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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
SSCprofiler Resource Report Resource Website 1+ mentions |
SSCprofiler (RRID:SCR_001282) | SSCprofiler | data analysis service, production service resource, analysis service resource, service resource | Tool which can be used to identify novel miRNA gene candidates in the human genome. | microrna, gene, genome, sequence, structure, conservation |
is listed by: OMICtools has parent organization: Institute of Molecular Biology and Biotechnology; Heraklion; Greece |
PMID:19324892 | Free, Freely available | OMICS_02055 | SCR_001282 | Sequence Structure and Conservation profiler | 2026-08-06 09:25:22 | 3 | ||||||
|
Bio Resource for Array Genes Database Resource Report Resource Website |
Bio Resource for Array Genes Database (RRID:SCR_000748) | database, data or information resource | Bio Resource for array genes is a free online resource for easy access to collective and integrated information from various public biological resources for human, mouse, rat, fly and c. elegans genes. The resource includes information about the genes that are represented in Unigene clusters. This resource provides interactive tools to selectively view, analyze and interpret gene expression patterns against the background of gene and protein functional information. Different query options are provided to mine the biological relationships represented in the underlying database. Search button will take you to the list of query tools available. This Bio resource is a platform designed as an online resource to assist researchers in analyzing results of microarray experiments and developing a biological interpretation of the results. This site is mainly to interpret the unique gene expression patterns found as biological changes that can lead to new diagnostic procedures and drug targets. This interactive site allows users to selectively view a variety of information about gene functions that is stored in an underlying database. Although there are other online resources that provide a comprehensive annotation and summary of genes, this resource differs from these by further enabling researchers to mine biological relationships amongst the genes captured in the database using new query tools. Thus providing a unique way of interpreting the microarray data results based on the knowledge provided for the cellular roles of genes and proteins. A total of six different query tools are provided and each offer different search features, analysis options and different forms of display and visualization of data. The data is collected in relational database from public resources: Unigene, Locus link, OMIM, NCBI dbEST, protein domains from NCBI CDD, Gene Ontology, Pathways (Kegg, Genmapp and Biocarta) and BIND (Protein interactions). Data is dynamically collected and compiled twice a week from public databases. Search options offer capability to organize and cluster genes based on their Interactions in biological pathways, their association with Gene Ontology terms, Tissue/organ specific expression or any other user-chosen functional grouping of genes. A color coding scheme is used to highlight differential gene expression patterns against a background of gene functional information. Concept hierarchies (Anatomy and Diseases) of MESH (Medical Subject Heading) terms are used to organize and display the data related to Tissue specific expression and Diseases. Sponsors: BioRag database is maintained by the Bioinformatics group at Arizona Cancer Center. The material presented here is compiled from different public databases. BioRag is hosted by the Biotechnology Computing Facility of the University of Arizona. 2002,2003 University of Arizona. | drug, experiment, expression, fly, functional, gene, array, biological, biology, c. elegans, cluster, database, disease, human, microarray, mouse, protein, rat, target, tissue | has parent organization: University of Arizona; Arizona; USA | nif-0000-10165 | SCR_000748 | BioRag | 2026-08-06 09:25:17 | 0 | |||||||||
|
Expression Patterns for C. elegans promoter GFP fusions Resource Report Resource Website 1+ mentions |
