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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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408 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
University of British Columbia Centre for Molecular Medicine and TherapeuticsOrganizationCenter is part of University of British Columbia Faculty of Medicine, located at British Columbia Children Hospital Research Institute (BCCHR) in Vancouver, British Columbia, Canada. Research at CMMT is focused on discovering genetic susceptibility to illnesses such as Huntington Disease, Type 2 diabetes and bipolar disorder.genetic, susceptibility, Huntington, disease, type 2 diabetes, bipolar disorderSCR_017241(University of British Columbia Centre for Molecular Medicine and Therapeutics, RRID:SCR_017241)Last checked up
Referral Center for Animal Models of Human Genetic DiseasesOrganization, biomaterial supply resource, material resourceCenter that aims to discover, characterize, maintain breeding colonies, and make available dog and cat models with hereditary diseases homologous to those found in human patients that can be used to translate preclinical trials from kennel to clinic. The animal models represent true orthologs of their respective human disease, involving defects in homologous genes resulting in similar molecular, biochemical, pathological, and clinical phenotype as in human patients.animal, dog, cat, disease, homologue, genetic, colony, breed, modelSCR_016453(Referral Center for Animal Models of Human Genetic Diseases, RRID:SCR_016453)University of Pennsylvania; Philadelphia; Pennsylvania NIH Office of the DirectorLast checked up
NIAIDOrganization, disease-related portal, organization portal, portal, topical portal, data or information resourceNational Institute of Allergy and Infectious Diseases is a leading research institution to understand, treat, and prevent infectious, immunologic, and allergic diseases.immunologic, allergic, infectious, disease, institute, treat, preventSCR_016598(NIAID, RRID:SCR_016598)NIHrelated to: The Immunology Database and Analysis Portal (ImmPort), The 10000 Immunomes, lists: Nephele, PaVE, ChemokineDB, SPICE, TRIAGE, NGlycPred, dCAS, HASP, ABC Bacterial Transporter Systems Database, TB PORTALS, JOINSOLVERLast checked up
Mayo ClinicOrganization, institutionNonprofit academic medical center based in Rochester, Minnesota, focused on integrated clinical practice, education, and research. Highly specialized in cardiovascular diseases and surgery. Practice specializes in treating difficult cases through tertiary care and destination medicine.medical, academic, center, integrated, clinical, practice, cardiovascular, disease, surgerySCR_011383(Mayo Clinic, RRID:SCR_011383)related to: Alzheimers Disease Genetics Consortium, Clinical and Translational Science Awards Consortium, Care Connectivity Consortium, uses: KaggleLast checked upnlx_158051
HIRN Consortium on Beta Cell Death and SurvivalOrganization, organization portal, portal, consortium, data or information resourceConsortium that is an independent research initiative of the Human Research Information Network (HIRN). It is using human tissues to discover highly specific biomarkers of beta cell injury in asymptomatic T1D and developing strategies to stop beta cell destruction early in the disease process.kidney, tissue, biomarker, beta, cell, t1d, disease, researchSCR_016198(HIRN Consortium on Beta Cell Death and Survival, RRID:SCR_016198)NIDDKsubmitted by: NIDDK Information NetworkLast checked up
HIRN Consortium on Modeling Autoimmune InteractionsOrganization, organization portal, portal, consortium, data or information resourceConsortium that is an independent research initiative of the Human Research Information Network (HIRN). It is developing innovative approaches to model basic aspects of human T1D immunobiology using novel in vivo and in vitro platforms.autoimmune, disease, immunobiology, in vitro, research, in vivoSCR_016200(HIRN Consortium on Modeling Autoimmune Interactions, RRID:SCR_016200)NIDDKsubmitted by: NIDDK Information NetworkLast checked up
Broad InstituteOrganization, software resource, organization portal, training resource, portal, data or information resourceBiomedical and genomic research center located in Cambridge, Massachusetts, United States. Nonprofit research organization under the name Broad Institute Inc., and is partners with Massachusetts Institute of Technology, Harvard University, and the five Harvard teaching hospitals. Dedicated to advance understanding of biology and treatment of human disease to improve human health.biomedical, genomic, research, center, nonprofit, organization, human, biology, diseaseSCR_007073(Broad Institute, RRID:SCR_007073)Eli and Edythe Broad, individual donorsrelated to: LINCS Information Framework, HMS LINCS Database, Cancer Cell Line Encyclopedia, affiliated with: Massachusetts Institute of Technology, Massachusetts, USA, Harvard University, Cambridge, United States, Integrative Human Microbiome Project, MIT, Cambridge, Massachusetts, United StatesLast checked upnif-0000-31438
