgh; Pennsylvania; USA |
NLM ; Fondazione RiMED |
PMID:23703208 PMID:23284279 |
Acknowledgement requested | OMICS_00395, biotools:comir | https://bio.tools/comir | SCR_013023 | Combinatorial miRNA targeting, ComiR: Combinatorial miRNA target prediction tool, ComiR - Combinatorial miRNA target prediction tool | 2026-08-10 09:34:41 | 26 | ||||
|
ExTopoDB Resource Report Resource Website 1+ mentions |
ExTopoDB (RRID:SCR_013143) | ExTopoDB | data or information resource, database | A publicly accessible database of experimentally derived topological models of transmembrane proteins. It contains experimental information about the topology of 2143 transmembrane proteins. This information was collected from studies in the literature that reported the use of biochemical methods for the determination of the topology of transmembrane proteins. Each record contains unique information about the given protein, such as its sequence, cross-references to many publicly available databases worldwide, the protein''s name and organism source. The web interface of the database offers the user the ability to submit advanced queries for text search within ExTopoDB''s protein entries and there is also an interface for running BLAST against the database. Furthermore, the results of topology prediction using the HMM-TM algorithm are included for each protein in the database (unconstrained prediction) and we also incorporated the experimental information about the topology of the proteins in the HMM-TM prediction procedure, producing more reliable topology models (constrained prediction). | transmembrane protein, protein structure, topological model, blast, transmembrane, protein, model |
is listed by: 3DVC has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
PMID:20601677 | Public | nlx_151724 | SCR_013143 | 2026-08-10 09:34:42 | 2 | |||||||
|
Retinal Information Network Resource Report Resource Website 10+ mentions |
Retinal Information Network (RRID:SCR_012733) | data or information resource, database | RetNet provides tables of genes and loci causing inherited retinal diseases, such as retinitis pigmentosa, macular degeneration and Usher syndrome, and related information. This information is provided to the research community and other interested individuals for research purposes only. The information should not be used for medical or commercial purposes. Although we strive for accuracy and completeness, we cannot guarantee that all information is correct and complete. We welcome comments and suggestions! | has parent organization: University of Texas System; Texas; USA | nif-0000-31454 | SCR_012733 | RetNet | 2026-08-10 09:34:43 | 34 | ||||||||||
|
AU-RICH ELEMENT-CONTAINING mRNA DATABASE Resource Report Resource Website 10+ mentions |
AU-RICH ELEMENT-CONTAINING mRNA DATABASE (RRID:SCR_012978) | data or information resource, database | The ARE-mRNA database (ARED) reveals that ARE-mRNAs encode a wide repertoire of functionally diverse proteins belonging to different biological processes and important in several disease states. Cluster analysis was performed using the ARE sequences to demonstrate potential relationships between the type and number of ARE motifs, and the functional characteristics of the proteins. Sponsors: This database is supported by The King Faisal Specialist Hospital and Research Center. Keywords: mRNA, Database, Au-rich, Element, Biological, Disease, State, Cluster, Analysis, Motif, Functional, Characterstic, Protein, | nif-0000-30039 | SCR_012978 | ARE Datebase | 2026-08-10 09:34:40 | 23 | |||||||||||
|
European ribosomal RNA database Resource Report Resource Website 500+ mentions |
European ribosomal RNA database (RRID:SCR_012735) | data or information resource, database | Database compiles all complete or nearly complete SSU (small subunit) and LSU (large subunit) ribosomal RNA sequences. Sequences are provided in aligned format. Alignment takes into account secondary structure information derived by comparative sequence analysis of thousands of sequences. Additional information such as literature references, taxonomy, secondary structure modles and nucleotide variability maps, is also available. | ribosomal RNA sequences, small subunit, large subunit, aligned format sequences, literature references, taxonomy, secondary structure modles, nucleotide variability maps, |
is related to: SILVA has parent organization: Ghent University; Ghent; Belgium |
Free, Freely available | nif-0000-02820 | http://www.psb.ugent.be/rRNA/ | SCR_012735 | European ribosomal RNA database, SILVA rRNA database, SILVA - high quality ribosomal RNA databases | 2026-08-10 09:34:37 | 654 | |||||||
|
SWISS-MODEL Repository Resource Report Resource Website 100+ mentions |
SWISS-MODEL Repository (RRID:SCR_013032) | data or information resource, database | Database of annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL. | protein structure, structural homology, model |
