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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
UNC Microarray Database Resource Report Resource Website 10+ mentions |
UNC Microarray Database (RRID:SCR_010979) | UNC MD, UNCMD | service resource, data or information resource, storage service resource, database, data repository | Database for microarray data storage, retrieval, analysis, and visualization. | microarray, FASEB list |
is listed by: OMICtools has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
Account required, The community can contribute to this resource | OMICS_00872 | SCR_010979 | UNC-Chapel Hill Microarray Database | 2026-08-11 09:42:10 | 33 | |||||||
|
DFLAT Resource Report Resource Website 1+ mentions |
DFLAT (RRID:SCR_010738) | DFLAT | data or information resource, standard specification, data set, narrative resource | We are an interdisciplinary team dedicated to annotating gene function related to human fetal development. We are contributing new functional annotation to the Gene Ontology, curating and mining gene sets suitable for the interpretation of developmental genomic data, and creating the computational tools needed to apply genomics for better understanding the molecular mechanisms of human development. Our GO annotation is in the process of being incorporated into the GOA public release. The GONE (Gene Ontology Non-Eligible) database is where we store annotations relevant to our research but that don''t quite meet GOA''s standards. Usually an annotation falls into this category because either the gene/protein described is a family of genes/proteins rather than a specific one, there is no UniProt ID to identify the gene/protein in the system, a GO term does not yet exist to describe the particular function, process, or location of the gene/protein, the species is not clearly identifiable in the paper, or the evidence is not as reliable (GO evidence codes TAS and NAS). As individual annotations these are more suspect than current GO annotation. However, for functional analysis of expression data, these gene sets can be valuable even with a certain amount of noise. We also include here a link to the supplementary data from our forthcoming PSB 2011 paper on gene set mining. | human, fetal, development | has parent organization: Tufts University; Massachusetts; USA | NICHD R01 HD058880 | PMID:21121032 | nlx_95610 | SCR_010738 | Developmental FunctionaL Annotation at Tufts | 2026-08-11 09:42:14 | 2 | ||||||
|
B-Fabric Resource Report Resource Website 1+ mentions |
B-Fabric (RRID:SCR_011827) | B-Fabric | service resource, data or information resource, storage service resource, database, data repository | An open infrastructure for managing projects and data in life sciences that allows to store and access experimental data together with its scientific context. The platform connects the data from scientific instruments with data analysis tools, including workflow, annotation, and data visualization support. All public data can be searched and used to carry out inter-experiment analyses. For a fee, B-Fabric Order allows you to order the following analytical services at the FGCZ independent of a User Lab research project: Mass spectrometry, Protein sequencing, peptide sequencing, Amino acid analysis, Chromatography, Electrophoresis. | project management, mass spectrometry, protein sequencing, peptide sequencing, amino acid analysis, chromatography, electrophoresis |
is listed by: OMICtools has parent organization: University of Zurich; Zurich; Switzerland |
PMID:21772064 | Account required | OMICS_01002 | SCR_011827 | 2026-08-11 09:42:20 | 1 | |||||||
|
TESS: Transcription Element Search System Resource Report Resource Website 100+ mentions |
TESS: Transcription Element Search System (RRID:SCR_010739) | TESS | service resource, analysis service resource, data or information resource, database, data analysis service, production service resource | TESS is a web tool for predicting transcription factor binding sites in DNA sequences. It can identify binding sites using site or consensus strings and positional weight matrices from the TRANSFAC, JASPAR, IMD, and our CBIL-GibbsMat database. You can use TESS to search a few of your own sequences or for user-defined CRMs genome-wide near genes throughout genomes of interest. Search for CRMs Genome-wide: TESS now has the ability to search whole genomes for user defined CRMs. Try a search in the AnGEL CRM Searches section of the navigation bar.. You can search for combinations of consensus site sequences and/or PWMs from TRANSFAC or JASPAR. Search DNA for Binding Sites: TESS also lets you search through your own sequence for TFBS. You can include your own site or consensus strings and/or weight matrices in the search. Use the Combined Search under ''Site Searches'' in the menu or use the box for a quick search. TESS assigns a TESS job number to all sequence search jobs. The job results are stored on our server for a period of time specified in the search submit form. During this time you may recall the search results using the form on this page. TESS can also email results to you as a tab-delimited file suitable for loading into a spreadsheet program. Query for Transcription Factor Info: TESS also has data browsing and querying capabilities to help you learn about the factors that were predicted to bind to your sequence. Use the Query TRANSFAC or Query Matrices links above or use the search interface provided from the home page. | transcription factor, dna sequence, genome, promoter, gene regulation, FASEB list | has parent organization: University of Pennsylvania; Philadelphia; USA | PMID:18428685 | nlx_97404 | http://www.pcbi.upenn.edu/tess | SCR_010739 | Transcription Element Search System | 2026-08-11 09:42:07 | 191 | ||||||
