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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
Rat Genome Database (RGD)Resource, service resource, data or information resource, data repository, storage service resource, databaseDatabase for genetic, genomic, phenotype, and disease data generated from rat research. Centralized database that collects, manages, and distributes data generated from rat genetic and genomic research and makes these data available to scientific community. Curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data is provided. Facilitates investigators research efforts by providing tools to search, mine, and analyze this data. Strain reports include description of strain origin, disease, phenotype, genetics, immunology, behavior with links to related genes, QTLs, sub-strains, and strain sources.mouse, rat, human, gene, qtl, marker, map, strain, sequence, est, genome, ontology, pathway, comparative genomics, physiology, phenotype, disease, model organism, proteomics, function, genetic, genomic, variation, immunology, behavior, knockout, inbred rat strain, mutant, congenic rat, recombinant inbred rat, data analysis service, organism supplier, genotype, gold standardSCR_006444(Rat Genome Database (RGD), RRID:SCR_006444)Medical College of Wisconsin; Wisconsin; USA NHLBIrelated to: Rat Gene Symbol Tracker, MPO, NIF Data Federation, MONARCH Disease Models View, Vertebrate Trait Ontology, Biositemaps, One Mind Biospecimen Bank Listing, AmiGO, Monarch Initiative, OMICtools, re3data.org, Integrated Manually Extracted Annotation, used by: ChannelPedia, Resource Identification Portal, DisGeNET, Integrated Animals, uses: InterMOD, recommended by: Resource Identification Portal, listed by: re3data.org, InterMOD, affiliated with: InterMODReferences (3)Last checked upnif-0000-00134, OMICS_01660
Repository of molecular brain neoplasia dataResource, topical portal, database, analysis service resource, production service resource, data analysis service, service resource, portal, data or information resourceREMBRANDT is a data repository containing diverse types of molecular research and clinical trials data related to brain cancers, including gliomas, along with a wide variety of web-based analysis tools that readily facilitate the understanding of critical correlations among the different data types. REMBRANDT aims to be the access portal for a national molecular, genetic, and clinical database of several thousand primary brain tumors that is fully open and accessible to all investigators (including intramural and extramural researchers), as well as the public at-large. The main focus is to molecularly characterize a large number of adult and pediatric primary brain tumors and to correlate those data with extensive retrospective and prospective clinical data. Specific data types hosted here are gene expression profiles, real time PCR assays, CGH and SNP array information, sequencing data, tissue array results and images, proteomic profiles, and patients'''' response to various treatments. Clinical trials'''' information and protocols are also accessible. The data can be downloaded as raw files containing all the information gathered through the primary experiments or can be mined using the informatics support provided. This comprehensive brain tumor data portal will allow for easy ad hoc querying across multiple domains, thus allowing physician-scientists to make the right decisions during patient treatments.gene, genetic, cancer, glioma, tumor, clinical genomics, functional genomics, clinical trial, genomics, gene expression, chromosomal aberration, clinical data, clinical, cellular pathway, gene ontology, molecule, brain, neoplasia, brain tumor, adult, pediatric, child, adolescent, gene expression profile, real time pcr assay, cgh array, snp array, sequence, tissue array, image, proteomic profile, treatment, protocol, molecular data, oncology, data mining, copy number array, gene expression array, secretion, kinase, membrane, gene-anomaly, translational research, personalized medicine, data integration, pathway, cell, phenotypeSCR_004704(Repository of molecular brain neoplasia data, RRID:SCR_004704)National Cancer Institute Glioma, Brain cancer, Brain tumorNCI, NINDSrelated to: Gene Ontology, Glioma Molecular Dignostic InitiativesPMID:19208739Last checked upnif-0000-00230
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
