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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MirSNP Resource Report Resource Website 50+ mentions |
MirSNP (RRID:SCR_001629) | MirSNP | data or information resource, database | Database of human SNPs in predicted miRNA-mRNA binding sites, based on information from dbSNP135 and mirBASE18. MirSNP is highly sensitive and covers most experiments confirmed SNPs that affect miRNA function. MirSNP may be combined with researchers' own GWAS or eQTL positive data sets to identify the putative miRNA-related SNPs from traits/diseases associated variants. They aim to update the MirSNP database as new versions of mirBASE and dbSNP database become available. | single nucleotide polymorphism, mirna, genome-wide association study, expression quantitative trait locus, mirna-mrna binding site, trait, disease, variant, gene, mrna, FASEB list | has parent organization: Peking University; Beijing; China | National Natural Science Foundation of China 81071087; National Natural Science Foundation of China 81071088; International Science and Technology Cooperation Program of China 2010DFB30820; National High Technology Research and Development Program of China 2009AA022702 |
PMID:23173617 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153896 | http://202.38.126.151/hmdd/mirsnp/search/ | SCR_001629 | 2026-02-14 02:06:02 | 73 | |||||
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Human Gene Mutation Database Resource Report Resource Website 1000+ mentions |
Human Gene Mutation Database (RRID:SCR_001621) | HGMD | data or information resource, database | Curated database of known (published) gene lesions responsible for human inherited disease. | gene, disease, gene lesion, mutation, deletion, insertion, duplication, rearrangement, nuclear gene, functional polymorphism, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: BIOBASE Corporation has parent organization: Cardiff University; Wales; United Kingdom |
Inherited disease | PMID:22948725 PMID:20368137 PMID:20038494 PMID:19348700 PMID:18428754 PMID:18245393 PMID:12754702 PMID:10612821 PMID:9399854 PMID:9066272 PMID:8882888 |
Free, Freely available | nlx_153887, SCR_001888, biotools:hgmd, nif-0000-10459, OMICS_00281 | http://www.hgmd.cf.ac.uk/ac/index.php https://bio.tools/hgmd |
SCR_001621 | The Human Gene Mutation Database, The Human Gene Mutation Database at the Institute of Medical Genetics in Cardiff | 2026-02-14 02:06:05 | 2462 | ||||
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GTEx eQTL Browser Resource Report Resource Website 100+ mentions |
GTEx eQTL Browser (RRID:SCR_001618) | data or information resource, database | Database and browser that provides a central resource to archive and display association between genetic variation and high-throughput molecular-level phenotypes. This effort originated with the NIH GTEx roadmap project: however the scope of this resource will be extended to include any available genotype/molecular phenotype datasets. | genetic variation, high-throughput, phenotype, genotype, molecular, molecule, gene, gene expression, snp, trait, expression, quantitative trait locus, expression quantitative trait locus, genome, probe, sequence, statistics, p-value, rna-seq, array, lymphoblastoid, liver, cerebellum, frontal cortex, temporal cortex, pons, gene regulation, tissue, mrna, data set | has parent organization: NCBI | NIH Common Fund 268201000029C-4-0-2 | Free, Freely available | nlx_153884 | http://www.gtexportal.org/home/ | SCR_001618 | NCBI GTEx eQTL Browser, Genotype-Tissue Expression eQTL Browser, GTEx (Genotype-Tissue Expression) eQTL Browser, NCBI GTeX eQTL Browser | 2026-02-14 02:06:02 | 111 | ||||||
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MAboya Gene Expression Patterns and Sequence Tags Resource Report Resource Website 1+ mentions |
MAboya Gene Expression Patterns and Sequence Tags (RRID:SCR_000763) | MAGEST | data or information resource, database | A database for maternal gene expression information for ascidia, colloquially known as sea squirts. Information available includes DNA sequences, expression patterns of ESTs, and cDNA data from uncleaved fertilized eggs. The goal is to utilize the database to understand molecular mechanisms of establishment of embryonic body plans of chordates and to understand evolution from invertebrates to vertebrates in the future. | ascidia, sea squirt, development, maternal, dna, rna, genetic, chordate, vertebrae, gene, expression | has parent organization: University of Tokyo; Tokyo; Japan | Ministry of Education Science Sports and Culture Japan 1016821; Ministry of Education Science Sports and Culture Japan 11149212; Research for the Future Program from the Japan Society for the promotion of Science 96L00404 |
PMID:11752271 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21247 | http://www.genome.ad.jp/magest | SCR_000763 | MAboya Gene Expression Patterns and Sequence Tags (MAGEST) | 2026-02-14 02:06:00 | 7 | ||||
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Neurospora crassa Database Resource Report Resource Website 1+ mentions |
