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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.

(last updated: Oct 12, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
BodyMap-XsResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A taxonomical and anatomical database of latest cross species animal EST data, clustered by UniGene and inter connected by Inparanoid. Users can search by Unigene, RefSeq, or Entrez Gene ID, or search for Gene Name or Tissue type. Data is also sortable and viewable based on qualities of normal, Neoplastic, or other. The last data import appears to be from 2008expressed sequence tag, comparative genomics, anatomy, taxonomy, brain, blood, connective, reproductive, muscular, alimentary, lung, liver, urinary, endocrine, exocrine, embryo, homology, gene expression, ortholog, paralogSCR_001147(BodyMap-Xs, RRID:SCR_001147)DDBJ - DNA Data Bank of Japan Neoplasm, NormalJapanese Ministry of Education Culture Sports Science and Technology MEXT, New Energy and Industrial Technology Development OrganizationReferences (3)Last checked downnif-0000-02617http://bodymap.jp/, http://bodymap.ims.u-tokyo.ac.jp/
Bloomington Drosophila Stock CenterResource, organism supplier, biomaterial supply resource, service resource, storage service resource, material resource, material storage repositoryDatabase that collects, maintains and distributes Drosophila melanogaster strains for research. Emphasis is placed on genetic tools that are useful to a broad range of investigations. These include basic stocks of flies used in genetic analysis such as marker, balancer, mapping, and transposon-tagging strains; mutant alleles of identified genes, including a large set of transposable element insertion alleles; defined sets of deficiencies and a variety of other chromosomal aberrations; engineered lines for somatic and germline clonal analysis; GAL4 and UAS lines for targeted gene expression; enhancer trap and lacZ-reporter strains with defined expression patterns for marking tissues; and a collection of transposon-induced lethal mutations.disease model, deficiency, deletion, transposon insertion, sequenced strain, duplication, protein trap, human disease model, transposon, fly, gene, genetic, genetic analysis, database, deficiency, germline, insertion, invertebrate, scientist, somatic, stock, transposon, mutation, genetic constructSCR_006457(Bloomington Drosophila Stock Center, RRID:SCR_006457)Indiana University; Indiana; USA Human disease modelNIH Office of the Directorrelated to: One Mind Biospecimen Bank Listing, NIF Data Federation, used by: Integrated Animals, listed by: One Mind Biospecimen Bank ListingLast checked upnif-0000-00241https://orip.nih.gov/comparative-medicine/programs/invertebrate-modelshttp://flystocks.bio.indiana.edu/bloomhome.htm
Aging Genes and Interventions DatabaseResource, service resource, data or information resource, data repository, storage service resource, databaseA database of genes and interventions connected with aging phenotypes including those with respect to their effects on life-span or age-related neurological diseases. Information includes: organism, aging phenotype, allele type, strain, gene function, phenotypes, mutant, and homologs. If you know of published data (or your own unpublished data that you'd like to share) not currently in the database, please use the Submit a Gene/Intervention link.allele, strain, gene function, phenotype, mutant, homolog, mutation, degeneration, gene, intervention, life-spanSCR_002701(Aging Genes and Interventions Database, RRID:SCR_002701)University of Washington; Seattle; USA Aging, Age-related neurological disease, Neurological diseaseEllison Medical Foundationrelated to: Monarch Initiative, used by: Aging Portal, NIF Data FederationPMID:12044961Last checked upnif-0000-23326http://sageke.sciencemag.org/highlights/gidb/
Lifespan Observations DatabaseResource, data or information resource, databaseDatabase that collects published lifespan data across multiple species. The entire database is available for download in various formats including XML, YAML and CSV.lifespan, phenotype, intervention, gene, compound, publicationSCR_001609(Lifespan Observations Database, RRID:SCR_001609)Sageweb Agingrelated to: Monarch Initiative, used by: NIF Data Federation, Aging PortalLast checked downnlx_153873http://sageweb.org/lifespandb
Drosophila Development OntologyResource, ontology, data or information resource, controlled vocabularyA structured controlled vocabulary of the development of Drosophila melanogaster.oboSCR_010310(Drosophila Development Ontology, RRID:SCR_010310)FlyBase used by: Virtual Fly Brain, listed by: BioPortalLast checked upnlx_157390
Drosophila Gross Anatomy OntologyResource, ontology, data or information resource, controlled vocabularyA structured controlled vocabulary of the anatomy of Drosophila melanogaster.oboSCR_010311(Drosophila Gross Anatomy Ontology, RRID:SCR_010311)used by: Virtual Fly Brain, listed by: BioPortalLast checked upnlx_157391