Expression Patterns for C. elegans promoter GFP fusions (RRID:SCR_001619) | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Database of expression patterns of C. elegans promoter::GFP constructs. A text description of the observed pattern is provided, indicating the stage(s) and tissue(s) in which GFP is expressed. Also available for some strains are the corresponding 2D and 3D images. Investigators may browse the entire list, search by gene name, tissue, stage, and pattern. Search results may be downloaded in .csv and .txt formats. All of the strains in the expression pattern database are displayed in the browse page. The records are organized by gene; information such as locus name, genomic location (WormBase), the presence of images and videos, and the actual expression pattern are shown in a tabular format. | expression, gene, gene expression, caenorhabditis elegans, c. elegans, genomic, green fluorescent protein, location, locus, pattern, stage, strain, tissue |
is listed by: One Mind Biospecimen Bank Listing is related to: WormAtlas is related to: WormBase is related to: Caenorhabditis Genetics Center is related to: NEXTDB has parent organization: Albert Einstein College of Medicine; New York; USA |
Genome Canada ; Genome British Columbia |
PMID:17850180 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153885, nif-0000-25220, SCR_008354 | SCR_001619 | Caenorhabditis elegans Expression Patterns | 2026-08-06 09:25:26 | 4 | ||||||
|
Cancer Gene Index Resource Report Resource Website 1+ mentions |
Cancer Gene Index (RRID:SCR_001117) | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on November 17, 2016. A database of genes that have been experimentally associated with human cancer diseases and/or pharmacological compounds, the evidence of these associations, and relevant annotations on the data. | gene, cancer, genetics, pharmacology, disease, database, data |
is listed by: OMICtools has parent organization: National Cancer Institute has parent organization: National Cancer Institute |
Cancer | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01575 | SCR_001117 | 2026-08-06 09:25:20 | 2 | ||||||||
|
WTCHG Genome Scan Viewer Resource Report Resource Website 1+ mentions |
WTCHG Genome Scan Viewer (RRID:SCR_001635) | GSCANDB | service resource, database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database / display tool of genome scans, with a web interface that lets the user view the data. It does not perform any analyses - these must be done by other software, and the results uploaded into it. The basic features of GSCANDB are: * Parallel viewing of scans for multiple phenotypes. * Parallel analyses of the same scan data. * Genome-wide views of genome scans * Chromosomal region views, with zooming * Gene and SNP Annotation is shown at high zoom levels * Haplotype block structure viewing * The positions of known Trait Loci can be overlayed and queried. * Links to Ensembl, MGI, NCBI, UCSC and other genome data browsers. In GSCANDB, a genome scan has a wide definition, including not only the usual statistical genetic measures of association between genetic variation at a series of loci and variation in a phenotype, but any quantitative measure that varies along the genome. This includes for example competitive genome hybridization data and some kinds of gene expression measurements. | genome, gene, snp, trait, genotype, phenotype, visualization, region, chromosome, quantitative trait locus, hybridization, gene expression | has parent organization: University of Oxford; Oxford; United Kingdom | NIAAA U01AA014425; NCRR R24RR015116; NIGMS R01GM072863; NINDS R01NS049445; NIMH P20-MH 62009; NIAAA U24AA13513 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153902 | SCR_001635 | Wellcome Trust Centre for Human Genetics Genome Scan Viewer, Genome Scan Viewer, Genome Scan Database | 2026-08-06 09:25:28 | 3 | ||||||
|
A Classification of Mobile genetic Elements Resource Report Resource Website 10+ mentions |
A Classification of Mobile genetic Elements (RRID:SCR_001694) | ACLAME | database, data or information resource | A database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. In addition to provide information on the full genomes and genetic entities, it aims at building a comprehensive classification of the functional modules of MGE's at the protein, gene, and higher levels. Prophinder, a tool dedicated to the detection of prophages in sequenced bacterial genomes, is available on ACLAME. | mobile genetic element, phage genome, plasmid, virus, prophage, transposon, protein, gene, classification, data analysis service, prophage prediction, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Free University of Brussels; Brussels; Belgium is parent organization of: MeGO |
ESTEC contract ESTEC 16370/02/NL/CK | PMID:19933762 PMID:14681355 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02533, OMICS_01528, biotools:aclame | https://bio.tools/aclame | SCR_001694 | ACLAME: A CLAssification of Mobile genetic Elements | 2026-08-06 09:25:27 | 31 | ||||