FiGSResource, analysis service resource, data analysis service, service resource, production service resourceA web-based workbench to conveniently compare the classification performances of many different filter-based gene selection procedures. In addition to the commonly used filter metric-classifier combinations, user can test various additive methodological options by specification of only up- or down-regulated genes to select, applying feature discretization and adding feature vectors to make a new feature. Throughout the comprehensive comparisons, user can identify the best performing gene selection procedure and subsequent classification performance measured by .632+ bootstrap error estimation for the given binary (two-class) microarray data.microarray, classification, parallel computing, disease, gene setSCR_012037(FiGS, RRID:SCR_012037)Korea Advanced Institute of Science and Technology; Daejeon; South Korea listed by: OMICtoolsPMID:20100357Last checked downOMICS_02293
FunDOResource, analysis service resource, data analysis service, service resource, production service resourceTool that takes a list of genes and finds relevant diseases based on statistical analysis of the Disease Ontology annotation database. It accepts Entrez gene ids or gene symbols, separated by tabs, newlines, or commas. This list of genes can be obtained by microarray, proteomics, sequencing or other high-throughput screening methods.gene, disease, ontology, functionSCR_001725(FunDO, RRID:SCR_001725)Northwestern University; Illinois; USA related to: Disease Ontology, KOBASLast checked upnif-0000-10225
PhevorResource, analysis service resource, data analysis service, service resource, production service resourceTool that integrates phenotype, gene function, and disease information with personal genomic data for improved power to identify disease-causing alleles. It works by combining knowledge resident in multiple biomedical ontologies with the outputs of variant prioritization tools. It does so using an algorithm that propagates information across and between ontologies. This process enables Phevor to accurately reprioritize potentially damaging alleles identified by variant prioritization tools in light of gene function, disease, and phenotype knowledge. Phevor is especially useful for single exome and family trio-based diagnostic analyses, the most commonly occurring clinical scenarios, and ones for which existing personal-genomes diagnostic tools are most inaccurate and underpowered. Phevor not only improves diagnostic accuracy for individuals presenting with established disease phenotypes, but also for those with previously undescribed and atypical disease presentations. Importantly, Phevor is not limited to known diseases, or known disease-causing alleles.genome interpretation, variant prioritization, disease gene prioritization, phenotype, gene function, disease, genomic, disease-causing allele, gene, function, alleleSCR_002273(Phevor, RRID:SCR_002273)University of Utah School of Medicine; Utah; USA PMID:24702956Last checked upSciRes_000139
Human Gene Connectome ServerResource, analysis service resource, data analysis service, service resource, production service resourceAn interactive web server that enables researchers to prioritize any list of genes by their biological proximity to defined core genes (i.e. genes that are known to be associated with the phenotype), and to predict novel gene pathways.gene, disease, phenotype, genome, connectomeSCR_002627(Human Gene Connectome Server, RRID:SCR_002627)Human Gene Connectome PMID:23509278Last checked upnlx_156049
SNPnexusResource, analysis service resource, data analysis service, service resource, production service resourceA web server for functional annotation of novel and publicly known genetic variants that was developed to assess the potential significance of known and novel SNPs on the major transcriptome, proteome, regulatory and structural variation models in order to identify the phenotypically important variants. A broader range of variations have been incorporated such as insertions / deletions, block substitutions, IUPAC codes submission and region-based analysis, expanding the query size limit, and most importantly including additional categories for the assessment of functional impact. SNPnexus provides a comprehensive set of annotations for genomic variation data by characterizing related functional consequences at the transcriptome/proteome levels of