Short Course on the Genetics and Epigenetics of Addiction National Institute on Drug Abuse: Archived VideoResource, narrative resource, short course material, training material, video resource, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. An archived video on the web providing comprehensive and hands-on training in genetics and epigenetic methodology. The purpose of the course is to provide an introduction to approaches and tools for identifying genes that confer vulnerability to addiction and individual differences in responses to treatments. The course is targeted to those who are new to the field of addiction genetics. The course was held over 5 days with lectures and hands-on demonstrations given each day. Viewers of the course will gain familiarity with conceptual and practical approaches to complex disorders using relevant genetic and epigenetic databases, and appropriate statistical and empirical approaches. Topics covered Behavioral genetics, genetic epidemiology, twin and adoption studies, statistical genetic concepts and approaches for mapping complex traits, haplotype based approaches for association mapping, genome-wide scans for addictive disorders, application of linkage for mapping genes and genetic loci for addictive disorders, pharmacogenomics of treatment of addictive disorders, Baysian Methods for identifying gene-gene interactions, analysis of copy number variation, practical use of genetic databases, mapping of complex traits in mice, methods for analyzing gene expression, and methods for doing epigenetic analysis are covered. The course was held April 4, 2008, at the Bethesda North Marriott Hotel and Conference Center, 5701 Marinelli Road, Bethesda, MD 20852.epigenetic, gene-gene interactions, genes, genetic, genetic epidemiology, genetic loci, addiction, addiction genetics, addictive disorders, adoption studies, association mapping, baysian methods, behavioral genetics, complex traits, copy number variation, genome-wide scans, haplotype, mapping, mapping genes, methodology, mice, pharmacogenomics, twin studiesSCR_002783(Short Course on the Genetics and Epigenetics of Addiction National Institute on Drug Abuse: Archived Video, RRID:SCR_002783)Last checked downnif-0000-00438http://drugabuse.gov/about/organization/Genetics/geneticsepigenetics/index.html
NUgene ProjectResource, biomaterial supply resource, biospecimen repository, service resource, storage service resource, data or information resource, material resource, material storage repositoryCollects and stores genetic (DNA) samples along with associated healthcare information from patients of Northwestern-affiliated hospitals and clinics. This resource is available to scientists to conduct groundbreaking genetic research. The information and blood samples provided will be used by researchers to examine the role genes play in the development and treatment of common diseases. The NUgene Project seeks to increase the understanding of genetic mechanisms underlying common diseases, assist in the development of DNA-based technology for diagnosis and treatment of disease, and aid physicians and other healthcare providers in the application of genetics to the practice of medicine. NUgene participants are recruited throughout the Northwestern-affiliated healthcare community in order to create an ethnically and medically diverse population for research. Participants must be 18 years of age or older and receive their medical care from a Northwestern-affiliated provider, regardless of health status. Consenting individuals complete all aspects of enrollment in a single meeting with a research coordinator. The enrollment process includes the donation of a single sample of blood and the completion of a self-administered questionnaire. Participants also sign a consent form during this encounter. The NUgene Project is an interdisciplinary project that relies on the expertise of individuals working in a variety of fields, including science, medicine, clinical research, statistics, epidemiology, and computational biology. NUgene''s multidisciplinary approach has spurred collaborations within Northwestern-affiliated institutions and with other outside institutions. This collaboration of ideas is the future of genetics and genomic research.human, clinical, gene, gene bank, genetic, genomic, translational, medicine, genetic assessment, dna, genomic research, blood, self-administered questionnaire, questionnaireSCR_007426(NUgene Project, RRID:SCR_007426)Northwestern University; Illinois; USA related to: Disease Ontology, DOAF, listed by: One Mind Biospecimen Bank ListingLast checked downnif-0000-00537
