Searching the RRID Resource Information Network
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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Arabidopsis thaliana Protein Interactome Database Resource Report Resource Website 1+ mentions |
Arabidopsis thaliana Protein Interactome Database (RRID:SCR_001896) | AtPID | data repository, data or information resource, database, service resource, storage service resource | Centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome. The Protein-protein interaction pairs are predicted by integrating several methods with the Naive Baysian Classifier. All other related information curated is manually extracted from published literature and other resources from some expert biologists. You are welcomed to upload your PPI or subcellular localization information or report data errors. Arabidopsis proteins is annotated with information (e.g. functional annotation, subcellular localization, tissue-specific expression, phosphorylation information, SNP phenotype and mutant phenotype, etc.) and interaction qualifications (e.g. transcriptional regulation, complex assembly, functional collaboration, etc.) via further literature text mining and integration of other resources. Meanwhile, the related information is vividly displayed to users through a comprehensive and newly developed display and analytical tools. The system allows the construction of tissue-specific interaction networks with display of canonical pathways. | gene, gene expression, domain, annotation, ineractome, metabolic pathway, phylogenetic, protein, protein-protein interaction, signaling pathway, proteome, protein subcellular location, ortholog, gene regulation, pathway, phenotype |
is listed by: OMICtools is related to: Gene Ontology has parent organization: Northeast Forest University; Harbin; China |
National Basic Research Program of China 2010CB945400; National Basic Research Program of China 2007CB108800; National High Technology Research and Development Program of China 2006AA02Z313; National High Technology Research and Development Program of China 2006AA10Z129; National Natural Science Foundation of China 30870575; National Natural Science Foundation of China 30730078; Science and Technology Commission of Shanghai Municipality 06DZ22923 |
PMID:21036873 PMID:17962307 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01898, nif-0000-02585 | http://atpid.biosino.org/ | SCR_001896 | AtPID Database | 2026-02-11 10:56:21 | 8 | ||||
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PBmice Resource Report Resource Website 1+ mentions |
PBmice (RRID:SCR_006978) | PBmice | data repository, data or information resource, database, software resource, source code, service resource, storage service resource | Database for storing, retrieving, and displaying the information derived from piggyBac (PB) insertions (Insert) and their characterizations in the mouse genome with piggyBac transposon system. Quick Search and Advanced Search tools have been provided to find information in the PBmice database, the result is centered on Inserts and provides information related to the Inserts. A mapping database is linked to PBmice too. This mapping database allows row experiment data to be inputted in. All the mature data can be allowed publish to PBmice. PBmice Source Code is available with a License Agreement. | c57bl/6j, insertional mutation, mutagenesis, piggybac, transposon, insert, mutation | has parent organization: Fudan University; Shanghai; China | Program for New Century Excellent Talents in University ; Chinese Key Projects for Basic Research 2006CB806700; Chinese Key Projects for Basic Research 2005CB321905; Chinese Key Projects for Basic Research 2002CB512801; Hi-tech Research and Development Project 2007AA022012; National Natural Science Foundation of China 60473124; Shanghai Pujiang Program 05PJ14024 |
PMID:17932058 | nlx_97993 | http://www.scbit.org/PBmice/, http://www.idmshanghai.cn/PBmice/ | SCR_006978 | PiggyBac Mutagenesis Information CEnter, PBmice: PiggyBac Mutagenesis Information CEnter | 2026-02-11 10:57:27 | 1 | |||||
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Consortium for Reliability and Reproducibility Resource Report Resource Website 1+ mentions |
Consortium for Reliability and Reproducibility (RRID:SCR_003774) | CoRR | portal, data or information resource, data set | Consortium that has aggregated resting state fMRI (R-fMRI) and diffusion imaging data from laboratories around the world, creating an open science resource for the imaging community, that facilitates the assessment of test-retest reliability and reproducibility for functional and structural connectomics. Given that this was a retrospective data collection, they have focused on basic phenotypic measures that are relatively standard in the neuroimaging field, as well as fundamental for analyses and sample characterization. Their phenotypic key is organized to reflect three classifications of variables: 1) core (i.e., minimal variables required to characterize any dataset), 2) preferred (i.e., variables that were strongly suggested for inclusion due to their relative import and/or likelihood of being collected by most sites), and 3) optional (variables that are data-set specific or only shared by a few sites). CoRR includes 33 datasets consisting of: * 1629 Subjects * 3357 Anatomical Scans * 5093 Resting Functional Scans * 1302 Diffusion Scans * 300 CBF and ASL Scans | consortium, connectomics, reproducibility, resting state fmri, fmri, diffusion mri, neuroimaging, metadata standard, functional image, dti, anatomical image, functional, anatomical |