MitoBreakResource, service resource, data or information resource, data repository, storage service resource, databaseDatabase with curated datasets of mitochondrial DNA (mtDNA) rearrangements. Users may submit new mtDNA rearrangements.mitochondrial dna rearrangement, mitochondrial dna, deletion, duplication, linearSCR_012949(MitoBreak, RRID:SCR_012949)listed by: OMICtoolsPMID:24170808Last checked upOMICS_01640
ComiRResource, analysis service resource, data analysis service, service resource, production service resourceData analysis service that predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression to improve and combine multiple miRNA targets for each of the four prediction algorithms: miRanda, PITA, TargetScan and mirSVR. The composite scores of the four algorithms are then combined using a support vector machine trained on Drosophila Ago1 IP data.mirnaSCR_013023(ComiR, RRID:SCR_013023)University of Pittsburgh; Pennsylvania; USA Fondazione RiMED, NLMlisted by: OMICtoolsReferences (2)Last checked upOMICS_00395
doRiNAResource, data or information resource, databaseIn animals, RNA binding proteins (RBPs) and microRNAs (miRNAs) post-transcriptionally regulate the expression of virtually all genes by binding to RNA. Recent advances in experimental and computational methods facilitate transcriptome-wide mapping of these interactions. It is thought that the combinatorial action of RBPs and miRNAs on target mRNAs form a post-transcriptional regulatory code. We provide a database that supports the quest for deciphering this regulatory code. Within doRiNA, we are systematically curating, storing and integrating binding site data for RBPs and miRNAs. Users are free to take a target (mRNA) or regulator (RBP and/or miRNA) centric view on the data. We have implemented a database framework with short query response times for complex searches (e.g. asking for all targets of a particular combination of regulators). All search results can be browsed, inspected and analyzed in conjunction with a huge selection of other genome-wide data, because our database is directly linked to a local copy of the UCSC genome browser. At the time of writing, doRiNA encompasses RBP data for the human, mouse and worm genomes. For computational miRNA target site predictions, we provide an update of PicTar predictions.binding site, rna binding protein, microrna, post-transcription, rna, gene, genome, mammal, population variation, gene expression, transcript, regulator, protein, bindingSCR_013222(doRiNA, RRID:SCR_013222)Max Delbruck Center for Molecular Medicine; Berlin; Germany BMBF, DFG, MDC Systems Biology Network, Senate of Berlin; Berlin; Germanyrelated to: UCSC Genome BrowserPMID:22086949Last checked downnlx_151321
Drosophila melanogaster Exon DatabaseResource, data or information resource, databaseDatabase on Drosophila melanogaster exons presented in a splicing graph form. Data is based on release 3.2 of the Drosophila melanogaster genome annotations available at FlyBase. The gene structure information extracted from the annotations were checked, clustered and transformed into splicing graph. The splicing graph form of the gene constructs were then used for classification of the various types of alternative splicing events. In addition, Pfam domains were mapped onto the gene structure. Users can query the database using the query page using BLAST, FlyBase Gene Name, FlyBase Gene Symbol, Pfam Accession Number and Pfam Identifier. This allows users to determine the Drosophila melanogaster homology of their gene using a BLAST search and to visualize the alternative splicing variants if any. Users can also determine genes containing a particular domain using the Pfam Accession Numbers and Identifiers.exon, gene, alternative splicing, annotation, classification, cluster, domain, genome, graph, homology, protein, splicing, structure, transcript, visualize, blastSCR_013441(Drosophila melanogaster Exon Database, RRID:SCR_013441)National University of Singapore; Singapore; Singapore Agency for Science Technology and Researchrelated to: FlyBase, listed by: OMICtoolsPMID:15581431Last checked upnif-0000-21118, OMICS_01894
MitoMinerResource, data or information resource, databaseA database of mitochondrial proteomics data. It includes two sets of proteins: the MitoMiner Reference Set, which has 10477 proteins from 12 species; and MitoCarta, which has 2909 proteins from mouse and human mitochondrial proteins. MitoMiner provides annotation from the Gene Ontology (GO) and UniProt databases. This reference set contains all proteins that are annotated by either of these resources as mitochondrial in any of the species included in MitoMiner. MitoMiner data via is available via Application Programming Interface (API). The client libraries are provided in Perl, Python, Ruby and Java.mitochondrion, proteomics, function, homolog, proteome, protein expression, mass-spectrometry, protein, metabolism, green fluorescent protein tag, orthologSCR_001368(MitoMiner, RRID:SCR_001368)MRCuses: HomoloGene, Universal Protein Resource, KEGG, OMIM, HPA, Gene OntologyReferences (2)Last checked upnlx_152504