aneurISTResource, topical portal, production service resource, analysis service resource, data analysis service, standard specification, narrative resource, service resource, portal, knowledge environment, data or information resourceAn IT infrastructure for the management, integration and processing of data associated with the diagnosis and treatment of cerebral aneurysm and subarachnoid hemorrhage. This new paradigm to understand and manage cerebral aneurysms, provides an integrated decision support system to assess the risk of aneurysm rupture in patients and to optimize their treatments. aneurIST benefits patients with better diagnostics, prevention and treatment because it combines efforts of clinicians and industry. Through research clinicians gain a greater insight in aneurysm understanding, while industry will be dragged by these achievements to develop more suitable medical devices to treat the disease. This infrastructure : * Facilitate clinicians the diagnosis and study of the disease, as a result of providing a seamless access to patient data using data fusion and processing of complex information spanning from the molecular to the personal level. * Provide a better planning and personalization of minimally invasive interventional procedures for patients, after linking modern diagnostic imaging to computational tools. * Collaborate in the development, extension and exploitation of standards and protocols at all project stages. * Share biomedical knowledge providing access to a set of software tools and platforms such as aneuLink, aneuFuse, aneuRisk, aneuEndo, aneuCompute and aneuInfo. * Create awareness through scientific dissemination and collaboration. * Explore the business opportunities directly arising from aneurIST. It intends to provide an integrated decision support system to assess the risk of aneurysm rupture in patients and to optimize their treatments. Software: * aneuLink will create an IT environment with the goal of establishing a link between genomics and disease. * aneuFuse will fuse diagnostic, modelling and simulation data into a coherent representation of the patient''s condition. * aneuRisk will provide clinicians with a tool to facilitate the personalized risk assessment and guidelines establishment to treat patients. * aneuEndo will develop computational tools to optimize and customize the design of endovascular devices. * aneuInfo will enable access to clinical and epidemiological data distributed in public and project-specific protected databases. * aneuCompute will provide aneurIST with distributed computing capabilities ensuring secure data transport.gene, genetic, adult, cerebral aneurysm, cerebral brain hemorrhage, cerebral hemorrhage, cerebral parenchymal hemorrhage, cerebral hemorrhage, clinical, genomic, human, intracerebral hemorrhage, intracranial aneurysm, subarachnoid hemorrhage, risk, aneurysm rupture, patient, treatment, infrastructure, platform, genomics, disease, personalized risk assessment, bioinformatics, clinical, data management, data integration, data processing, software tool, cerebrumSCR_007427(aneurIST, RRID:SCR_007427)Pompeu Fabra University; Barcelona; Spain Cerebral aneurysm, Subarachnoid hemorrhage, AgingEuropean Union, Sixth FPPriority 2 of the Information Society Technologies ISTLast checked downnif-0000-00538http://www.cilab.upf.edu/aneurist1/
eMERGE Network: electronic Medical Records and GenomicsResource, topical portal, portal, data or information resourceA national consortium formed to develop, disseminate, and apply approaches to research that combine DNA biorepositories with electronic medical record (EMR) systems for large-scale, high-throughput genetic research. The consortium is composed of seven member sites exploring the ability and feasibility of using EMR systems to investigate gene-disease relationships. Themes of bioinformatics, genomic medicine, privacy and community engagement are of particular relevance to eMERGE. The consortium uses data from the EMR clinical systems that represent actual health care events and focuses on ethical issues such as privacy, confidentiality, and interactions with the broader community.human, clinical, dna, alzheimer's disease, genome, genomics, gene, genetic, nervous system disease, nucleotide polymorphism, phenotype, bioinformatics, genomic medicine, privacy, community engagement, emr, electronic medical recordSCR_007428(eMERGE Network: electronic Medical Records and Genomics, RRID:SCR_007428)Vanderbilt University; Tennessee; USA AgingNHGRI, NIGMSrelated to: PheKB, NCBI database of Genotypes and Phenotypes, PheWAS CatalogLast checked upnif-0000-00539