uses: Mind Research Network - COINS uses: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: 1000 Functional Connectomes Project |
NIDA ; National Natural Science Foundation of China ; Child Mind Institute ; Institute of Psychology ; Chinese Academy of Sciences ; Nathan S. Kline Institute for Psychiatric Research; New York; USA |
Registration required, (NITRC), Open unspecified license | nlx_158048 | SCR_003774 | Consortium for Reliability and Reproducibility (CoRR) | 2026-02-11 10:56:46 | 6 | ||||||
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International HapMap Project Resource Report Resource Website 5000+ mentions |
International HapMap Project (RRID:SCR_002846) | HapMap | narrative resource, experimental protocol, data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A multi-country collaboration among scientists and funding agencies to develop a public resource where genetic similarities and differences in human beings are identified and catalogued. Using this information, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. All of the information generated by the Project will be released into the public domain. Their goal is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. HapMap project related data, software, and documentation include: bulk data on genotypes, frequencies, LD data, phasing data, allocated SNPs, recombination rates and hotspots, SNP assays, Perlegen amplicons, raw data, inferred genotypes, and mitochondrial and chrY haplogroups; Generic Genome Browser software; protocols and information on assay design, genotyping and other protocols used in the project; and documentation of samples/individuals and the XML format used in the project. | genetic variant, disease, genetic sequence, genetic variation, single nucleotide polymorphism, genetic diversity, dna, sequence, catalog, genome, chromosome, bio.tools |
is used by: BioSample Database at EBI is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SNAP - SNP Annotation and Proxy Search is related to: Haploview is related to: NHGRI Sample Repository for Human Genetic Research is related to: DistiLD - Diseases and Traits in LD is related to: SNP at Ethnos is related to: GBrowse has parent organization: NCBI |
Chinese Academy of Sciences ; Chinese Ministry of Science and Technology ; Delores Dore Eccles Foundation ; Genome Canada ; Genome Quebec ; Hong Kong Innovation and Technology Commission ; Japanese Ministry of Education Culture Sports Science and Technology MEXT ; National Natural Science Foundation of China ; SNP Consortium ; University Grants Committee of Hong Kong ; Wellcome Trust ; W. M. Keck Foundation ; NIH |
PMID:14685227 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02940, biotools:int_hapmap_project, r3d100011835, OMICS_00273 | http://www.hapmap.org/ https://bio.tools/int_hapmap_project https://doi.org/10.17616/R3H06Q |
http://snp.cshl.org | SCR_002846 | HapMap Project | 2026-02-11 10:56:34 | 6817 | |||
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PopLDdecay Resource Report Resource Website 100+ mentions |
PopLDdecay (RRID:SCR_022509) | software resource, software application, data processing software, data analysis software | Software tool for linkage disequilibrium decay analysis based on variant call format files. | linkage disequilibrium decay analysis, variant call format, VCF) files | National Natural Science Foundation of China ; China Postdoctoral Science Foundation |
PMID:30321304 | Free, Available for download, Freely available | SCR_022509 | 2026-02-11 11:00:27 | 117 | |||||||||
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PharmMapper Resource Report Resource Website 50+ mentions |
PharmMapper (RRID:SCR_022604) | data access protocol, software resource, web service | Web server for potential drug target identification using pharmacophore mapping approach.Designed to identify potential target candidates for given probe small molecules including drugs, natural products, or other newly discovered compounds with binding targets unidentified using pharmacophore mapping approach. Used for potential drug target identification with comprehensive target pharmacophore database. | potential drug target identification, given probe small molecules, identify potential target candidates, binding targets unidentified, pharmacophore mapping approach, drug target identification, target pharmacophore database | National Natural Science Foundation of China ; Shanghai Committee of Science and Technology ; Major National Scientific and Technological Project of China |
