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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Oak Ridge Collection at JAX Resource Report Resource Website |
Oak Ridge Collection at JAX (RRID:SCR_016409) | ORNL, ORC | biomaterial supply resource, material resource, organism supplier | Supplier of mice for research purposes. | mouse, strain, supply, research, repository, subject, genetic engineering, knockout, mice, gene, model | is listed by: International Mouse Strain Resource | SCR_016409 | Oak Ridge Collection, Oak Ridge Laboratory, JAX Oak Ridge, Oak Ridge Lab, Oakridge, The Oak Ridge National Laboratory (ORNL), Oak Ridge National Laboratory, Oak Ridge | 2026-09-12 12:58:39 | 0 | |||||||||
|
Oriental BioService Inc. Resource Report Resource Website 1+ mentions |
Oriental BioService Inc. (RRID:SCR_016404) | OBS | biomaterial supply resource, material resource, organism supplier | Supplier of mice for research purposes. | mouse, strain, supply, research, repository, subject, genetic engineering, knockout, mice, gene, model, transgenic | is listed by: International Mouse Strain Resource | SCR_016404 | Oriental BioService, Oriental BioServices | 2026-09-12 12:58:39 | 8 | |||||||||
|
Monocle2 Resource Report Resource Website 100+ mentions |
Monocle2 (RRID:SCR_016339) | data analysis software, data processing software, software application, software resource, software toolkit | Software package for analyzing single cell gene expression, classifying and counting cells, performing differential expression analysis between subpopulations of cells, and reconstructing cellular trajcectories. Works well with very large single-cell RNA-Seq experiments containing tens of thousands of cells or more. Used in computational analysis of gene expression data in single cell gene expression studies to profile transcriptional regulation in complex biological processes and highly heterogeneous cell populations. | analysis, heterogenous, population, single, cell, gene, expression, data, large, single-cell RNA-Seq, transcriptional, regulation, heterogen | Alfred P. Sloan Foundation Research Fellowship ; NIH DP2 HD088158 |
PMID:24658644 | Free, Available for download, Freely available | SCR_016339 | Monocle 2 | 2026-09-12 12:58:38 | 227 | ||||||||
|
GEO2R Resource Report Resource Website 50+ mentions |
GEO2R (RRID:SCR_016569) | data analysis software, data processing software, software application, software resource | Software as an interactive web tool to compare two or more groups of samples in a Gene Expression Omnibus (GEO) series regardless of data type and quality. Used to identify genes that are differentially expressed across experimental conditions. Results are presented as a table of genes ordered by significance. | compare, group, sample, gene, expression, omnibus, data, identify, differentially, expressed, across, condition, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Bioconductor is related to: GEOquery is related to: LIMMA |
Free, Available for download, Freely available | biotools:GEO2R | https://bio.tools/GEO2R | SCR_016569 | 2026-09-12 12:58:41 | 76 | ||||||||
|
AbundantOTU+ Resource Report Resource Website 1+ mentions |
AbundantOTU+ (RRID:SCR_016527) | AbundantOTU | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for analysis of large 16S rRNA pyrosequences by using a consensus alignment algorithm, utilizing the sequence redundancy of abundant species in the pyrosequence dataset. | pyrosequencing, 16S, rRNA, gene, operational, taxonomic, unit, abundant, species, dataset |
is listed by: OMICtools has parent organization: Indiana University; Indiana; USA |
NHGRI R01 HG004908; NHLBI U01 HL09896001 |
PMID:22102981 | Free, Available for download, Freely available | SCR_016527 | AbundantOTU:Abundant Operational Taxonomic Unit, Abundant OTU, AbundantOTU+ | 2026-09-12 12:58:40 | 1 | ||||||
|
TRANSIT Resource Report Resource Website 1+ mentions |
TRANSIT (RRID:SCR_016492) | data analysis software, data processing software, software application, software resource | Software tool Python based and open source for statistical analysis of TnSeq data. Provides a graphical interface to three different statistical methods for analyzing TnSeq data capable of identifying essential genes in individual datasets as well as comparative analysis between conditions. | statistical, analysis, TnSeq, data, identify, gene, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Texas A and M University; Texas; USA |
PMID:26447887 | Free, Available for download, Freely available | biotools:transit | https://github.com/mad-lab/transit, https://bio.tools/transit | SCR_016492 | 2026-09-12 12:58:40 | 4 | |||||||