Integrated AnimalsResource, biomaterial supply resource, data or information resource, material resource, organism supplier, databaseIntegrated Animals is a virtual database currently indexing available animal strains and mutants from: AGSC (Ambystoma), BCBC (mice), BDSC (flies), CWRU Cystic Fibrosis Mouse Models (mice), DGGR (flies), FlyBase (flies), IMSR (mice), MGI (mice), MMRRC (mice), NSRRC (pig), NXR (Xenopus), RGD (rats), Sperm Stem Cell Libraries for Biological Research (rats), Tetrahymena Stock Center (Tetrahymena), WormBase (worms), XGSC (Xiphophorus), ZFIN (zebrafish), and ZIRC (zebrafish).non human animal, mutant, database, integrated, nifSCR_001421(Integrated Animals, RRID:SCR_001421)Integrated used by: NIF Data Federation, NIDDK Information Network, uses: Mouse Genome Informatics (MGI), Beta Cell Biology Consortium , Zebrafish Information Network, International Mouse Strain Resource, Bloomington Drosophila Stock Center, Rat Genome Database (RGD), Zebrafish International Resource Center, Ambystoma Genetic Stock Center, Kyoto Stock Center, FlyBase, Mutant Mouse Regional Resource Center, National Swine Resource and Research Center, National Xenopus Resource, CWRU In Vivo Animal Facilities, Sperm Stem Cell Libraries for Biological Research, A Resource Center For Tetrahymena Thermophila, WormBase, Xiphophorus Genetic Stock CenterLast checked downnif-0000-08137https://legacy.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nlx_154697-1 http://neuinfo.org/nif/nifgwt.html?query=nif-0000-08137, https://www.neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nif-0000-08137-1
DrososhareResource, organism supplier, biomaterial supply resource, portal, material resource, community building portal, data or information resourceWebsite resource for researchers to order and send Drosophilia specimens to each other. This community-driven supplier also works with the FlyBase Drosophilia database to search for synonyms for fly species.community driven, organism supplier, community building portal, drosophila, fly, specimenSCR_014976(Drososhare, RRID:SCR_014976)uses: FlyBaseLast checked down
BABAMResource, software resource, data visualization software, data analysis resource, data processing software, software applicationGraphical user interface for exploring hypotheses of correlations between neural activity in regions of the brain and behavior for Drosophila melanogaster. These correlation hypotheses are the result of our thermogenetic neural activation screen from the Janelia GAL4 collection.drosophila melanogaster, correlation hypothesis, neural activity, thermogenetic neural activation screenSCR_015632(BABAM, RRID:SCR_015632)uses: MATLABLast checked up
MINTResource, data or information resource, databaseA database that focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. The curated data can be analyzed in the context of the high throughput data and viewed graphically with the MINT Viewer. This collection of molecular interaction databases can be used to search for, analyze and graphically display molecular interaction networks and pathways from a wide variety of species. MINT is comprised of separate database components. HomoMINT, is an inferred human protein interatction database. Domino, is database of domain peptide interactions. VirusMINT explores the interactions of viral proteins with human proteins. The MINT connect viewer allows you to enter a list of proteins (e.g. proteins in a pathway) to retrieve, display and download a network with all the interactions connecting them.protein-protein interaction, protein, interaction, virus, peptide, organelle co-localization, pathway, molecular interaction, papillomavirus, epstein-barr virus, hepatitis b virus, hepatitis c virus, human adenovirus, human herpesvirus, human immunodeficiency virus, influenza a virus, vaccinia virus, simian virus 40, virus strains, virus protein, orthologous protein, network, proteomics, orthologSCR_001523(MINT, RRID:SCR_001523)University of Rome Tor Vergata; Rome; Italy AIRC Associazione Italiana per la Ricerca sul Cancro, ENFIN, European Union, HUPO Proteomics Standards Initiative, IMEx - The International Molecular Exchange Consortium, Interaction Proteome Projectrelated to: MPIDB, TissueNet - The Database of Human Tissue Protein-Protein Interactions, InteroPorc, Interaction Reference Index, Pathway Commons, ConsensusPathDB, VirusMINT, PSICQUIC Registry, Agile Protein Interactomes DataServer, uses: IntAct, PSI-MI, listed by: re3data.org, affiliated with: IMEx - The International Molecular Exchange Consortium, works_with: IMEx - The International Molecular Exchange ConsortiumReferences (8)Last checked upnlx_152821