Zebrafish Gene CollectionResource, biomaterial supply resource, data or information resource, material resource, portal, project portalPart of zebrafish genome project. ZGC project to produce cDNA libraries, clones and sequences to provide complete set of full-length (open reading frame) sequences and cDNA clones of expressed genes for zebrafish. All ZGC sequences are deposited in GenBank and clones can be purchased from distributors of IMAGE consortium. With conclusion of ZGC project in September 2008, GenBank records of ZGC sequences will be frozen, without further updates. Since definition of what constitutes full-length coding region for some of genes and transcripts for which we have ZGC clones will likely change in future, users planning to order ZGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene).cdna library, clone, sequence, full-length open reading frame, cdna clone, frozen, fish, gene, genetic, genome, genomicSCR_007054(Zebrafish Gene Collection, RRID:SCR_007054)National Cancer Institute NIH Blueprint for Neuroscience Researchrelated to: One Mind Biospecimen Bank Listing, NIDDK Information Network, Mammalian Gene Collection, GenBank, ATCC, listed by: One Mind Biospecimen Bank Listing, submitted by: NIDDK Information NetworkLast checked upnif-0000-00567https://genecollections.nci.nih.gov/ZGC/
HuGE Navigator - Human Genome Epidemiology NavigatorResource, data computation service, data or information resource, bibliography, databaseKnowledge base of genetic associations and human genome epidemiology including information on population prevalence of genetic variants, gene-disease associations, gene-gene and gene- environment interactions, and evaluation of genetic tests. This tool explores HuGENet, the Human Genome Epidemiology Network, which is a global collaboration of individuals and organizations committed to the assessment of the impact of human genome variation on population health and how genetic information can be used to improve health and prevent disease. What does HuGE Navigator offer? *HuGEpedia - an encyclopedia of human genetic variation in health and disease, includes, Phenopedia and Genopedia. Phenopedia allows you to look up gene-disease association summaries by disease, and Genopedia allows you to look up gene-disease association summaries by gene. In general, HuGEpedia is a searchable database that summarizes published articles about human disease and genetic variation, including primary studies, reviews, and meta-analyses. It provides links to Pubmed abstracts, researcher contact info, trends, and more. *HuGEtools - searching and mining the literature in human genome epidemiology, includes, HuGE Literature Finder, HuGE Investigator Browser, Gene Prospector, HuGE Watch, Variant Name Mapper, and HuGE Risk Translator. *HuGE Literature Finder finds published articles in human genome epidemiology since 2001. The search query can include genes, disease, outcome, environmental factors, author, etc. Results can be filtered by these categories. It is also possible to see all articles in the database for a particular topic, such as genotype prevalence, pharmacogenomics, or clinical trial. *HuGE Investigator Browser finds investigators in a particular field of human genome epidemiology. This info is obtained using a behind-the-scenes tool that automatically parses PubMed affiliation data. *Gene Prospector is a gateway for evaluating genes in relation to disease and risk factors. This tool allows you to enter a disease or risk factor and then supplies you with a table of genes associated w/your query that are ranked based on strength of evidence from the literature. This evidence is culled from the HuGE Literature Finder and NCBI Entrez Gene - And you're given the scoring formula. The Gene Prospector results table provides access to the Genopedia entry for each gene in the list, general info including links to other resources, SNP info, and associated literature from HuGE, PubMed, GWAS, and more. It is a great place to locate a lot of info about your disease/gene of interest very quickly. *HuGE Watch tracks the evolution of published literature, HuGE investigators, genes studied, or diseases studied in human genome epidemiology. For example, if you search Trend/Pattern for Diseases Studied you'll initially get a graph and chart of the number of diseases studied per year since 1997. You can refine these results by limiting the temporal trend to a category or study type such as Gene-gene Interaction or HuGE Review. *Variant Name Mapper maps common names and rs numbers of genetic variants using information from SNP500Cancer, SNPedia, pharmGKB, ALFRED, AlzGene, PDGene, SZgene, HuGE Navigator, LSDBs, and user submissions. *HuGE Risk Translator calculates the predictive value of genetic markers for disease risk. To do so, users must enter the frequency of risk variant, the population disease risk, and the odds ratio