|
Transcriptome Analysis Console Resource Report Resource Website 10+ mentions |
Transcriptome Analysis Console (RRID:SCR_016519) | TAC | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for microarray analysis designed for biologists . Used for identification of differential expression by providing interactive visualizations. | transcriptome, analysis, console, data, array, gene, visualization, identify | Commercially available | SCR_016519 | TAC:Transcriptome Analysis Console | 2026-09-12 12:58:40 | 21 | |||||||||
|
Generalized Relevance Network Resource Report Resource Website 1+ mentions |
Generalized Relevance Network (RRID:SCR_016488) | GenRelNet | data analysis software, data processing software, network analysis software, software application, software resource | Software tool with approaching infers network structure by measuring the pairwise associations between the data observed in the individual network nodes. It follows the more general statistical perspective of GRN inference, where no explicit model of the data is built or assumed. | network, inference, reconstruction, relevance, approach, gene, regulatory | Free, Available for download, Freely available | SCR_016488 | GenRelNet:Generalized Relevance Network | 2026-09-12 12:58:40 | 1 | |||||||||
|
CODEHOP Resource Report Resource Website 50+ mentions |
CODEHOP (RRID:SCR_002898) | CODEHOP | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.Service to design PCR primers from protein multiple sequence alignments. NOTICE: This version of CODEHOP is no longer maintained. | degenerate, primer, primer design, degenerate primer, oligonucleotide, pcr assay, gene, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Fred Hutchinson Cancer Center |
PMID:20967601 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:codehop, OMICS_02339 | https://bio.tools/codehop | SCR_002898 | COnsensus-DEgenerate Hybrid Oligonucleotide Primers, CODEHOP: COnsensus-DEgenerate Hybrid Oligonucleotide Primers | 2026-09-12 01:01:27 | 75 | |||||
|
Ligand-Gated Ion Channel Database Resource Report Resource Website 1+ mentions |
Ligand-Gated Ion Channel Database (RRID:SCR_002418) | LGICdb | data or information resource, database | Database providing access to information about transmembrane proteins that exist under different conformations, with three primary subfamilies: the cys-loop superfamily, the ATP gated channels superfamily, and the glutamate activated cationic channels superfamily. Due to the lack of evolutionary relationship, these three superfamilies are treated separately. It currently contains 554 entries of ligand-activated ion channel subunits. In this database one may find: the nucleic and proteic sequences of the subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Additionally, the atomic coordinates of subunits, or portion of subunits, are provided when available. Redundancy is kept to a minimum, i.e. one entry per gene. Each entry in the database has been manually constructed and checked by a researcher of the field in order to reduce the inaccuracies to a minimum. NOTE: This database is not actively maintained anymore. People should not consider it as an up-to-date trustable resource. For any new work, they should consider using alternative sources, such as UniProt, Ensembl, Protein Databank etc. | equilibrium, extracellular, gabaa, gated, gene, genetics, 3d model, alignment, anionic, atomic, atp, cationic, cellular, molecular, channel, compartment, computation, conformation, coordinate, cys-loop, glutamate, glycine, histamine, homologous, ion, ion channel, ligand, membrane, nicotinic, nucleic acid, phylogenetic, pore, portion, proteic, nucleic acid, protein, phylogeny, receptor, segment, sequence, sequence data, serotonin, subunit, superfamily, transmembrane |
is listed by: re3data.org has parent organization: European Bioinformatics Institute |
College of France; Paris; France ; Centre National de la Recherche Scientifique ; European Union ; Biotech and Biomed contracts ; French Ministry of Higher Education and Research ; Institut Pasteur |
PMID:16381861 PMID:11125117 |
nif-0000-00037, r3d100010796 | https://doi.org/10.17616/R3Q90D | SCR_002418 | LGIC Database | 2026-09-12 01:01:25 | 1 | |||||
|
GeneCards Resource Report Resource Website 5000+ mentions |