PMID:20430828 PMID:28472422 |
Free, Freely available | SCR_022604 | PharmMapper 2017 | 2026-02-11 11:00:34 | 97 | ||||||||
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TAM Resource Report Resource Website 1+ mentions |
TAM (RRID:SCR_023800) | data access protocol, software resource, web service | Web server for miRNA set enrichment analysis. TAM 2.0 is updated version of this web server. Allows to test functional and disease annotations of miRNAs by overrepresentation analysis and to compare input de-regulated miRNAs with those de-regulated in other disease conditions via correlation analysis. | miRNA set enrichment analysis, functional and disease annotations testing, miRNAs, overrepresentation analysis, | National Natural Science Foundation of China ; Fundamental Research Funds for Central Universities of China ; Natural Science Foundation of Hebei Province ; Doctoral Fund of Ministry of Education of China |
PMID:29878154 PMID:20696049 |
Free, Freely available | SCR_023800 | TAM 2.0 | 2026-02-11 11:00:44 | 2 | ||||||||
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miRBaseConverter Resource Report Resource Website 1+ mentions |
miRBaseConverter (RRID:SCR_023873) | software resource, software application, data processing software, data analysis software | Software R package for converting and retrieving information of miRNAs in different miRBase versions. Used for converting and retrieving miRNA Name, Accession, Sequence, Version, History and Family information in different miRBase versions. Can process huge number of miRNAs in short time without other depends. | converting and retrieving miRNAs information, miRNAs information, different miRBase versions, miRNA Name, miRNA Accession, miRNA Sequence, miRNA Version, miRNA History, miRNA Family, miRNA | Australian Research Council Discovery Project ; National Health and Medical Research council ; Presidential Foundation of Hefei Institutes of Physical Science ; Chinese Academy of Sciences ; National Natural Science Foundation of China ; Applied Basic Research Foundation of Science and Technology of Yunnan Province ; Shanghai Key Laboratory of Intelligent Information Processing China |
PMID:30598108 | Free, Available for download, Freely available | https://github.com/taoshengxu/miRBaseConverter | SCR_023873 | 2026-02-11 11:00:40 | 3 | ||||||||
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CLEAR Resource Report Resource Website 10+ mentions |
CLEAR (RRID:SCR_021663) | software resource, software application, data processing software, data analysis software | Software tool as computational pipeline for circular and linear RNA expression analysis from ribosomal-RNA depleted RNA-seq. CIRCexplorer3-CLEAR is CLEAR pipeline for direct comparison of circular and linear RNA expression. | Strategic Priority Research Program of Chinese Academy of Sciences ; National Natural Science Foundation of China ; Howard Hughes Medical Institute International Program |
PMID:31904419 DOI:10.1101/668657 |
Free, Available for download, Freely available | SCR_021663 | CLEAR/circExplorer3, Circular and Linear RNA Expression Analysis from Ribosomal-RNA depleted (Ribo–) RNA-seq, CIRCexplorer3-CLEAR | 2026-02-11 11:00:12 | 15 | |||||||||
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IPEV Resource Report Resource Website 1+ mentions |
IPEV (RRID:SCR_023702) | software resource, software application, data processing software, data analysis software | Software tool to identify of Prokaryotic and Eukaryotic virus derived sequences in virome using deep learning. Used to calculate set of scores that reflect probability that input sequence fragments are prokaryotic and eukaryotic viral sequences. | Prokaryotic and Eukaryotic virus derived sequences, identify sequences, virome, eukaryotic viral sequences, prokaryotic viral sequences, | National Key Research and Development Program of China ; National Natural Science Foundation of China |
DOI:10.1101/2023.05.28.541705 | Free, Available for download, Freely available | SCR_023702 | Identification of Prokaryotic and Eukaryotic Virus | 2026-02-11 11:00:44 | 1 | ||||||||
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RNALocate Resource Report Resource Website 10+ mentions |
RNALocate (RRID:SCR_024418) | data access protocol, software resource, web service | Web tool for RNA subcellular localizations analysis. RNALocate v2.0 is updated resource for RNA subcellular localization with increased coverage and annotation. | RNA subcellular localizations analysis, | is listed by: SoftCite | Scientific Research Fund of Heilongjiang Provincial Education Department ; National Key Research and Development Project of China ; National Natural Science Foundation of China ; Paul K. and Diane Shumaker Endowment Fund at University of Missouri ; Guangdong Basic and Applied Basic Research Foundation |