between the gene and disease. This information is necessary in order to yield a useful predictive result. *HuGEmix - a series of HuGE related informatics utilities and projects, includes, GAPscreener, HuGE Track, Open Source. GAPscreener is a screening tool for published literature on human genetic associations; HuGE Track is a custom track built for HuGE data in the UCSC Genome Browser; and Open Source is infrastructure for managing knowledge and information from PubMed.environment, epidemiology, gene, genetic, genetic associations, genetic markers, genome, disease, human, human disease, predictive value, prevalence, publications, risk factors, test evaluations, varianceSCR_003172(HuGE Navigator - Human Genome Epidemiology Navigator, RRID:SCR_003172)Centers for Disease Control and Prevention Last checked downnif-0000-00573http://hugenavigator.net/HuGENavigator/home.do
Human Genome Epidemiology NetworkResource, organization portal, portal, data or information resourceHuman Genome Epidemiology Network, or HuGENet, is a global collaboration of individuals and organizations committed to the assessment of the impact of human genome variation on population health and how genetic information can be used to improve health and prevent disease. Its goals include: establishing an information exchange that promotes global collaboration in developing peer-reviewed information on the relationship between human genomic variation and health and on the quality of genetic tests for screening and prevention; providing training and technical assistance to researchers and practitioners interested in assessing the role of human genomic variation on population health and how such information can be used in practice; developing an updated and accessible knowledge base on the World Wide Web; and promoting the use of this knowledge base by health care providers, researchers, industry, government, and the public for making decisions involving the use of genetic information for disease prevention and health promotion. HuGENet collaborators come from multiple disciplines such as epidemiology, genetics, clinical medicine, policy, public health, education, and biomedical sciences. Currently, there are 4 HuGENet Coordinating Centers for the implementation of HuGENet activities: CDC''s Office of Public Health Genomics, Atlanta, Georgia; HuGENet UK Coordinating Center, Cambridge, UK; University of Ioannina, Greece; University of Ottawa , Ottawa, Canada. HuGENet includes: HuGE e-Journal Club: The HuGE e-Journal Club is an electronic discussion forum where new human genome epidemiologic (HuGE) findings, published in the scientific literature in the CDC''s Office of Public Health Genomics Weekly Update, will be abstracted, summarized, presented, and discussed via a newly created HuGENet listserv. HuGE Reviews: A HuGE Review identifies human genetic variations at one or more loci, and describes what is known about the frequency of these variants in different populations, identifies diseases that these variants are associated with and summarizes the magnitude of risks and associated risk factors, and evaluates associated genetic tests. Reviews point to gaps in existing epidemiologic and clinical knowledge, thus stimulating further research in these areas. HuGE Fact Sheets: HuGE Fact Sheets summarize information about a particular gene, its variants, and associated diseases. HuGE Case Studies: An on-line presentation designed to sharpen your epidemiological skills and enhance your knowledge on genomic variation and human diseases. Its purpose is to train health professionals in the practical application of human genome epidemiology (HuGE), which translates gene discoveries to disease prevention by integrating population-based data on gene-disease relationships and interventions. Students will acquire conceptual and practical tools for critically evaluating the growing scientific literature in specific disease areas. HUGENet Publications: Articles related to the HuGENet movement written by our HuGENet collaborators. HuGE Navigator: An integrated, searchable knowledge base of genetic associations and human genome epidemiology, including information on population prevalence of genetic variants, gene-disease associations, gene-gene and gene- environment interactions, and evaluation of genetic tests. HuGE Workshops: HuGENet has sponsored meetings and workshops with national and international partners since 2001. Available are detailed summaries, agendas or the ability to download speaker slides. HuGE Book: Human Genome Epidemiology: A Scientific Foundation for Using Genetic Information to Improve Health and Prevent Disease. (The