is listed by: 3DVC has parent organization: SIB Swiss Institute of Bioinformatics has parent organization: University of Basel; Basel; Switzerland is provided by: SWISS-MODEL |
nif-0000-03522, r3d100010605 | SCR_013032 | SWISS-MODEL Repository | 2026-08-10 09:34:48 | 331 | |||||||||
|
Zebrafish Genome Project Resource Report Resource Website 50+ mentions |
Zebrafish Genome Project (RRID:SCR_013157) | data or information resource, database | Database of zebrafish genome. | Zebrafish, genome |
is related to: Genome Reference Consortium is related to: Zebrafish Information Network (ZFIN) has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Free, Freely available | SCR_017503, nif-0000-31931 | https://www.sanger.ac.uk/science/data/zebrafish-genome-project | SCR_013157 | Danio rerio Sequencing Project | 2026-08-10 09:34:49 | 67 | |||||||
|
Elephant shark genome sequencing Resource Report Resource Website 50+ mentions |
Elephant shark genome sequencing (RRID:SCR_013158) | data or information resource, database, service resource | To explore the elephant shark genome, we have conducted a survey-sequencing and comparative analysis of the elephant shark genome in collaboration with J. Craig Venter Institute. The elephant shark sequences generated under this project have been deposited at GenBank under the project accession number AAVX01000000. The sequences can also be searched using BLAST and retrieved here. Cartilaginous fishes (Chondrichthyes) represented by sharks, rays, skates and chimaeras, are phylogenetically the oldest group of living jawed vertebrates. They constitute an important group for our understanding of the origins of the complex developmental and physiological systems of jawed vertebrates. They are also an useful outgroup for bony vertebrates such as tetrapods and teleost fishes and help in identifying specialized features that have led to the evolution of diverse groups of bony vertebrates. The elephant shark (Callorhinchus milii), also known as the elephant fish and ghost shark, is a chimaera belonging to the Order Chimaeriformes and Family Callorhynchidae. It has the smallest genome among the known cartilaginous fish genomes. Thus, it was proposed as a model cartilaginous fish genome for whole-genome sequencing and comparative analysis (Venkatesh et al. 2005. Curr. Biol. 15: R82-R83). The following resources of the elephant shark are available for the scientific community: *Elephant Shark 1.4x assembly fasta sequences zipped 227 megabytes *Genomic DNA *~8x coverage BAC library (average insert size, ~150 kb) *cDNA libraries (under construction) *cDNA (dated 11 April 2008) with orthologs in 5 vertebrates (human, opossum, chicken, frog, fugu) | FASEB list | has parent organization: Institute of Molecular and Cell Biology; Singapore; Singapore | Agency for Science Technology and Research | PMID:9254694 PMID:17185593 PMID:17407382 |
nif-0000-30511 | SCR_013158 | 2026-08-10 09:34:42 | 84 | ||||||||
|
Replication Domain Resource Report Resource Website 10+ mentions |
Replication Domain (RRID:SCR_012941) | data or information resource, database | ReplicationDomain is an online database resource for storing, sharing and visualizing DNA replication timing and transcription data, as well as other numerical epigenetic data types. Data is typically obtained from DNA microarrays or DNA sequencing. Our site has a user registration system that allows registered users to upload their own data sets. While non-registered users may freely view and download public data sets, registered users may upload their own data sets and view them privately, share them with other registered users, or make published data sets publicly available. In addition we have implemented additional mechanisms that allow users to restrict sharing of data sets to a user designated group of registered users. Further details on the database usage are in the User Guide Page, while data set details are in the Documentation Page. Replication timing data were obtained by hybridizing early and late replication intermediates to Nimblegen oligonucleotide arrays, as described in Hiratani et al [PLoS Biology (2008) 6: e245]. Briefly, replication intermediates are prepared from cells that are first pulse-labeled with BrdU and then sorted into early and late stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. After unbiased amplification of recovered DNA, the samples are differentially labeled with Cy3 and Cy5 and hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 5.8 kb across the mouse genome (Nimblegen, 2006-07-26_MM8_WG_CGH). Raw data from two independent biological replicates in which the early and late replicating DNA were labeled reciprocally with Cy3 and Cy 5 (dye switch) are loess-normalized and scaled to have the same median-absolute deviation using the limma package (R/Bioconductor) and then averaged. Finally, the data are smoothed with a weighted moving average (loess: local polynomial smoothing). | nif-0000-31444 | SCR_012941 | Replication Domain | 2026-08-10 09:34:39 | 20 | |||||||||||
|