Neurospora crassa Database (RRID:SCR_001372) | NCD | data or information resource, database | It's strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated and reassembled. This method is standard for microbial genome sequencing, and has been successfully applied to Drosophila. Neurospora is an ideal candidate for this approach because of the low repeat content of the genome. Neurospora crassa Database has expanded the scope of its database by including a mitochondrial annotation, incorporating information from the Neurospora compendium, and assigning NCU numbers to tRNA and rRNAs. They have improved the annotation process to predict untranslated regions and to reduce the number of spurious predictions. As a result, version 3 contains 9,826 genes, 794 fewer than version 2. During the initial phase of a WGS project they sequence both ends of the 4 kb inserts from a plasmid library prepared using randomly sheared and sized-selected DNA. The shotgun reads are assembled by recognizing overlapping regions of sequence and making use of the knowledge of the orientation and distance of the paired reads from each plasmid. Obtaining deep sequence coverage though high levels of sequence redundancy assures that the majority of the genome is represented in the initial assembly and that the consensus sequence is of high quality. Their approach toward the initial assembly was conservative, meaning they would rather fail to join sequence contigs that might overlap each other than risk making false joins between two closely related but non-overlapping genomic regions. Hence, the initial assembly contains many sequence contigs and over time these contigs will increase in size and decrease in number as they are joined together. After shotgun sequencing and assembly there was a second phase of sequencing in which additional sequence was obtained from specific regions that were missing from the original assembly or are recognized to be of low quality in the consensus. The Neurospora crassa sequencing project reflects a close collaboration between the Broad Institute and the Neurospora research community. Principal investigators include Bruce Birren and Chad Nusbaum from the Broad Institute, Matt Sachs at the Oregon Graduate Institute of Science and Technology, Chuck Staben at the University of Kentucky and Jak Kinsey at the Fungal Genetics Stock Center at the University of Kansas Medical Center. In addition, we have a larger Advisory Board made up of a number of Neurospora researchers. Sponsors: They have been funded by the National Science Foundation to sequence the N. crassa genome and make the information publicly available. | gene, annotation, compendium, contig, distance, drosophila, genome, mitochondrial, neurospora crassa, plasmid, region, rrna, sequence, trna, untranslated | Free, Freely available, | nif-0000-20965 | http://www.broadinstitute.org/annotation/genome/neurospora/Home.html | SCR_001372 | Neurospora crassa Database | 2026-02-14 02:06:01 | 4 | |||||||
|
BloodExpress Resource Report Resource Website 1+ mentions |
BloodExpress (RRID:SCR_001142) | data or information resource, database | A database of gene expression in mouse haematopoiesis, integrating 271 individual microarray experiments derived from 15 distinct studies done on most characterized mouse blood cell types. Gene expression information has been discretized to absent/present/unknown calls. It supports gene-centric searches to find out where a gene of interest is expressed, and what other genes follow the same (or a similar) pattern of expression. It also supports cell-centric searches to find out what genes are expressed in specific cell types/studies and not others. | blood, hematopoiesis, microarray, red blood cell, gene expression, expression profile, gene, cell, haematopoietic stem cell |
uses: StemBase uses: Gene Expression Omnibus has parent organization: University of Cambridge; Cambridge; United Kingdom |
Leukemia Research Foundation ; Leukemia and Lymphoma Society ; MRC |
PMID:18987008 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02615 | SCR_001142 | Blood Express | 2026-02-14 02:06:01 | 1 | ||||||
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STIFDB Resource Report Resource Website 10+ mentions |
STIFDB (RRID:SCR_002131) | STIFDB | data or information resource, database | Database of biotic and abiotic stress responsive genes in Arabidopsis thaliana and Oryza sativa L. with options to identify probable Transcription Factor Binding Sites in their promoters. In the response to biotic stress like Bacteria and abiotic stresses like ABA, drought, cold, salinity, dehydration, UV-B, high light, heat,heavy metals etc, ten specific families of transcription factors in Arabidopsis thaliana and six in Oryza sativa L. are known to be involved. HMM-based models are used to identify binding sites of transcription factors belonging to these families. They have also consulted literature reports to cross-validate the Transcription Factor Binding Sites predicted by the method. | stress responsive, transcription factor, biotic, abiotic, gene, transcription factor binding site, promoter, stress, chromosome, blast |