PMID:27543076 PMID:34551440 |
Free, Freely available | http://www.rna-society.org/rnalocate/ http://www.rnalocate.org/ |
SCR_024418 | RNALOCATE, RNALocate v2.0 | 2026-02-11 11:00:49 | 12 | ||||||
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HPEPDOCK Server Resource Report Resource Website 10+ mentions |
HPEPDOCK Server (RRID:SCR_018561) | production service resource, software resource, web service, data access protocol, service resource, analysis service resource | Web server for blind peptide protein docking based on hierarchical algorithm. Blind peptide-protein docking by fast modeling of peptide conformations and global sampling of binding orientations. | Blind peptide protein docking, peptide conformation modeling, global sampling, blind orientation, protein, modeling, docking, bio.tools |
is listed by: bio.tools is listed by: Debian |
National Key Research and Development Program of China ; National Natural Science Foundation of China ; Huazhong University of Science and Technology |
PMID:29746661 | Free, Freely available | biotools:hpepdock | https://bio.tools/hpepdock | SCR_018561 | 2026-02-11 10:59:56 | 46 | ||||||
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SC2diseases Resource Report Resource Website 1+ mentions |
SC2diseases (RRID:SCR_019093) | production service resource, data or information resource, database, service resource, analysis service resource | Manually curated database of single cell transcriptome for human diseases. scRNA-seq database derived from numerous human studies. Provides researchers with encyclopedia of biomarkers at level of genes, cells, and diseases. | Human disease, single cell transcriptome, data, manually curated data, biomarker | National Natural Science Foundation of China | PMID:33010177 | Free, Freely available | SCR_019093 | 2026-02-11 10:59:51 | 5 | |||||||||
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HLAsupE Resource Report Resource Website 1+ mentions |
HLAsupE (RRID:SCR_016277) | data or information resource, database | Database of HLA supertype-specific epitopes. It describes major histocompatibility complex (MHC) molecules that bind short peptides derived from endogenous or exogenous antigens and present them onto the surface of antigen-presenting cells (APCs) for T-cell receptor (TCR) recognition. | hla, supertype, epitope, t cell, immunology, immune, mhc, antigen, histocompatibility | National Natural Science Foundation of China 91442203; National Natural Science Foundation of China 31470899; National Natural Science Foundation of China 31270788; National Science and Technology Major Project 2012ZX09103301014; 863 Project 2012AA02A407 |
PMID:27307005 | Freely available, Tutorial available | SCR_016277 | integrated database of HLA supertype specific epitopes | 2026-02-11 10:59:22 | 1 | ||||||||
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lnc2cancer Resource Report Resource Website 10+ mentions |
lnc2cancer (RRID:SCR_023781) | data or information resource, database | Manually curated database of experimentally supported lncRNAs associated with various human cancers. Cancer long non coding RNA database. Lnc2Cancer 3.0 is updated resource for experimentally supported lncRNA/circRNA cancer associations and web tools based on RNA-seq and scRNA-seq data. | Manually curated database, experimentally supported lncRNAs, human cancer, cancer long non coding RNA, lncRNA/circRNA cancer, | National High Technology Research and Development Program of China ; National Natural Science Foundation of China ; Postdoctoral Science Foundation of China ; Postdoctoral Foundation of Heilongjiang Province ; National Key R and D Program of China ; Heilongjiang Touyan Innovation Team Program ; Heilongjiang Provincial Natural Science Foundation |
PMID:26481356 PMID:33219685 |
Free, Freely available | SCR_023781 | lnc2Cancer 3.0 | 2026-02-11 11:00:38 | 17 | ||||||||
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Group Information Guided ICA Resource Report Resource Website |
Group Information Guided ICA (RRID:SCR_009491) | GIG-ICA | software resource, software toolkit | Software toolbox for group-information guided Independent Component Analysis (ICA). In GIG-ICA, group information captured by standard Independent Component Analysis (ICA) on the group level is used as guidance to compute individual subject specific Independent Components (ICs) using a multi-objective optimization strategy. For computing subject specific ICs, GIG-ICA is applicable to subjects that are involved or not involved in the computation of the group information. Besides the group ICs, group information captured from other imaging modalities and meta analysis could be used as the guidance in GIG-ICA too. | computational neuroscience, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Chinese Academy of Sciences; Beijing; China |