OMA Browser Resource Report Resource Website 10+ mentions |
OMA Browser (RRID:SCR_011978) | OMA | data or information resource, database | A database that identifies orthologs among publicly available, complete genomes. It offers a comprehensive search and numerous display options for 4.7 million proteins from 1000 species. The main features are the orthologous relationships which can be accessed either group-wise, where all group members are orthologous to all other group members, or on a sequence-centric basis, where for a given protein all its orthologs in all other species are displayed. | protein |
is listed by: OMICtools is related to: GermOnline has parent organization: ETH Zurich; Zurich; Switzerland |
PMID:21113020 PMID:17545180 |
Creative Commons Attribution-ShareAlike License, 2.5 | OMICS_01690 | SCR_011978 | Orthologous MAtrix | 2026-08-10 09:34:22 | 10 | ||||||
|
NCL Resource - A gateway for Batten disease Resource Report Resource Website 10+ mentions |
NCL Resource - A gateway for Batten disease (RRID:SCR_012826) | data or information resource, database | It serves as a gateway for clinicians, families and researchers who have an interest in or are affected by Batten disease or who wish to find out more. Information can be accessed via four main routes - Clinicians, Families, Researchers, Professional Support. The Clinical route describes Batten disease and includes details on diagnosis and diagnostic services. The Family route also describes Batten disease and lists support groups. The Research route includes the NCL Mutation Database, established in 1998, and other useful information. The Professional Support route includes details of coordinated initiatives to support those affected by Batten disease. A fifth route, Research Consortia, serves to meet research needs and currently act as a focus for collaborative efforts to identify the remaining human and animal NCL genes and facilitate functional approaches. An additional route, Creativity, has been launched to display creative items from families with Batten disease, and to celebrate life, in both its fullness and fragility. | FASEB list | has parent organization: University College London; London; United Kingdom | nif-0000-03182 | SCR_012826 | NCL Resource | 2026-08-10 09:34:38 | 34 | |||||||||
|
NASCs International Affymetrix Service Resource Report Resource Website 10+ mentions |
NASCs International Affymetrix Service (RRID:SCR_012825) | data or information resource, database | The NASC International Affymetrix Service is a commercial website that provides transcripomics services for a fee. This data is available for any available species, any consortium chip, and any kind of experiment. The website also provides open source and free Xspecies software and techniques that can be (examples) used to perform GeneChip transcriptomics experiments on species for which no current Affymetrix chip exists. | FASEB list | nif-0000-03176 | SCR_012825 | NASCarrays | 2026-08-10 09:34:45 | 44 | ||||||||||
|
OrthoDB Resource Report Resource Website 1000+ mentions |
OrthoDB (RRID:SCR_011980) | data or information resource, database | Database of orthologous protein coding genes across vertebrates, arthropods, fungi, basal metazoans, and bacteria. | Hierarchical catalog, ortholog, protein coding genes, mapping genomics to functional data, FASEB list |
is listed by: OMICtools has parent organization: University of Geneva; Geneva; Switzerland |
Swiss National Foundation | PMID:23180791 | Free, Freely available | OMICS_01692 | http://cegg.unige.ch/orthodb7 | SCR_011980 | OrthoDB: Database of Orthologous Groups, OrthoDB v7, OrthoDB - The Hierarchical Catalog of Orthologs, OrthoDB v10 | 2026-08-10 09:34:23 | 1143 | |||||
|
Household Products Database Resource Report Resource Website 1+ mentions |
Household Products Database (RRID:SCR_013006) | data or information resource, database | A database of ingredients in brand-name household products linked to health information from Material Safety Data Sheets (MSDS) provided by manufacturers. The database is designed to help answer the following typical questions: *What are the chemical ingredients and their percentage in specific brands? *Which products contain specific chemical ingredients? *Who manufactures a specific brand? How do I contact this manufacturer? *What are the acute and chronic effects of chemical ingredients in a specific brand? *What other information is available about chemicals in the toxicology-related databases of the National Library of Medicine? NLM and its Contractor (the Database Providers) do not test products nor investigate to determine if this information is complete or accurate. | drug, chemical, consumer, health, toxicology, toxicology databases | has parent organization: National Library of Medicine | National Center for Environmental Health of the Centers for Disease Control and Prevention | nif-0000-21198 | SCR_013006 | HPD | 2026-08-10 09:34:48 | 4 |
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.