findings and conclusions in this book are those of the author(s) and do not necessarily represent the views of the funding agency.) HuGENet Collaborators: HuGENet is interested in establishing collaborations with individuals and organizations working on population based research involving genetic information. HuGE Funding: Funding opportunities for specific population-based genetic epidemiology research projects are available. Research initiatives whose aims include assessing the prevalence of human genetic variation, the association between genetic variants and human diseases, the measurement of gene-gene or gene-environment interaction, and the evaluation of genetic tests for screening and prevention are compiled to create a posted listing. Additional information and application details can be found by clicking on the respective links.epidemiology, gene, genetic, genetic variants, genome, articles, collaboration, disease, disease prevention, genomics, health promotion, human, human diseasesSCR_013117(Human Genome Epidemiology Network, RRID:SCR_013117)Centers for Disease Control and Prevention Last checked upnif-0000-00574
dbSNPResource, service resource, data or information resource, data repository, storage service resource, databaseDatabase as central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. Distinguishes report of how to assay SNP from use of that SNP with individuals and populations. This separation simplifies some issues of data representation. However, these initial reports describing how to assay SNP will often be accompanied by SNP experiments measuring allele occurrence in individuals and populations. Community can contribute to this resource.insertion, polymorphism, short, deletion, single, nucleotide, genetic, variation, genomics, genotype, disease, allele, microsatellite, marker, multinucleotide, heterozygous, sequence, gold standardSCR_002338(dbSNP, RRID:SCR_002338)NCBI , National Human Genome Research Institute NLMrelated to: Ensembl Variation, Monarch Initiative, GWAS Central, TopoSNP, Human Genome Variation database of Genotype-to-Phenotype information, used by: ExAc, GEMINI, recommended by: National Library of Medicine, BRAIN Initiative, listed by: OMICtools, re3data.org, works_with: Open Regulatory Annotation DatabaseLast checked upnif-0000-02734, OMICS_00264http://www.ncbi.nlm.nih.gov/projects/SNP/
GeneCardsResource, data or information resource, databaseDatabase 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 reagentSCR_002773(GeneCards, RRID:SCR_002773)related to: MOPED - Model Organism Protein Expression Database, listed by: OMICtoolsPMID:20689021Last checked downnif-0000-02879, OMICS_01652http://bioinfo.weizmann.ac.il/genecards/
GrameneResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceA curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species to facilitate the study of cross-species comparisons using information generated from projects supported by public funds. It currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database. In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data. Additionally you can access Gramene through an FTP site.crop, plant genome, genetic, blast, gene, genome, genetic diversity, pathway, protein, marker, quantitative trait locus, comparative map, phenotype, genomics, physiology, comparative, grain, expressed sequence tag, trait, mutation, environment, taxonomy, web serviceSCR_002829(Gramene, RRID:SCR_002829) Cornell University; New York; USA , Cold Spring Harbor Laboratory NSF, USDA, USDA IFAFSrelated to: AmiGO, Gene Ontology, PO, Trait Ontology, EnvO, BioCyc, used by: NIF Data Federation, listed by: re3data.orgReferences (3)Last checked upnif-0000-02926, nlx_65829, SCR_000532
Rice Proteome DatabaseResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER AVAILABLE, documented July 22, 2016.\\n\\nA database on the proteome of rice that contains reference maps based on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) of proteins from rice tissues and subcellular compartments.rice, proteome, gene, genetic, eleoctrophoresis, 2d-page, tissue, subcellular compartmentsSCR_000743(Rice Proteome Database, RRID:SCR_000743)National Institute of Agrobiological Sciences; Ibaraki; Japan PMID:16217611Last checked upnif-0000-03409http://dbarchive.biosciencedbc.jp/en/rpd/desc.html