is listed by: OMICtools has parent organization: Tata Institute of Fundamental Research; Mumbai; India |
PMID:23314754 PMID:19841686 |
Free, Freely Available | OMICS_01866 | SCR_002131 | Stress Responsive Transcription Factor Database | 2026-02-14 02:05:38 | 10 | ||||||
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Rice Metabolic Pathway Database Resource Report Resource Website 1+ mentions |
Rice Metabolic Pathway Database (RRID:SCR_002128) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. RiceCyc is a catalog of known and/or predicted biochemical pathways from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database project on the release 5 of the TIGR-assembly of Oryza sativa japonica cv. Nipponbare genome sequenced by IRGSP. | gene, biochemical pathway, rice | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20922 | http://www.gramene.org/pathway/ricecyc.html | SCR_002128 | Rice Metabolic Pathways, RiceCyc | 2026-02-14 02:05:46 | 9 | ||||||||
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pSTIING Resource Report Resource Website 1+ mentions |
pSTIING (RRID:SCR_002045) | pSTIING | data or information resource, database | A publicly accessible knowledgebase about protein-protein, protein-lipid, protein-small molecules, ligand-receptor interactions, receptor-cell type information, transcriptional regulatory and signal transduction modules relevant to inflammation, cell migration and tumourigenesis. It integrates in-house curated information from the literature, biochemical experiments, functional assays and in vivo studies, with publicly available information from multiple and diverse sources across human, rat, mouse, fly, worm and yeast. The knowledgebase allowing users to search and to dynamically generate visual representations of protein-protein interactions and transcriptional regulatory networks. Signalling and transcriptional modules can also be displayed singly or in combination. This allow users to identify important "cross-talks" between signalling modules via connections with key components or "hubs". The knowledgebase will facilitate a "systems-wide" understanding across many protein, signalling and transcriptional regulatory networks triggered by multiple environmental cues, and also serve as a platform for future efforts to computationally and mathematically model the system behavior of inflammatory processes and tumourigenesis. | protein-protein, protein-lipid, protein-small molecule, ligand-receptor interaction, receptor-cell type, transcriptional regulatory module, signal transduction module, inflammation, cell migration, tumorigenesis, protein-protein interaction, transcriptional regulatory network, signalling pathway, interaction, protein interaction, motif, domain, protein, gene |
is listed by: OMICtools is related to: Gene Ontology has parent organization: University College London; London; United Kingdom |
Inflammation, Tumor, Cancer | PMID:16381926 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01916 | SCR_002045 | Protein Signalling Transcriptional Interactions and Inflammation Networks Gateway, Protein Signalling Transcriptional Interactions & Inflammation Networks Gateway | 2026-02-14 02:05:37 | 2 | |||||
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RegPrecise Resource Report Resource Website 50+ mentions |
RegPrecise (RRID:SCR_002149) | RegPrecise | data or information resource, database | Collection of manually curated inferences of regulons in prokaryotic genomes. Database for capturing, visualization and analysis of transcription factor regulons that were reconstructed by comparative genomic approach in wide variety of prokaryotic genomes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | regulon, genome, transcription factor, gene, operon, transcription factor binding site, taxonomy, rna, effector, pathway, ortholog, function, FASEB list |
is listed by: OMICtools has parent organization: Lawrence Berkeley National Laboratory |
Department of Energy ; NSF DBI-0850546 |
PMID:24175918 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01869 | SCR_002149 | 2026-02-14 02:06:08 | 80 | ||||||
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Primate Orthologous Exon Database Resource Report Resource Website 1+ mentions |
Primate Orthologous Exon Database (RRID:SCR_002065) | Primate Orthologous Exon Database | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of orthologous exon regions in the genomes of human, chimpanzee, and rhesus macaque. It can be used in analysis of multi-species RNA-seq expression data, allowing for comparisons of exon-level expression across primates, as well as comparative examination of alternative splicing and transcript isoforms. | alternative splicing, transcript isoform, ortholog, exon, gene, rna-seq, primate, genome |
is listed by: OMICtools has parent organization: University of Chicago; Illinois; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01895 | SCR_002065 | 2026-02-14 02:06:06 | 1 | ||||||||