|
Published Association Database Resource Report Resource Website |
Published Association Database (RRID:SCR_001841) | PADB | database, data or information resource | It aims to help researchers to utilize information more efficiently from the published association data. This database is freely accessible only for academic users under the GNU GPL PADB indexes the sentences containing "associat*" or "case-control*" or "cohort*" or "meta-analysis" or "systematic review" or "odds ratio*" or "hazard ratio*" or "risk ratio*" or "relative risk*" from PubMed abstracts and automatically extracts the numeric values of odds ratios, hazard ratios, risk ratios and relative risks data when available. PADB automatically identifies HUGO official symbols of human genes using NCBI Entrez Gene data, and each gene is linked to the UCSC genome browser and International HapMap Project database. Furthermore, molecular pathways listed in BioCarta or KEGG databases can be accessed through the link using CGAP gene annotation data. Also, each record in PADB is linked to GAD or HPLD if it is available from those databases. Currently, (Last Update of Database Contents : Dec. 20, 2006) PADB indexes more than 1,500,000 abstracts including about 190,000 risk values ranging from 0.00001 to 4878.9 and 3,442 human genes related to 461 molecular pathways. Sponsors: This work was supported by the Brain Korea 21 Project for Medical Science, Yonsei University, Seoul, Korea and a faculty research grant of Yonsei University College of Medicine for 2006, Seoul, Korea. | gene, genome, hazard ratio, hugo, human, index, molecular pathway, ncbi, numeric value, ratio, risk ration, symbol | PMID:17877839 | Free, Freely available | nif-0000-10405 | http://medclue.com/padb/ | SCR_001841 | Published Association Database | 2026-08-06 09:25:32 | 0 | ||||||
|
5 prime end Serial Analysis of Gene Expression Database Resource Report Resource Website |
5 prime end Serial Analysis of Gene Expression Database (RRID:SCR_001680) | 5'SAGE, 5SAGE | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on October 30, 2012. A database that displays the observed frequencies of individual 5' end SAGE tags and previously unknown transcription start sites in the promoter regions, introns and intergenic regions of known genes. 5'SAGE will be useful for analyzing promoter regions and start site variation in different tissues, and is freely available. | gene expression, dna, rna, serial analysis, transcription start site, promoter region, intron, intergenic region, gene | has parent organization: University of Tokyo; Tokyo; Japan | Japanese Ministry of Education Culture Sports Science and Technology MEXT | PMID:15608259 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02525 | SCR_001680 | 5'end Serial Analysis of Gene Expression Database, 5end Serial Analysis of Gene Expression Database | 2026-08-06 09:25:27 | 0 | |||||
|
Spliceosome Database Resource Report Resource Website 10+ mentions |
Spliceosome Database (RRID:SCR_002097) | Spliceosome Database | database, data or information resource | A database of proteins and RNAs that have been identified in various purified splicing complexes. Various names, orthologs and gene identifiers of spliceosome proteins have been cataloged to navigate the complex nomenclature of spliceosome proteins. Links to gene and protein records are also provided for the spliceosome components in other databases. To navigate spliceosome assembly dynamics, tools were created to compare the association of spliceosome proteins with complexes that form at specific stages of spliceosome assembly based on a compendium of mass spectrometry experiments that identified proteins in purified splicing complexes. | splicing, mass spectrometry, protein, rna, complex, spliceosome, small nuclear rna, structure, dynamics, ortholog, gene |
is listed by: OMICtools has parent organization: University of California at Santa Cruz; California; USA |
PMID:23118483 | Free, Freely available | OMICS_01891 | SCR_002097 | Spliceosome Database - A source of information for the SLPICEOSOME: The large ribonucleoprotein complex responsible for pre-mRNA splicing, Spliceosome Component Database | 2026-08-06 09:25:34 | 11 | ||||||
|
MPromDb Resource Report Resource Website 1+ mentions |