|
miRTar Resource Report Resource Website 50+ mentions |
miRTar (RRID:SCR_010851) | miRTar | service resource, analysis service resource, data or information resource, data analysis service, production service resource, data set | An integrated web server for identifying miRNA-target interactions in human. The tool enables biologists easily to identify the biological functions and regulatory relationships between a group of known/putative miRNAs and protein coding genes. It also provides perspective of information on the miRNA targets on alternatively spliced transcripts. |
is listed by: OMICtools has parent organization: National Chiao Tung University; Hsinchu; Taiwan |
OMICS_00410 | SCR_010851 | MicroRNA Target prediction | 2026-08-11 09:42:14 | 55 | |||||||||
|
SRS Resource Report Resource Website 1+ mentions |
SRS (RRID:SCR_010736) | SRS | service resource, analysis service resource, data or information resource, database, data analysis service, production service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The EBI SRS server is a primary gateway to major databases in the field of molecular biology produced and supported at EBI as well as European public access point to the MEDLINE database provided by US National Library of Medicine (NLM). It is a reference server for latest developments in data and application integration. Features include: concept of virtual databases, integration of XML databases like the Integrated Resource of Protein Domains and Functional Sites (InterPro), Gene Ontology (GO), MEDLINE, Metabolic pathways, etc., user friendly data representation in ''Nice views'', SRSQuickSearch bookmarklets. Quick Searches allow users to make a number of searches without needing to learn how to use SRS in depth. The searches query some of the common databanks without having to go and select them explicitly and without the need to understand the SRS Query Forms. Quick Searches can be performed from either the Start page (when you first open SRS) or the SRS Quick Search page (when you are already in a project). SRS also has the ability to search for links between your current results and related information in other databanks. Additionally, it is able to analyze the results of your search using many bioinformatics analysis tools or applications. This enables you to seek out further information that may be relevant to your initial search. | data set, gold standard |
is listed by: 3DVC has parent organization: European Bioinformatics Institute |
PMID:11847095 PMID:12176845 PMID:8435768 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_95251 | SCR_010736 | EBI SRS, EBI SRS server, Sequence Retrieval System | 2026-08-11 09:42:19 | 1 | ||||||
|
MetAMOS Resource Report Resource Website 10+ mentions |
MetAMOS (RRID:SCR_011914) | MetAMOS | software application, workflow software, data processing software, software resource | A modular and open source metagenomic assembly and analysis pipeline. | microbiome, pipeline, microbiome, workflow software, metagenomic assembly, metagenomic assembly, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: bio.tools is listed by: Debian is hosted by: GitHub |
Open source, Available for download | OMICS_01426, biotools:metamos | https://github.com/marbl/metAMOS, https://bio.tools/metamos | SCR_011914 | 2026-08-11 09:42:18 | 14 | |||||||
|
HUPO - Human Proteome Organisation Resource Report Resource Website 10+ mentions |
HUPO - Human Proteome Organisation (RRID:SCR_010707) | HUPO | portal, meeting resource, data or information resource, training resource, knowledge environment, organization portal, journal article | The Human Proteome Organisation (HUPO) is an international scientific organization representing and promoting proteomics through international cooperation and collaborations by fostering the development of new technologies, techniques and training. |
is parent organization of: HUPO Proteomics Standards Initiative is parent organization of: HUPO Antibody Initiative is parent organization of: HUPO Brain Proteome Project |
nlx_85721 | SCR_010707 | Human Proteome Organisation | 2026-08-11 09:42:07 | 38 | |||||||||
|
ABySS Resource Report Resource Website 500+ mentions |