GeneCards (RRID:SCR_002773) | GeneCards | data or information resource, database | Database of human genes that provides concise genomic, proteomic, transcriptomic, genetic and functional information on all known and predicted human genes. Information featured in GeneCards includes orthologies, disease relationships, mutations and SNPs, gene expression, gene function, pathways, protein-protein interactions, related drugs and compounds and direct links to cutting edge research reagents and tools such as antibodies, recombinant proteins, clones, expression assays and RNAi reagents. | genome, human gene, genome, gene, genomic, proteomic, transcriptomic, genetic, function, ortholog, disease, mutation, single nucleotide polymorphism, gene expression, gene function, pathway, protein-protein interaction, drug, compound, reagent, antibody, recombinant protein, clone, expression assay, rnai reagent, FASEB list |
is listed by: OMICtools is related to: MOPED - Model Organism Protein Expression Database |
PMID:20689021 | Free, Freely available | nif-0000-02879, OMICS_01652, r3d100012015 | http://bioinfo.weizmann.ac.il/genecards/, https://doi.org/10.17616/R3D643 | SCR_002773 | GeneCards - The Human Gene Compendium | 2026-09-12 01:01:26 | 7635 | |||||
|
HomoloGene Resource Report Resource Website 100+ mentions |
HomoloGene (RRID:SCR_002924) | HomoloGene | data or information resource, database, service resource | 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 | 2026-09-12 01:01:27 | 459 | |||||
|
Zebrafish Information Network (ZFIN) Resource Report Resource Website 500+ mentions |
Zebrafish Information Network (ZFIN) (RRID:SCR_002560) | ZFIN | data or information resource, database | Model organism database that serves as central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. Data represented are derived from three primary sources: curation of zebrafish publications, individual research laboratories and collaborations with bioinformatics organizations. Data formats include text, images and graphical representations.Serves as primary community database resource for laboratory use of zebrafish. Developed and supports integrated zebrafish genetic, genomic, developmental and physiological information and link this information extensively to corresponding data in other model organism and human databases. | expression, gene, anatomy, development, disease, genomic, model, molecular, mutant, neuronal, organism, phenotype, physiological, synteny, zebrafish, gene expression, genome sequence, molecular neuroanatomy resource, genotype, anatomical structure, publication, genome, image collection, gold standard, bio.tools, FASEB list, RRID Community Authority |
uses: InterMOD is used by: NIF Data Federation is used by: Resource Identification Portal is used by: Morpholino Database is used by: Integrated Animals is used by: NIH Heal Project is recommended by: Resource Identification Portal is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: InterMOD is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: Phenoscape Knowledgebase is related to: MONARCH Initiative is related to: Bgee: dataBase for Gene Expression Evolution is related to: NIH Data Sharing Repositories is related to: HomoloGene is related to: Zebrafish International Resource Center is related to: Integrated Manually Extracted Annotation is related to: Zebrafish Genome Project has parent organization: University of Oregon; Oregon; USA is parent organization of: ZFIN Antibody Database is parent organization of: Zebrafish Anatomical Ontology is parent organization of: ZFIN Protocol Wiki is parent organization of: ZFIN Antibody Wiki is organization facet of: Alliance of Genome Resources |
NHGRI P41 HG002659; NHGRI R01 HG004834 |
PMID:23074187 PMID:21036866 PMID:16381936 |
Free, Available for download, Freely available | OMICS_01666, nif-0000-21427, biotools:zfin, r3d100010421, SCR_017504 | http://zfin.org/ZFIN/misc_html/tips.html#newrecord, https://wiki.zfin.org/display/general/ZFIN+Data+Submissions, https://bio.tools/zfin, https://doi.org/10.17616/R3CK5Z | SCR_002560 | Zebrafish Database, The Zebrafish Model Organism Database, Zebra Model Organism Database, ZebraFish Information Network, ZFIN | 2026-09-12 01:01:26 | 978 | ||||
|
Knowledgebase for Addiction Related Genes Resource Report Resource Website 1+ mentions |
Knowledgebase for Addiction Related Genes (RRID:SCR_002687) | KARG | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Database of data and knowledge linking genes and chromosome regions to addiction that were extracted from reviewing more than 1,000 peer-reviewed publications from between 1976 and 2006. This list of publications included review papers on addiction selected from results of PUBMED query "(addiction OR drug abuse) AND review" as well as research papers selected from PUBMED query "(addiction OR drug abuse) AND (gene OR microarray OR proteomics OR QTL OR population association OR genetic linkage)". The data spanned multiple technology platforms including classical hypothesis-testing of single