MPromDb (RRID:SCR_002136) | MPromDb | database, data or information resource | A curated database that strives to annotate gene promoters identified from ChIP-Seq experiment results. The long term goal of the database is to provide an integrated resource for mammalian gene transcriptional regulation and epigenetics. Users can search based on Enterz gene id/symbol, or by tissue/cell specific activity and filter results based on any combination of tissue/cell specificity, known/novel, CpG/NonCpG, and protein-coding/non-coding gene promoters. It is also integrated with GBrowse genome browser for visualiztion of ChIP-seq profiles and display the annotations. | gene, promoter, chip-seq, chip-chip, visualization, gene promoter, annotation, rna pol-ii chip-seq, protein-coding gene |
is listed by: OMICtools is related to: Gene Expression Omnibus has parent organization: Wistar Institute |
PMID:21097880 PMID:16381984 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01876 | SCR_002136 | Mammalian Promoter Database | 2026-08-06 09:25:36 | 8 | ||||||
|
Mouse Neuronal Expression Database Resource Report Resource Website |
Mouse Neuronal Expression Database (RRID:SCR_002043) | MNED | database, data or information resource | Database of microarray analysis of twelve major classes of fluorescent labeled neurons within the adult mouse forebrain that provide the first comprehensive view of gene expression differences. The publicly available datasets demonstrate a profound molecular heterogeneity among neuronal subtypes, represented disproportionately by gene paralogs, and begin to reveal the genetic programs underlying the fundamental divisions between neuronal classes including that between glutamatergic and GABAergic neurons. Five of the 12 populations were chosen from cingulate cortex and included several subtypes of GABAergic interneurons and pyramidal neurons. The remaining seven were derived from the somatosensory cortex, hippocampus, amygdala and thalamus. Using these expression profiles, they were able to construct a taxonomic tree that reflected the expected major relationships between these populations, such as the distinction between cortical interneurons and projection neurons. The taxonomic tree indicated highly heterogeneous gene expression even within a single region. This dataset should be useful for the classification of unknown neuronal subtypes, the investigation of specifically expressed genes and the genetic manipulation of specific neuronal circuit elements. Datasets: * Full: Here you can query gene expression results for the neuronal populations * Strain: Here you can query the same expression results accessed under the full checkbox, with one additional population (CT6-CG2) included as a control for the effects of mouse strain. This population is identical to CT6-CG (YFPH) except the neurons were derived from wild-type mice of three distinct strains: G42, G30, and GIN. * Arlotta: Here you can query the same expression results accessed under the full checkbox, with nine additional populations from the dataset of Arlotta et al., 2005. These populations were purified by FACS after retrograde labeling with fluorescent microspheres. Populations are designated by the prefix ACS for corticospinal neurons, ACC for corticocallosal neurons and ACT for corticotectal neurons, followed by the suffix E18 for gestational age 18 embryos, or P3, P6 and P14 for postnatal day 3, 6 and 14 pups. For each successful gene query the following information is returned: # Signal level line plot: Signal level is plotted on Y-axis (log base 2) for each sample. Samples include the thirty six representing the twelve populations profiled in Sugino et al. In addition, six samples from homogenized (=dissociated and but not sorted) cortex are included representing two different strains: G42-HO is homogenate from strain G42, GIN-HO is homogenate from stain GIN. # Signal level raster plots: Signal level is represented by color (dark red is low, bright red is high) for all samples. Color scale is set to match minimum (dark red) and maximum (bright yellow) signal levels within the displayed set of probe sets. # Scaled signal level raster plots: Same as 2) except color scale is adjusted separately for each gene according to its maximum and minimum signal level. # Table: Basic information about the returned probe sets: * Affymetrix affyid of probe set * NCBI gene symbol, NCBI gene name * NCBI geneID * P-value score from ANOVA for each gene is also given if available (_anv column). P-value represents the probability that there is no difference in the expression across cell types. | expression profile, forebrain, functional, gabaergic neuron, amygdala, array, cell type, cell type comparison, microarray, cingulate cortex, classify, genomics, glutamatergic, hippocampus, interneuron, molecular, adult mouse, neuron, pyramidal neuron, somatosensory cortex, taxonomy, thalamus, gene, embryonic mouse | has parent organization: CRE Driver Network | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-12084 | http://mouse.bio.brandeis.edu:8080/ | SCR_002043 | NIH Neuroscience Blueprint Cre Driver Network Expression DB, NIH Neuroscience Blueprint Cre Driver Network - Expression DB | 2026-08-06 09:25:33 | 0 | ||||||