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Alignable Tight Genomic Cluster Resource Report Resource Website 1+ mentions |
Alignable Tight Genomic Cluster (RRID:SCR_001894) | ATGC | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. ATGC stands for Alignable Tight Genomic Cluster, which is cluster of closely related prokaryotic genomes. ATGC is the principal notion of this web resource. The purpose of this web resource is to prepare ATGC-derived data sets for a variety of research projects in functional and evolutionary genomics. Unique features of ATGC include: * Reliable identification of orthologs (high degree of similarity between the genomes in the set allow an extensive use of synteny in ortholog identification); * Fine granularity of protein classification (in comparisons of more distant genomes, proteins belonging to families of paralogs are often lumped into a singlegroup; under the ATGC approach, comparison of genomic sequences from highly similar genomes allows one to track each set of orthologs separately); * Relative rarity of changes of any kind (in sequence, genome organization and gene content) allows the use of parsimony-related methods of analysis. | gene, genomic cluster, genomic sequence, ortholog, paralog, prokaryotic genomic, protein, protein classification | has parent organization: Lawrence Berkeley National Laboratory | Department of Energy Joint Genome Institute ; NLM ; DOE DE-AC02-05CH11231 |
PMID:28053163 PMID:18845571 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02581 | SCR_001894 | 2026-02-14 02:06:03 | 1 | ||||||
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PubGene Resource Report Resource Website 10+ mentions |
PubGene (RRID:SCR_002119) | data or information resource, database | It helps users retrieve information on genes and proteins. The underlying structure of PubGene can be viewed as a gene-centric database. Gene and protein names are cross-referenced to each other and to terms that are relevant to understanding their biological function, importance in disease and relationship to chemical substances. The result is a literature network organizing information in a form that is easy to navigate. | gene, information, protein, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is parent organization of: Coremine Medical |
Free, Freely Available | biotools:pubgene, nif-0000-20908 | https://bio.tools/pubgene | SCR_002119 | PubGene | 2026-02-14 02:06:07 | 39 | |||||||
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Cell Signaling Pathways Resource Report Resource Website 1+ mentions |
Cell Signaling Pathways (RRID:SCR_002070) | data or information resource, database | Cell signaling pathways can be explored using PathFinder, the interactive, online graphical representation of cell signaling pathways. The user can use PathFinder to explore the relationships between different cell signaling pathway components while being presented with our high quality small molecules, antibodies, enzymes, siRNA for gene knockdown and qPCR components to aid them in their research. | enzyme, gene, antibody, cell signaling, molecule, pathway, qpcr, research, sirna | PMID:17854489 | Free, Freely available | nif-0000-20825 | http://www.sigmaaldrich.com/Area_of_Interest/Life_Science/PathFinder.html | SCR_002070 | PathFinder | 2026-02-14 02:05:37 | 3 | |||||||
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COSMIC - Catalogue Of Somatic Mutations In Cancer Resource Report Resource Website 1000+ mentions |
COSMIC - Catalogue Of Somatic Mutations In Cancer (RRID:SCR_002260) | COSMIC | data or information resource, database |
Database to store and display somatic mutation information and related details and contains information relating to human cancers. The mutation data and associated information is extracted from the primary literature. In order to provide a consistent view of the data a histology and tissue ontology has been created and all mutations are mapped to a single version of each gene. The data can be queried by tissue, histology or gene and displayed as a graph, as a table or exported in various formats. Some key features of COSMIC are: * Contains information on publications, samples and mutations. Includes samples which have been found to be negative for mutations during screening therefore enabling frequency data to be calculated for mutations in different genes in different cancer types. * Samples entered include benign neoplasms and other benign proliferations, in situ and invasive tumours, recurrences, metastases and cancer cell lines. |
cancer, mutation, somatic mutation, tumor, cancer genome, genome, gene, dna, tissue, histology, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Cancer | Wellcome Trust 077012/Z/05/Z | PMID:20952405 | Free | nif-0000-02690, biotools:cosmic, OMICS_00082 | http://www.sanger.ac.uk/perl/CGP/cosmic https://bio.tools/cosmic |
SCR_002260 | Catalogue Of Somatic Mutations In Cancer | 2026-02-14 02:06:06 | 4486 | |||