SMARTResource, data analysis service, data access protocol, production service resource, analysis service resource, database, web service, service resource, software resource, data or information resourceSoftware tool for identification and annotation of genetically mobile domains and analysis of domain architectures.extracellular, gene, genetic, genetically, genome, architecture, chromatin, domain, mobile, phyletic, protein, proteome, signaling, structure, taxonomic, tertiarySCR_005026(SMART, RRID:SCR_005026)EMBL - Bork Group European Unionrelated to: Eukaryotic Linear Motif, Conserved Domain Database, GOTaxExplorer, used by: Mutation Annotation and Genomic InterpretationReferences (6)Last checked upnif-0000-03471http://smart.embl-heidelberg.de/
YanHuang ProjectResource, data or information resource, databaseThis database presents the entire DNA sequence of the first diploid genome sequence of a Han Chinese, a representative of Asian population. The genome, named as YH, represents the start of YanHuang Project, which aims to sequence 100 Chinese individuals in 3 years. It was assembled based on 3.3 billion reads (117.7Gbp raw data) generated by Illumina Genome Analyzer. In total of 102.9Gbp nucleotides were mapped onto the NCBI human reference genome (Build 36) by self-developed software SOAP (Short Oligonucleotide Alignment Program), and 3.07 million SNPs were identified. The personal genome data is illustrated in a MapView, which is powered by GBrowse. A new module was developed to browse large-scale short reads alignment. This module enabled users track detailed divergences between consensus and sequencing reads. In total of 53,643 HGMD recorders were used to screen YH SNPs to retrieve phenotype related information, to superficially explain the donor's genome. Blast service to align query sequences against YH genome consensus was also provided.genome, genetic, adult, chromosome, clinical, control, genomic, human, normalSCR_006077(YanHuang Project, RRID:SCR_006077)BGI; Shenzhen; China Last checked upnif-0000-03654
Biological Pathways ExchangeResource, data or information resource, databaseBioPAX (Biological Pathway Exchange) aims to facilitate the integration and exchange of data maintained in biological pathway databases. BioPAX Level 3 covers metabolic pathways, molecular interactions, signaling pathways (including molecular states and generics), gene regulation and genetic interactions. BioPAX Level 2 covers metabolic pathways, molecular interactions and protein post-translational modifications and is backwards compatible with Level 1. Future levels will expand support for signaling pathways, gene regulatory networks and genetic interactions. And lastly, BioPAX Level 1 represents metabolic pathway information. Sponsors: The BioPAX project is funded in part by U.S. Department of Energy Workshop Grant #DE-FG02-04ER63931 and by Award Number P41HG004118 from the National Human Genome Research Institute.exchange, gene, generic, genetic, biological, biological pathway, data, database, integration, interaction, metabolic, modifications, molecular, pathway, post-translational, protein, regulation, signaling, stateSCR_001681(Biological Pathways Exchange, RRID:SCR_001681)related to: cPathLast checked upnif-0000-10171
Center for Disease Control and Prevention: Genetic Testing Reference Materials Coordination ProgramResource, topical portal, portal, data or information resourceThe goal of the Genetic Testing Reference Materials Coordination Program (GeT-RM) is to coordinate a self-sustaining community process to improve the availability of appropriate and characterized reference materials for: Quality control (QC), Proficiency testing (PT), Test development & validation, Research. The purpose of this program is: - To help the genetic testing community obtain appropriate and characterized reference materials - To facilitate and coordinate information exchange between users and providers of QC and reference materials - To coordinate efforts for contribution, development, characterization and distribution of reference materials for genetic testing Get-RM provides information about cell lines, DNA, and other kinds of materials that could be used as reference materials for molecular genetic testing. Some of these materials have been characterized by the GeT-RM program and can be divided into three categories: - Genetic Inherited Disease & Pharmacogenetics This section includes information about cell lines, DNA, and other samples that can be used as reference materials for various inherited diseases (including cystic fibrosis, fragile X, Huntington disease, and Ashkenazi Jewish-related diseases), pharmacogenetic loci, and biochemical genetics. The GeT-RM program has confirmed the genotype of many of the genomic DNA samples through testing in multiple clinical genetic laboratories. - Molecular Oncology This section includes information about commercially available cell lines, DNA, and other kinds of