|
Genome Network Platform Resource Report Resource Website 10+ mentions |
Genome Network Platform (RRID:SCR_001737) | GNP | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Integrated database of experiment data generated by participating research institutes and public databases relating to: 1) transcription starting position of human genes in the human genome, 2) conjunction to control region on transcriptional factors and the human genome 3) protein-protein interaction with a central focus on transcription factors organized for use in genome level research. Gene Search is the function to search the integrated database by using keywords and public IDs. The search results can be visualized by: * Genome Explorer : provides annotation of landmarks (genes, transcription start sites, etc.) aligned in accordance with their genome locations. * PPI Network : provides a graphical view of protein-protein interaction (PPI) network from the experimental data generated under the project and the public datasets. * Expression Profile : clusters genes by expression pattern and display the result with heatmap. The function provides genes which have relation of coregulation and anti-coregulation. * Comparison Viewer : This function gives the view to compare the genomic regions between human and mouse homologous genes. The viewer shows the distribution of transcription start sites (TSS) as the way of separable by tissues or time points with other landmarks on genome region. * Gene Stock : This is the function to save the gene list that you are interested until the session is closed. | gene, genome, chip, human, interaction, micro array, protein, protein-protein interaction, qrt-pcr, rat, rna, sequence, short rna, tiling array, transcription, transcription control, transcription factor, transcription starting position, yeast two hybrid, data set, cage, data analysis service |
is listed by: 3DVC has parent organization: National Institute of Genetics; Shizuoka; Japan |
PMID:24927841 | Free, Freely Available | nif-0000-10237 | http://genomenetwork.nig.ac.jp/index_e.html | SCR_001737 | 2026-08-06 09:25:27 | 20 | ||||||
|
ASPicDB Resource Report Resource Website 1+ mentions |
ASPicDB (RRID:SCR_002102) | ASPicDB | database, data or information resource | A database to access reliable annotations of the alternative splicing pattern of human genes, obtained by ASPic algorithm (Castrignano et al. 2006), and to the functional annotation of predicted isoforms. Users may select and extract specific sets of data related to genes, transcripts and introns fulfilling a combination of user-defined criteria. Several tabular and graphical views of the results are presented, providing a comprehensive assessment of the functional implication of alternative splicing in the gene set under investigation. ASPicDB also includes information on tissue-specific splicing patterns of normal and cancer cells, based on available EST data and their library source annotation. | annotation, splicing pattern, gene, transcript, intron, protein, variant, alternative splicing, splicing, blast, exon, u2, u12, isoform |
is listed by: OMICtools is listed by: SoftCite has parent organization: University of Bari; Bari; Italy |
Normal, Cancer | PMID:21051348 PMID:18388144 |
Free, Freely available | OMICS_01882 | http://srv00.ibbe.cnr.it/ASPicDB/ | SCR_002102 | Alternative Splicing Prediction Data Base, ASPicDB - A Database tool for alternative splicing analysis | 2026-08-06 09:25:32 | 7 | ||||
|
The Alternatve Splicing Database Resource Report Resource Website 1+ mentions |