genes, identification of significantly differentially expressed genes in microarray experiments, identification of significantly differentially expressed proteins in proteomics assays, identification of addiction-vulnerable chromosome regions in animal QTL studies, genetic linkage studies, population association studies, and OMIM annotations. From each publication they collected the genes, proteins, or chromosome regions linked to addiction, as well as metadata such as species, nature of the addictive substance, studied brain regions, technology platforms, and experimental parameters. In total, they collected 2,343 items of evidence linking 1,500 human genes to addiction. Among them 396 genes were supported by two or more items of evidence. The interface supports browsing of the genes by chromosome or pathways, advanced text search by gene ID, organism, type of addictive substance, technology platform, protein domain, and/or PUBMED ID, and sequence search by BLAST similarity. All data, database schema, and MySQL commands are freely available for download. | molecular neuroanatomy resource, gwas, meta-analysis, genetic susceptibility, gene, protein, chromosome, pathway, drug of abuse, blast, addiction, substance abuse, drug abuse, microarray, proteomics, qtl, population association, genetic linkage |
uses: PubMed has parent organization: Peking University; Beijing; China |
PMID:18179280 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00411 | SCR_002687 | KARG: Knowledgebase for Addiction-Related Gene, Knowledgebase for Addiction-Related Gene, KARG: Knowledgebase for Addiction Related Genes | 2026-09-12 01:01:26 | 8 | ||||||
|
EcoGene Resource Report Resource Website 50+ mentions |
EcoGene (RRID:SCR_002437) | ECK, ECOGENE, ECOGENE G | data or information resource, database | Database that contains updated information about the Escherichia coli K-12 genome and proteome sequences, including extensive gene bibliographies. Users are able to download customized tables, perform Boolean query comparisons, generate sets of paired DNA sequences, and download any E. coli K-12 genomic DNA sub-sequence. BLAST functions, microarray data, an alphabetical index of genes, and gene overlap queries are also available. The Database Table Downloads Page provides a full list of EG numbers cross-referenced to the new cross-database ECK numbers and other common accession numbers, as well as gene names and synonyms. Monthly release archival downloads are available, but the live, daily updated version of EcoGene is the default mysql database for download queries. | life sciences, genomics, proteomics, gene, gene expression, genetics, protein, protein binding, protein-protein interaction, membrane, rna, dna, structure, function, functional annotation, annotation, blast, FASEB list |
is listed by: re3data.org is related to: RefSeq is related to: Colibri has parent organization: University of Miami Miller School of Medicine; Florida; USA |
NIH ; Lucille P. Markey Foundation ; NIGMS 5-R01-GM58560-05 |
PMID:23197660 PMID:10592181 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02784, r3d100010546 | https://doi.org/10.17616/R3KP5V | http://bmb.med.miami.edu/ http://bmb.med.miami.edu/EcoGene/EcoWeb/ http://www.ecogene.org/old/ | SCR_002437 | EcoGene Database of Escherichia coli Sequence and Function | 2026-09-12 01:01:25 | 58 | |||
|
object-oriented Transcription Factors Database Resource Report Resource Website 1+ mentions |
object-oriented Transcription Factors Database (RRID:SCR_002435) | data or information resource, database | ooTFD (object-oriented Transcription Factors Database) is a successor to TFD, the original Transcription Factors Database. This database is aimed at capturing information regarding the polypeptide interactions which comprise and define the properties of transcription factors. ooTFD contains information about transcription factor binding sites, as well as composite relationships within transcription factors, which frequently occur as multisubunit proteins that form a complex interface to cellular processes outside the transcription machinery through protein-protein interactions. ooTFD contains information represented in TFD but also allows the representation of containment, composite, and interaction relationships between transcription factor polypeptides. It is designed to represent information about all transcription factors, both eukaryotic and prokaryotic, basal as well as regulatory factors, and multiprotein complexes as well as monomers. | eukaryotic, expression, factor, gene, basal, binding site, biochemical, biology, cellular, complex, genome, genomic, information, interaction, molecule, monomer, multisubunit, nucleotide sequences, transcriptional regulator sites, transcription factors, object, polypeptide, process, prokaryotic, property, protein, protein-protein interaction, regulatory, sequence, transcription | has parent organization: IFTI-Mirage | PMID:10592257 PMID:9847215 PMID:9399874 |