ABySS (RRID:SCR_010709) | ABySS | data analysis software, software application, software resource, data processing software, sequence analysis software | Software providing de novo, parallel, paired-end sequence assembler that is designed for short reads. ABySS 1.0 originally showed that assembling human genome using short 50 bp sequencing reads was possible by aggregating half terabyte of compute memory needed over several computers using standardized message passing system. ABySS 2.0 is Resource Efficient Assembly of Large Genomes using Bloom Filter. ABySS 2.0 departs from MPI and instead implements algorithms that employ Bloom filter, probabilistic data structure, to represent de Bruijn graph and reduce memory requirements. | paired-end sequence assembler, short reads, assembling human genome, large genomes, bloom filter, |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
Genome Canada ; Genome British Columbia ; British Columbia Cancer Foundation ; NHGRI R01HG007182 |
PMID:19251739 DOI:10.1101/068338 DOI:10.1101/gr.214346.116 |
Free, Available for download, Freely available | biotools:abyss, OMICS_00006 | https://github.com/bcgsc/abyss, https://sources.debian.org/src/abyss/, https://bio.tools/abyss, | SCR_010709 | ABySS 1.0, ABySS 2.0 | 2026-08-11 09:42:13 | 808 | ||||
|
LIMMA Resource Report Resource Website 10000+ mentions |
LIMMA (RRID:SCR_010943) | LIMMA | data analysis software, data processing software, software resource, software application | Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression. | analysis, gene, expression, microarray, data, linear, model, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: GEO2R is related to: Bioconductor |
Free, Available for download, Freely available | biotools:limma, OMICS_00769 | https://omictools.com/limma-tool, https://bio.tools/limma, https://sources.debian.org/src/r-bioc-limma/ | SCR_010943 | Linear Models for Microarray Data | 2026-08-11 09:42:19 | 27197 | ||||||
|
RNAsnp Resource Report Resource Website 10+ mentions |
RNAsnp (RRID:SCR_010837) | RNAsnp | service resource, analysis service resource, software resource, data analysis service, production service resource | Software / Web Server to predict the effect of SNPs on local RNA secondary structure based on the RNA folding algorithms implemented in the Vienna RNA package. |
is listed by: OMICtools has parent organization: University of Copenhagen; Copenhagen; Denmark |
PMID:23630321 | OMICS_00392 | SCR_010837 | RNAsnp Web Server, RNAsnp Web Server: Predicting SNP effects on local RNA secondary structure | 2026-08-11 09:42:19 | 34 | ||||||||
|
CiteXplore literature searching Resource Report Resource Website 1+ mentions |
CiteXplore literature searching (RRID:SCR_010676) | data or information resource, database, web service, software resource, data access protocol | CiteXplore combines literature search with text mining tools for biology. Search results are cross referenced to EBI applications based on publication identifiers. Links to full text versions are provided where available. The underlying database is populated with data from Medline, Patents, C.B.A. and Citeseer. The site offers a quick search as well as an advanced search. Results of queries can be saved in formats compatible with commonly-used bibliographic management software and exported. We provide a Simple Object Access Protocol (SOAP) based service to retrieve data from the Citation database. Text mining is provided internally by Whatizit and externally by iHOP. | gold standard | has parent organization: European Bioinformatics Institute | nlx_76807 | SCR_010676 | CiteXplore | 2026-08-11 09:42:13 | 8 | |||||||||
|
PSI-MI Resource Report Resource Website 1+ mentions |
PSI-MI (RRID:SCR_010710) | MI | data or information resource, standard specification, narrative resource | The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics to facilitate data comparison, exchange and verification. As a first step, the PSI is developing standards for two key areas of proteomics: mass spectrometry and protein-protein interaction data. The document describes the molecular interaction data exchange format. PSI is following a leveled approach to building this specification. Level 1 will describe protein interactions at a basic level that covers a large amount of currently available data. Subsequent levels will add capability to represent new molecular interaction information that the community wishes to exchange. The scope of PSI MI is currently limited to protein-protein interactions. Other molecules, such as small molecules, DNA and RNA maybe taken into account in the future. The PSI MI format is a data exchange format for protein-protein interactions. It is not a proposed database structure. The purpose of the document is to describe the general structure of the PSI MI XML specification in a more user-friendly manner than the specification does itself. PSI MI was designed by a group of people including representatives from database providers and users in both academia and industry. PSI MI is supported by the DIP, MINT, IntAct, BIND and HPRD databases. |