Hundred Talent Program of the Chinese Academy of Sciences ; National Basic Research Program of China 973 Program ; National Natural Science Foundation of China 91132707; National Natural Science Foundation of China 30970770 |
PMID:23194820 | Available for download | nlx_155639 | SCR_009491 | 2026-02-11 10:57:57 | 0 | ||||||
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WEGO - Web Gene Ontology Annotation Plot Resource Report Resource Website 100+ mentions |
WEGO - Web Gene Ontology Annotation Plot (RRID:SCR_005827) | WEGO | data analysis service, service resource, production service resource, analysis service resource | Web Gene Ontology Annotation Plot (WEGO) is a simple but useful tool for plotting Gene Ontology (GO) annotation results. Different from other commercial software for chart creating, WEGO is designed to deal with the directed acyclic graph (DAG) structure of GO to facilitate histogram creation of GO annotation results. WEGO has been widely used in many important biological research projects, such as the rice genome project and the silkworm genome project. It has become one of the useful tools for downstream gene annotation analysis, especially when performing comparative genomics tasks. Platform: Online tool | visualization, gene ontology, gene, annotation, comparative genomics, histogram, directed acyclic graph, genomics, genome, ontology or annotation visualization, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: BGI; Shenzhen; China |
Zhejiang University ; Chinese Academy of Sciences ; Danish Basic Research Foundation ; Ministry of Science and Technology 2002AA104250; Ministry of Science and Technology CNGI-04-15-7A; National Natural Science Foundation of China 30399120; National Natural Science Foundation of China 90208019; National Natural Science Foundation of China 30200163; National Natural Science Foundation of China 90403130 |
PMID:16845012 | Free for academic use | biotools:wego, nlx_149334 | https://bio.tools/wego | SCR_005827 | BGI WEGO - Web Gene Ontology Annotation Plotting, Web Gene Ontology Annotation Plot | 2026-02-11 10:57:10 | 386 | ||||
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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 | 2026-02-11 10:57:32 | 36 | |||||
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iNPS Resource Report Resource Website 10+ mentions |
iNPS (RRID:SCR_015750) | software resource, algorithm resource | Software for nucleosome detection that builds on the NPS software. Its application to T-cell activation data demonstrates a greater ability to facilitate detection of nucleosome repositioning, uncovering additional biological features underlying the activation process., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | nucleosome, detection, nps, sequencing data, nucleosome positioning | is related to: NPS | National Natural Science Foundation of China 31210103916; National Natural Science Foundation of China 91019019; Chinese Ministry of Science and Technology 2011CB504206; Chinese Academy of Sciences KSCX2-EW-R-02; Chinese Academy of Sciences KSCX2-EW-J-15; Chinese Academy of Sciences YZ201243; Stem Cell Leading Project XDA01010303; Shanghai Academic Leader Project 11XD1405700; Fundamental Research Funds for the Central Universities 2014JBZ005 |
PMID:25233085 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015750 | iNPS: An improved algorithm for accurate nucleosome positioning from sequencing data | 2026-02-11 10:59:22 | 25 | |||||||
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Resting State Hemodynamic Response Function Retrieval and Deconvolution Resource Report Resource Website 1+ mentions |
Resting State Hemodynamic Response Function Retrieval and Deconvolution (RRID:SCR_023663) | rsHRF | software resource, software toolkit | Software toolbox for resting state HRF estimation and deconvolution analysis. Matlab and Python toolbox that implements HRF estimation and deconvolution from resting state BOLD signal. Used to retrieve optimal lag between events and HRF onset, as well as HRF shape. Once that HRF has been retrieved for each voxel/vertex, it can be deconvolved from time series or one can map shape parameters everywhere in brain and use it as pathophysiological indicator. Input can be 2D GIfTI, 3D or 4D NIfTI images, but also on time series matrices/vectors. Output are three HRF shape parameters for each voxel/vertex, plus deconvolved time series, and number of retrieved pseudo events. All can be written back to GIfTI or NIfTI images. | hemodynamic response function, HRF estimation and deconvolution, resting state BOLD signal, GIfTI images, NIfTI images, brain | National Natural Science Foundation of China ; Fund for Scientific Research-Flanders ; European Union Horizon 2020 Framework Programme |
PMID:34560269 | Free, Available for download, Freely available | https://github.com/compneuro-da/rsHRF | SCR_023663 | 2026-02-11 11:00:38 | 3 |
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