larvalignResource, data analysis software, data processing software, software application, sequence analysis software, data set, software resource, software toolkit, data or information resourceSoftware package including computational methods for aligning gene expression patterns from the larval brain of Drosophila melanogaster. Its method includes evaluation of the registration framework involved in template generation and mapping.drosophila melanogaster, computational method, gene expression, alignment, larval brain, larvae, template generation, mappingSCR_015815(larvalign, RRID:SCR_015815)submitted by: Resource Identification PortalLast checked up
Drosophila anatomy and development ontologiesResource, ontology, data or information resource, controlled vocabularyA structured controlled vocabulary of the anatomy of Drosophila melanogaster. These ontologies are query-able reference sources for information on Drosophila anatomy and developmental stages. They also provide controlled vocabularies for use in annotation and classification of data related to Drosophila anatomy, such as gene expression, phenotype and images. They were originally developed by FlyBase, who continue to maintain them and have used them for over 200,000 annotations of phenotypes and expression. Extensive use of synonyms means that, given a suitably sophisticated autocomplete, users can find relevant content by searching with almost any anatomical term they find in the literature. These ontologies are developed in the web ontology language OWL2. Their extensive formalization in OWL can be used to drive sophisticated query systems.anatomy, development, developmental stage, gene expression, phenotype, owlSCR_001607(Drosophila anatomy and development ontologies, RRID:SCR_001607) SourceForge , FlyBase NHGRIrelated to: OBO, Flannotator, REDfly Regulatory Element Database for Drosophilia, Bgee: a dataBase for Gene Expression EvolutionLast checked downnlx_153871
MikadoResource, software resource, source codeMikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data * and to select the best models in each locus.annotation, rna-seq, genomics, transcriptomicsSCR_016159(Mikado, RRID:SCR_016159)BBSRCrelated to: PortcullisDOI:10.1101/216994Last checked uphttp://mikado.readthedocs.io/
AncoraResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceWeb resource that provides data and tools for exploring genomic organization of highly conserved noncoding elements (HCNEs) for multiple genomes. It includes a genome browser that shows HCNE locations and features novel HCNE density plots as a powerful tool to discover developmental regulatory genes and distinguish their regulatory elements and domains. They identify HCNEs as non-exonic regions of high similarity between genome sequences from distantly related organisms, such as human and fish, and provide tools for studying the distribution of HCNEs along chromosomes. Major peaks of HCNE density along chromosomes most often coincide with developmental regulatory genes. Their aim with this site is to aid discovery of developmental regulatory genes, their regulatory domains and their fundamental regulatory elements.genome, highly conserved noncoding element, noncoding element, regulatory gene, regulatory domain, regulatory element, developmental regulatory gene, evolution, enhancerSCR_001623(Ancora, RRID:SCR_001623)University of Bergen; Bergen; Norway Bergen Research Foundation, Research Council of Norway, Sars Centrerelated to: Monarch InitiativePMID:18279518Last checked upnlx_153891
Ensembl VariationResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourcePublic database that stores areas of genome that differ between individual genomes (variants) and, where available, associated disease and phenotype information. Different types of variants for several species: single nucleotide polymorphisms (SNPs), short nucleotide insertions and/or deletions, and longer variants classified as structural variants (including CNVs). Effects of variants on the Ensembl transcripts and regulatory features for each species are predicted. You can run same analysis on your own data using Variant Effect Predictor. These data are integrated with other data sources in Ensembl, and can be accessed using the API or website. For several different species in Ensembl, they import variation data (SNPs, CNVs, allele frequencies, genotypes, etc) from a variety of sources (e.g. dbSNP). Imported variants and alleles are subjected to quality control process to flag suspect data. In human, they calculate linkage disequilibrium for each variant, by population.genome, disease, phenotype, genomic variant, single nucleotide polymorphism nucleotide, insertion, deletion, structural variant, copy number variation, inversion, translocation, somatic variant, allele frequency, genotype, disease phenotype, inherited diseaseSCR_001630(Ensembl Variation, RRID:SCR_001630)Ensembl related to: dbSNP, Database of Genomic Variants Archive, PubMed, Animal QTLdb, OMIA - Online Mendelian Inheritance in Animals, used by: Monarch InitiativeReferences (4)Last checked downnlx_153897
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