is used by: MINT is related to: DOMINO: Domain peptide interactions is related to: PathGuide: the pathway resource list is related to: VirusMINT is related to: MatrixDB is related to: cPath is related to: IMEx - The International Molecular Exchange Consortium is related to: IntAct is related to: Biological General Repository for Interaction Datasets (BioGRID) |
nlx_87297 | SCR_010710 | PSI MI, PSI, Proteomic Standard Initiative for Molecular Interaction, Proteomics Standards Initiative, Proteomics Standards Initiative Molecular Interaction XML Format Documentation | 2026-08-11 09:42:07 | 2 | |||||||||
|
973 Program Resource Report Resource Website 100+ mentions |
973 Program (RRID:SCR_011494) | service resource, training service resource, funding resource, regional funding resource | A Chinese-based national program for furthering basic scientific research. The program has three main aims, which include: supporting research on issues concerning national socioeconnomic development, creating a highly-skilled cohort of scientists, and improving program management to encourage innovation. | china, basic science, research, socioeconomic development, scientists | nlx_156931 | http://www.973.gov.cn/English/Index.aspx | SCR_011494 | National Basic Research Program of China | 2026-08-11 09:42:20 | 137 | |||||||||
|
KisSplice Resource Report Resource Website 10+ mentions |
KisSplice (RRID:SCR_011893) | KisSplice | data analysis software, data processing software, software resource, software application | Software tool that enables analysis of RNA-seq data with or without reference genome. Local transcriptome assembler for SNPs, indels and AS events. | RNA-seq data analysis, with reference genome, without reference genome, local transcriptome assembler, SNPs, indels, AS events., bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1186/1471-2105-13-S6-S5 | Free, Available for download, Freely available | biotools:KisSplice, OMICS_01321 | https://bio.tools/KisSplice, https://sources.debian.org/src/kissplice/ | SCR_011893 | 2026-08-11 09:42:19 | 21 | ||||||
|
ECHO Resource Report Resource Website 100+ mentions |
ECHO (RRID:SCR_011851) | ECHO | data analysis software, software application, algorithm resource, software resource, data processing software, sequence analysis software | Error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina''s Genome Analyzer II. | error correction, rnaseq, rna sequence, short-read, next-generation sequencing, ngs, illumina, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21482625 DOI:10.1101/gr.111351.110 |
Free, Available for download | biotools:echo, OMICS_01102 | https://bio.tools/echo, https://sources.debian.org/src/uc-echo/ | SCR_011851 | ECHO: A reference-free short-read error correction algorithm | 2026-08-11 09:42:17 | 312 | |||||
|
oPOSSUM Resource Report Resource Website 100+ mentions |
oPOSSUM (RRID:SCR_010884) | oPOSSUM | service resource, analysis service resource, software resource, data analysis service, production service resource | A web-based system for the detection of over-represented conserved transcription factor binding sites and binding site combinations in sets of genes or sequences. | transcription factor binding site | is listed by: OMICtools | PMID:22973536 PMID:17576675 PMID:15933209 |
Acknowledgement requested | OMICS_00488 | SCR_010884 | oPOSSUM-3 | 2026-08-11 09:42:19 | 101 | ||||||
|
ArrayAnalysis.org Resource Report Resource Website 50+ mentions |
ArrayAnalysis.org (RRID:SCR_010932) | ArrayAnalysis.org | service resource, analysis service resource, software resource, data analysis service, production service resource | Tools for microarray quality control and pre-processing. | r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23620278 | Acknowledgement requested | OMICS_00742, biotools:arrayanalysis.org | https://bio.tools/arrayanalysis.org | SCR_010932 | ArrayAnalysis | 2026-08-11 09:42:09 | 72 | |||||
|
nsSNPAnalyzer Resource Report Resource Website 50+ mentions |
nsSNPAnalyzer (RRID:SCR_010780) | nsSNPAnalyzer | service resource, data analysis software, software application, analysis service resource, software resource, data analysis service, production service resource, data processing software | A tool to predict whether a nonsynonymous single nucleotide polymorphism (nsSNP) has a phenotypic effect. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
OMICS_00156, biotools:nssnpanalyzer | https://bio.tools/nssnpanalyzer | SCR_010780 | nsSNPAnalyzer: predicting disease-associated nonsynonymous single nucleotide polymorphisms | 2026-08-11 09:42:14 | 50 | |||||||
|
CANGS Resource Report Resource Website 1+ mentions |
CANGS (RRID:SCR_011837) | CANGS | data analysis software, data processing software, software resource, software application | A user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies. | windows, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
PMID:20180949 | biotools:cangs, OMICS_01084 | https://bio.tools/cangs | SCR_011837 | 2026-08-11 09:42:17 | 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.