materials that could be used as reference materials for various types of cancers, including leukemia/lymphoma and solid tumors. - Infectious Disease This section includes information about commercially available cell lines, DNA, and other kinds of materials that could be used as reference materials for various infectious disease pathogens including viruses, bacteria, and protozoa.fragile x, genetic, genetics, genetic testing, ashkenazi, bacteria, biochemical, cancer, cell, cell line, coordination, cystic fibrosis, development, disease, dna, genomic, genotype, huntington disease, inherited, jewish, leukemia, locus, lymphoma, material, molecular, oncology, pathogen, pharmacogentic, protozoa, quality, solid, testing, tumor, virusSCR_013029(Center for Disease Control and Prevention: Genetic Testing Reference Materials Coordination Program, RRID:SCR_013029)Centers for Disease Control and Prevention Last checked upnif-0000-10189
Centre dEtude du Polymorphisme HumainResource, laboratory portal, portal, organization portal, data or information resourceThe Centre d''Etude du Polymorphisme Humain (CEPH) is a research laboratory, the main activities of which are the setting up, storage, processing and distribution of DNA collections for the identification of genetic factors conferring susceptibility to complex disorders. These collections are established in partnership and full collaboration with external French or international research groups. The Foundation currently hosts the CEPH reference panel, the HGDP panel (Human genome Diversity Cell Line Panel) and several collections amounting mid-2008 to more than 250 000 samples. The goal of CEPH is to understand complex multifactorial disorders necessitates the establishment of structures facilitating access to large and integrated collection of individuals, characterized by a large number of variables emanating from different technologies and platforms. To achieve this goal, CEPH facilitates the setting up of integrated analyses combining clinical, genetic and environmental data, for the identification of susceptibility factors to complex multifactorial disorders Additionally, CEHP allows the reception, storage, processing and distribution of biological sample collections. At the same time, it promotes and participates in the design and setting up of genetic studies: - in partnership and full collaboration with external research groups - giving access to a large number of variables - in a sufficient number of subjects - allowing large scale integrated analysesenvironmental, genome, genetic, analysis, biological, cell, clinical, disorder, distribution, diversity, dna, human, individual, laboratory, polymorphism, process, procession, reception, research, storage, structure, subject, technology, variableSCR_008026(Centre dEtude du Polymorphisme Humain, RRID:SCR_008026)related to: International AMD Genetics ConsortiumLast checked upnif-0000-10191
Phelan-McDermid Syndrome FoundationResource, disease-related portal, topical portal, portal, community building portal, funding resource, data or information resourceThe Phelan-McDermid Syndrome Foundation, established in 2002, is a 501(c)3 nonprofit group that provides support services for those who have family members affected by 22q13 Deletion Syndrome / Phelan-McDermid Syndrome. It also raises money to further awareness of the syndrome through research and sponsoring an international conference every two years that brings together families, researchers and therapists. The Foundation facilitates connections between families through networking, communications and support services. We also build alliances with other rare diseases groups to expand our reach and exposure. The syndrome, which affects families worldwide, is a rare genetic occurrence and is the result of a damaged or missing protein on the 22nd chromosome. Our Foundation works with researchers who are looking into the cause and possible cure for the syndrome. PMSF's grants and fellowships program is intended to encourage research projects that will advance the development of treatments and cures for PMS. Our mission is to bring together everyone affected by 22q13 Deletion Syndrome/Phelan-McDermid Syndrome to help them through the challenges they face every day and to raise awareness in the medical and research communities.22q13 deletion syndrome, phelan-mcdermid syndrome, rare disease, genetic, meeting, child, chromosome 22, treatment, therapy, research, grant, fellowshipSCR_001707(Phelan-McDermid Syndrome Foundation, RRID:SCR_001707)Phelan-McDermid SyndromeLast checked upnif-0000-10203
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