The Alternatve Splicing Database (RRID:SCR_001883) | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Alternative Splicing and Transcript Diversity (ASTD) database project is creating a database of alternative splice events and transcripts of genes from human, mouse and rat. Full length transcripts are generated with the aim of understanding the mechanism of alternative splicing on a genome-wide scale. The current release of the human genome consists of: 16715 genes, 14101 have more than one splice isoform, with an average of 5.6 splice patterns per gene. 10831 transcripts are annotated as full length with a transcription start site and a poly(A). The current release of the mouse genome consists of: 16491 genes, 13028 have more than one splice isoform, with an average of 4 splice patterns per gene. 6011 transcripts are annotated as full length with a transcription start site and a poly(A). The current release of the rat genome consists of: 10424 genes, 6344 have more than one splice isoform, with an average of 2.6 splice patterns per gene. 1250 transcripts are annotated as full length with a transcription start site and a poly(A). Sponsors: The ASTD project at EBI is supported by a grant from the EC: Eurasnet Network of Excellence (LSHG-CT-2005-518238). It was also supported by the ASD grant from the EC (QLRT-CT-2001-02062) until November 2005 and the ATD grant from the EC (LSHG-CT-2003-503329) until May 2007. | exon, exon splice site, gene, gene structure, alternative splicing, human genome, intron, intron splice site, mouse genome, nucleotide sequence database, rat genome, splice isoform, transcript, transcription, transcription diversity, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
PMID:19059335 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02579, biotools:astd | https://bio.tools/astd | SCR_001883 | ASTD | 2026-08-06 09:25:30 | 5 | ||||||
|
AREX Resource Report Resource Website 10+ mentions |
AREX (RRID:SCR_002170) | AREX | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Arabidopsis gene Expression Database collects Arabidopsis gene expression data from genome-wide and gene-specific sources and integrative search tools are provided. Currently the database contains only root gene expression data, but has the capability to contain data from any part of the plant. The aim of Arabidopsis gene Expression Database is to: (1) Integrate genome-wide and gene-specific ("traditional") types of expression pattern data, using ontologies to describe data whenever possible, in particular to describe expression patterns. (2) Provide user-friendly search tools, for example to search for genes expressed with a certain pattern, or to search for the expression pattern of specific genes (from gene-specific experiments and from microarray data). Expression pattern predicted from the microarray data is called digital in situ. | expression, gene, arabidopsis, genome, microarray, pattern | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20955 | SCR_002170 | The Arabidopsis Gene Expression Database, Arabidopsis Gene Expression Database | 2026-08-06 09:25:36 | 14 | ||||||||
|
Biospecimen Research Database Resource Report Resource Website 1+ mentions |
Biospecimen Research Database (RRID:SCR_001944) | database, data or information resource | Database to find literature, established protocols, and best practices for collecting, storing, and handling biological samples. Its main purpose is to help researchers improve the quality and reproducibility of biospecimen-based medical and genetic research. Provides a library of validated protocols that laboratories use to properly process human biospecimens (like blood or tissue) without degrading their molecular integrity. Offers procedural guidelines (BEBPs) backed by scientific literature to protect samples from pre-analytical variables (e.g., storage temperature, time-to-freezing). Catalogs thousands of peer-reviewed articles focused on biospecimen science. | NCI, biospecimen, biomarker, gene, standard operating procedure, sop, database |
is related to: Biorepositories and Biospecimens Research Branch has parent organization: National Cancer Institute has parent organization: National Institutes of Health |
NCI | PMID:25757745 | Free, Freely available | SciRes_000169 | https://dctd.cancer.gov/programs/cdp/organization/bbrb | https://brd.nci.nih.gov/brd/ | SCR_001944 | NCI Biospecimen Research Database, Biospecimen Research Database (BRD) | 2026-08-06 09:25:30 | 3 | ||||
|
HEXEvent Resource Report Resource Website 1+ mentions |