Free, Freely available | nif-0000-21303 | SCR_002435 | ooTFD | 2026-09-12 01:01:25 | 2 | |||||||
|
Database oDatabase of Predicted Subcellular Localization for Eukaryotic PDB Chainsf Predicted Subcellular Localization for Eukaryotic PDB Chains Resource Report Resource Website |
Database oDatabase of Predicted Subcellular Localization for Eukaryotic PDB Chainsf Predicted Subcellular Localization for Eukaryotic PDB Chains (RRID:SCR_002831) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. LOC3d is a database of predicted subcellular localization for eukaryotic proteins of known 3-D structure taken from the Protein Databank. Subcellular localization is currently predicted using four different methods: predictNLS (nuclear localization signal), LOChom (using homology), LOCkey (using keywords) and LOC3d (neural network based prediction). The reported localization is based on the method which predicts localization of a given protein with the highest confidence. LOCtree is a novel system of support vector machines (SVMs) that predict the subcellular localization of proteins, and DNA-binding propensity for nuclear proteins, by incorporating a hierarchical ontology of localization classes modeled onto biological processing pathways. Biological similarities are incorporated from the description of cellular components provided by the gene ontology consortium (GO). GO definitions have been simplified and tailored to the problem of protein sorting. Technically the ontology has been implemented using a decision tree with SVMs as the nodes. LOCtree, was extremely successful at learning evolutionary similarities among subcellular localization classes and was significantly more accurate than other traditional networks at predicting subcellular localization. Whenever available, LOCtree also reports predictions based on the following: 1) Nuclear localization signals found by PredictNLS, 2) Localization inferred using Prosite motifs and Pfam domains found in the protein, and 3) SWISS-PROT keywords associated with a protein. Localization is inferred in the last two cases using the entropy-based LOCkey algorithm. Additional information can be found in the LOCtree manuscript and associated PredictNLS and LOCkey publications. | eukaryotic, gene, binding, biological, dna, localization, nuclear, pathway, protein, structure, subcellular, vector, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Columbia University; New York; USA |
PMID:12824321 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25200, biotools:loc3d | https://bio.tools/loc3d | SCR_002831 | LOC3d | 2026-09-12 01:01:26 | 0 | ||||||
|
Exonic Splicing Enhancer Finder Resource Report Resource Website 50+ mentions |
Exonic Splicing Enhancer Finder (RRID:SCR_002835) | analysis service resource, data analysis service, production service resource, service resource | A web-based analysis service for identifying exonic splicing enhancers in eukaryotic genes. ESEfinder accept sequences in the FASTA format. A typical mammalian gene is composed of several relatively short exons that are interrupted by much longer introns. To generate correct mature mRNAs, the exons must be identified and joined together precisely and efficiently, in a process that requires the coordinated action of five small nuclear (sn)RNAs (U1, U2, U4, U5 and U6) and more than 60 polypeptides. The inaccurate recognition of exon/intron boundaries or the failure to remove an intron generates aberrant mRNAs that are either unstable or code for defective or deleterious protein isoforms. Exonic enhancers are thought to serve as binding sites for specific serine/arginine-rich (SR) proteins, a family of structurally related and highly conserved splicing factors characterized by one or two RNA-recognition motifs (RRM) and by a distinctive C-terminal domain highly enriched in RS dipeptides (the RS domain). The RRMs mediate sequence-specific binding to the RNA, and so determine substrate specificity, whereas the RS domain appears to be involved mainly in protein-protein interactions. SR proteins bound to ESEs can promote exon definition by directly recruiting the splicing machinery through their RS domain and/or by antagonizing the action of nearby silencer elements. Sponsors: ESEfinder is supported by the Cold Spring Harbor Laboratory. | element, enhancer, eukaryotic, exon, exonic, gene, analysis, arginine, boundary, c-terminal, dipeptide, intron, isoform, mammalian, mrna, nuclear, polypeptide, protein, recognition, rna, serine, service, snrna, splice | has parent organization: Cold Spring Harbor Laboratory | Free, Freely available | nif-0000-25204 | SCR_002835 | ESEfinder | 2026-09-12 01:01:26 | 66 | ||||||||