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Human Proteomics Initiative Resource Report Resource Website |
Human Proteomics Initiative (RRID:SCR_002373) | HPI | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 03, 2011. IT HAS BEEN REPLACED BY A NEW UniProtKB/Swiss-Prot ANNOTATION PROGRAM CALLED UniProt Chordata protein annotation program. The Human Proteome Initiative (HPI) aims to annotate all known human protein sequences, as well as their orthologous sequences in other mammals, according to the quality standards of UniProtKB/Swiss-Prot. In addition to accurate sequences, we strive to provide, for each protein, a wealth of information that includes the description of its function, domain structure, subcellular location, similarities to other proteins, etc. Although as complete as currently possible, the human protein set they provide is still imperfect, it will have to be reviewed and updated with future research results. They will also create entries for newly discovered human proteins, increase the number of splice variants, explore the full range of post-translational modifications (PTMs) and continue to build a comprehensive view of protein variation in the human population. The availability of the human genome sequence has enabled the exploration and exploitation of the human genome and proteome to begin. Research has now focused on the annotation of the genome and in particular of the proteome. With expert annotation extracted from the literature by biologists as the foundation, it has been possible to expand into the areas of data mining and automatic annotation. With further development and integration of pattern recognition methods and the application of alignments clustering, proteome analysis can now be provided in a meaningful way. These various approaches have been integrated to attach, extract and combine as much relevant information as possible to the proteome. This resource should be valuable to users from both research and industry. We maintain a file containing all human UniProtKB/Swiss-Prot entries. This file is updated at every biweekly release of UniProt and can be downloaded by FTP download, HTTP download or by using a mirroring program which automatically retrieves the file at regular intervals. | function, gene, alignment, biologist, clustering, coding, development, genome, human, location, mammalian, modification, ortholog, population, post-translational, protein, proteome, proteomic, proteomics, sequence, splice, structure, subcellular, variant, variation, gold standard |
is related to: UniProt Chordata protein annotation program has parent organization: SIB Swiss Institute of Bioinformatics |
PMID:11301130 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21199 | SCR_002373 | Human Proteome Initiative, UniProtKB/Swiss-Prot Human Proteome Initiative | 2026-02-14 02:05:47 | 0 | ||||||
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Human Gene and Protein Database (HGPD) Resource Report Resource Website 1+ mentions |
Human Gene and Protein Database (HGPD) (RRID:SCR_002889) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.The Human Gene and Protein Database presents SDS-PAGE patterns and other informations of human genes and proteins. The HGPD was constructed from full-length cDNAs. For conversion to Gateway entry clones, we first determined an open reading frame (ORF) region in each cDNA meeting the criteria. Those ORF regions were PCR-amplified utilizing selected resource cDNAs as templates. All the details of the construction and utilization of entry clones will be published elsewhere. Amino acid and nucleotide sequences of an ORF for each cDNA and sequence differences of Gateway entry clones from source cDNAs are presented in the GW: Gateway Summary window. Utilizing those clones with a very efficient cell-free protein synthesis system featuring wheat germ, we have produced a large number of human proteins in vitro. Expressed proteins were detected in almost all cases. Proteins in both total and supernatant fractions are shown in the PE: Protein Expression window. In addition, we have also successfully expressed proteins in HeLa cells and determined subcellular localizations of human proteins. These biological data are presented on the frame of cDNA clusters in the Human Gene and Protein Database. To build the basic frame of HGPD, sequences of FLJ full-length cDNAs and others deposited in public databases (Human ESTs, RefSeq, Ensembl, MGC, etc.) are assembled onto the genome sequences (NCBI Build 35 (UCSC hg17)). The majority of analysis data for cDNA sequences in HGPD are shared with the FLJ Human cDNA Database (http://flj.hinv.jp/) constructed as a human cDNA sequence analysis database focusing on mRNA varieties caused by variations in transcription start site (TSS) and splicing. | gene, cdna clusters, cdnas, cdna sequences, human, in vitro, mrna varieties, protein, sds-page | has parent organization: National Institute of Advanced Industrial Science and Technology | PMID:22140100 PMID:19073703 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02956 | SCR_002889 | HGPD | 2026-02-14 02:06:11 | 6 | |||||||