HEXEvent (RRID:SCR_002106) | HEXEvent | database, data or information resource | A free database that provides a list of human internal exons and reports all their known splice events based on EST information from the UCSC Genome Browser. This list can be restricted by the user to either only a specific region in the genome (by specifying the chromosome, the strand and the start and end position), to a whole chromosome or to a group of genes. Furthermore, exons can be filtered according to their splicing type (constitutive exons, cassette exons and exons with one or more alternative 3' and/or 5' splice sites). In order to extract a customized set of exons, the user-specific definitions of exon types can be fixed. The user needs to specify in what fraction of ESTs an exon is allowed to be alternatively spliced in order to still be called constitutive. Furthermore, the user can restrict the set of requested cassette exons by a certain upper inclusion level, which, for instance, is useful when only looking for low-inclusion exons. | exon, splicing, est, splice event, gene, chromosome, genome, splice |
is listed by: OMICtools is related to: UCSC Genome Browser has parent organization: University of California at Irvine; California; USA |
PMID:23118488 | THIS RESOURCE IS NO LONGER IS SERVICE. | OMICS_01888 | SCR_002106 | HEXEvent - a database of Human EXon splicing Events | 2026-08-06 09:25:32 | 3 | ||||||
|
Bacteriome.org Resource Report Resource Website 1+ mentions |
Bacteriome.org (RRID:SCR_001934) | Bacteriome.org | database, data or information resource | Database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase. Presently the resource offers access to two types of network: * A network of functional interactions derived through exploiting available functional genomic datasets within a Bayesian framework * Two networks of experimentally derived protein-protein interactions - a "core" network consisting of interactions deemed to be of "high quality"; and an "extended" network which extends the "core" network by including interactions for which experimental evidence is less strong. | functional interaction, genetics, genome, protein, protein-protein interaction, protein interaction, function, evolution, structure, gene, phylogenetic profile, chromosome, blast, phylogenetic, complex, network |
is listed by: OMICtools has parent organization: University of Toronto; Ontario; Canada |
Canadian Institutes of Health Research | PMID:219798435 PMID:17942431 |
nif-0000-02592, OMICS_01899, r3d100012726 | http://128.100.134.188/bacteriome/ | SCR_001934 | Bacteriome.org - Bacterial Protein Interaction Database | 2026-08-06 09:25:34 | 4 | |||||
|
Parasite Databases of Clustered ESTs Resource Report Resource Website 1+ mentions |
Parasite Databases of Clustered ESTs (RRID:SCR_002262) | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. These databases were constructed by extracting the organism specific ESTs from dbEST, removing polyA sequences from the ends and trimming 5' and 3' regions with greater than 25% N's in a 20 base pair window. These quality sequences were then aligned using the cap2 program and the consensus sequences thus generated put into a database that is available on the web. A number of parasitic organisms were chosen that have between 3000 and 15000 ESTs. The attempt here is to provide useful information and analyses to the scientific community without curating the results in any way. A total of 55192 ESTs, deposited into dbEST/GenBank, were included in the analyses. The resulting sequences have been clustered into nonredundant gene assemblies and deposited into a relational database that supports a variety of sequence and text searches. This database has been used to compare the gene assemblies using BLAST similarity comparisons to the public protein databases to identify putative genes. Of these new entries, approximately 15%-20% represent putative homologs with a conservative cutoff of p < 10(-9), thus identifying many conserved genes that are likely to share common functions with other well-studied organisms. Gene assemblies were also used to identify strain polymorphisms, examine stage-specific expression, and identify gene families. An interesting class of genes that are confined to members of this phylum and not shared by plants, animals, or fungi, was identified. These genes likely mediate the novel biological features of members of the Apicomplexa and hence offer great potential for biological investigation and as possible therapeutic targets. | est, expression, fungus, gene, animal, apicomplexa, biological, organism, parasitic, phylum, plants, polya, protein, sequence, therapeutic | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20980 | SCR_002262 | PDCEST | 2026-08-06 09:25:38 | 2 | |||||||||
|
CODEHOP Resource Report Resource Website 50+ mentions |
CODEHOP (RRID:SCR_002898) | CODEHOP | data analysis service, production service resource, analysis 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 | 2026-08-06 09:25:45 | 75 |
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.