|
ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters Resource Report Resource Website 1+ mentions |
ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters (RRID:SCR_002276) | ABS | data or information resource, database | Public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. For each gene, TFBSs conserved in orthologous sequences from at least two different species must be available. Promoter sequences as well as the original GenBank or RefSeq entries are additionally supplied in case of future identification conflicts. The final TSS annotation has been refined using the database dbTSS. Up to this release, 500 bps upstream the annotated transcription start site (TSS) according to REFSEQ annotations have been always extracted to form the collection of promoter sequences from human, mouse, rat and chicken. For each regulatory site, the position, the motif and the sequence in which the site is present are available in a simple format. Cross-references to EntrezGene, PubMed and RefSeq are also provided for each annotation. Apart from the experimental promoter annotations, predictions by popular collections of weight matrices are also provided for each promoter sequence. In addition, global and local alignments and graphical dotplots are also available. | gene, alignment, annotation, binding, computational, genome, nucleotide, ortholog, prediction, promoter, sequence, target, transcription, transcriptional factor, binding site, promoter sequence, protein motif, benchmark, transcription factor binding site, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: IntegromeDB has parent organization: Center for Genomic Regulation; Barcelona; Spain |
European Union FP6 contract LSHG-CT-2003-503265 | PMID:16381947 | Acknowledgement requested, GNU General Public License, v2 | biotools:alggen, nif-0000-21006 | https://bio.tools/alggen | SCR_002276 | A database of Annotated regulatory Binding Sites from orthologous promoters | 2026-09-12 01:01:25 | 3 | ||||
|
T3DB Resource Report Resource Website 10+ mentions |
T3DB (RRID:SCR_002672) | T3DB | data or information resource, database | Database that combines detailed toxin data with comprehensive toxin target information. The database currently houses 3,053 toxins described by 32,276 synonyms, including pollutants, pesticides, drugs, and food toxins, which are linked to 1,670 corresponding toxin target records. Altogether there are 37,084 toxin, toxin target associations. (March 2014) Each toxin record (ToxCard) contains over 50 data fields and holds information such as chemical properties and descriptors, toxicity values, molecular and cellular interactions, and medical information. This information has been extracted from over 5,454 sources sources, which include other databases, government documents, books, and scientific literature. The focus of the T3DB is on providing mechanisms of toxicity and target proteins for each toxin. This dual nature of the T3DB, in which toxin and toxin target records are interactively linked in both directions, makes it unique from existing databases. It is also fully searchable and supports extensive text, sequence, chemical structure, and relational query searches | toxicology, toxin, pollutant, pesticide, drug, food, gene-drug, interaction, gene, phenotype, mechanism, bio.tools |
is used by: NIF Data Federation is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: FMA has parent organization: University of Alberta; Alberta; Canada |
Alberta Advanced Education and Technology ; Canadian Institutes of Health Research ; Genome Alberta ; Genome Canada |
PMID:19897546 | Free, Available for download, Freely available | r3d100012189, nif-0000-22933, biotools:t3db, OMICS_01592 | https://bio.tools/t3db, https://doi.org/10.17616/R3VM0R | SCR_002672 | Toxin-Target Database, Toxin Toxin-Target Database, Toxin and Toxin Target Database, Toxin, Toxin Toxin Target Database | 2026-09-12 01:01:26 | 27 |
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 NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF 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 NIF then you can log in from here to get additional features in NIF 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 NIF 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.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