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EchoBASE Resource Report Resource Website 1+ mentions |
EchoBASE (RRID:SCR_002430) | EchoBASE | data or information resource, database | A database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655. It has been created to integrate information from post-genomic experiments into a single resource with the aim of providing functional predictions for the 1500 or so gene products for which we have no knowledge of their physiological function. While EchoBASE provides a basic annotation of the genome, taken from other databases, its novelty is in the curation of post-genomic experiments and their linkage to genes of unknown function. Experiments published on E. coli are curated to one of two levels. Papers dealing with the determination of function of a single gene are briefly described, while larger dataset are actually included in the database and can be searched and manipulated. This includes data for proteomics studies, protein-protein interaction studies, microarray data, functional genomic approaches (looking at multiple deletion strains for novel phenotypes) and a wide range of predictions that come out of in silico bioinformatic approaches. The aim of the database is to provide hypothesis for the functions of uncharacterized gene products that may be used by the E. coli research community to further our knowledge of this model bacterium. | gene, bio.tools |
is listed by: bio.tools is listed by: Debian |
GlaxoSmithKline ; BBSRC |
PMID:15608209 | nif-0000-02781, biotools:echobase, r3d100011646 | https://bio.tools/echobase https://doi.org/10.17616/R38W6H |
SCR_002430 | EchoBASE: an integrated post-genomic database for Escherichia coli | 2026-02-14 02:06:10 | 6 | |||||
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Greengenes Resource Report Resource Website 1000+ mentions |
Greengenes (RRID:SCR_002830) | data or information resource, database | Database that provides access to the current and comprehensive 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading. The data and tools can assist the researcher in choosing phylogenetically specific probes, interpreting microarray results, and aligning/annotating novel sequences. The 16S rRNA gene database provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. ARB users can use Greengenes to update local databases., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | microbiome, rrna, 16s rrna, gene, dna, rna, chimera, alignment, taxonomic classification, taxonomy, FASEB list |
is listed by: OMICtools is listed by: re3data.org is listed by: Human Microbiome Project has parent organization: Lawrence Berkeley National Laboratory |
Department of Energy contract DE-AC02-05CH11231 | PMID:16820507 | Free, Freely available | OMICS_01512, r3d100010549, nif-0000-02927 | http://greengenes.lbl.gov https://doi.org/10.17616/R36C8G |
SCR_002830 | 2026-02-14 02:05:48 | 3125 | ||||||
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AceView Resource Report Resource Website 100+ mentions |
AceView (RRID:SCR_002277) | AceView/WormGenes | data or information resource, database | 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., documented August 29, 2016. AceView offers an integrated view of the human, nematode and Arabidopsis genes reconstructed by co-alignment of all publicly available mRNAs and ESTs on the genome sequence. Our goals are to offer a reliable up-to-date resource on the genes and their functions and to stimulate further validating experiments at the bench. AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammals' transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release. Alternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been observed are listed in order of representation; diseases, phenotypes, pathways, functions, localization or interactions are annotated by mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm. In this way, both the anatomy and physiology of the experimentally cDNA supported human, mouse and nematode genes are thoroughly annotated. Our goals are to offer an up-to-date resource on the genes, in the hope to stimulate further experiments at the bench, or to help medical research. AceView can be queried by meaningful words or groups of words as well as by most standard identifiers, such as gene names, Entrez Gene ID, UniGene ID, GenBank accessions. | est, exon, expression, function, gene, alignment, arabidopsis, cdna, co-alignment, coding, disease, genome, genomic, human, intron, localization, mammal, mouse, mrna, nematode, pathway, phenotype, plant, polyadenylation, promoter, rat, sequence, signal, tissue, transcript, transcriptome, worm, blast, gold standard | has parent organization: NCBI | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21007, r3d100010651 | https://doi.org/10.17616/R3260G | http://www.ncbi.nih.gov/IEB/Research/Acembly/ | SCR_002277 | AceView genes, AceView/WormGenes, The AceView Genes | 2026-02-14 02:05:39 | 186 |
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