seven major annotation systems with in-depth analysis of potential deleterious effects, inferring physical and cytogenetic mapping, reporting information on HapMap genotype/allele data, finding overlaps with potential regulatory elements, structural variations and conserved elements, and retrieving links with previously reported genetic disease studies.single nucleotide polymorphism, genetic variant, gene, variant, insertion, deletion, block substitution, functional annotation, genotyping, phenotype, disease, regulatory element, conservation, non-synonymous coding snp, gene, protein, hapmap, population, structural variationSCR_005192(SNPnexus, RRID:SCR_005192)Queen Mary University of London; London; United Kingdom listed by: OMICtoolsReferences (3)Last checked upOMICS_00188
PolySearchResource, analysis service resource, data analysis service, service resource, production service resourceA web-based tool that supports more than 50 different classes of queries against nearly a dozen different types of text, scientific abstract or bioinformatic databases. The typical query supported by PolySearch is Given X, find all Y''s where X or Y can be diseases, tissues, cell compartments, gene/protein names, SNPs, mutations, drugs and metabolites. PolySearch also exploits a variety of techniques in text mining and information retrieval to identify, highlight and rank informative abstracts, paragraphs or sentences.text mining, disease, gene, protein, drug, metabolite, snp, gene sequence, pathway, tissue, gene family, subcellular localization, organSCR_005291(PolySearch, RRID:SCR_005291)University of Alberta; Alberta; Canada listed by: OMICtoolsLast checked upOMICS_01194
SNPsandGOResource, analysis service resource, data analysis service, service resource, production service resourceA server for the prediction of single point protein mutations likely to be involved in the insurgence of diseases in humans.prediction, protein, mutation, disease, single nucleotide polymorphismSCR_005788(SNPsandGO, RRID:SCR_005788)University of Bologna; Bologna; Italy related to: Gene Ontology, used by: HmtVar, listed by: OMICtoolsPMID:19514061Last checked upOMICS_02219
PIDFinderResource, analysis service resource, data analysis service, service resource, production service resourcePIDFinder is a tool for the exploration of the Primary Immunodeficiency Disease Ontology. Apart from browsing the knowledge contained in the ontology, it can also be used for the identification of PIDs based on a set of observed Phenotypes. The PidFinder web application is a developing prototype application that allows non-bioinformaticians to quickly view and use the knowledge contained in the Primary Immunodeficiency Disease Ontology. The application consists of a number of components: * The PIDFinder: allows the selection of a set of phenotypes and subsequently compares the set with the canonical set of phenotypes defined in the PID Ontology. The phenotypes, that can be selected are grouped by biomarker and are thus available in a number of different facets. Once phenotypes have been selected, the application compares them to canonical phenotypes associated with PIDs in the PID Ontology, by computing a semantic similarity measure. The similarity is determined using a Tanimoto Distance - the more closely related an observed phenotype is to a canonical ontology phenotype, the closer the calculated Tanimoto Distance is to 1 - with increasing dissimilarity, the Tanimoto Coefficient tends towards 0. * The Phenotype Explorer: a rudimentary browser for phenotypes currently contained in the PID Ontology. The browser allows the user to find phenotypes based on biomarker categories and provides some basic definitions (not all definitions are available at this stage) and disease association information. * A Heatmap comparing the phenotypic overlap of PIDs: In essence, the heatmap is a many-to-many comparison of the phenotypic overlap between all Primary Immunodeficiency Diseases contained in the PID Ontology. Again, overlap is calculated using a Tanimoto Distance. The heatmap is a matrix, plotting the Tanimoto coefficients for every PID/PID pair. Increased off-diagonal overlap between PIDs most likely indicates genes in the same pathway. * A Phenotype Frequency Visualization: The phenotype frequency visualization is a simple bar chart indicating how often a particular phenotype is associated with a Primary Immunodeficiency Disease in the Ontology. * A PID Expert map: All of the phenotypes and knowledge contained in the Primary Immunodeficiency Disease Ontology has been extracted from primary clinical or research literature. To construct the map, we have extracted the affiliations and locations of the authors of the literature sources and overlayed them on a map. The hope is that this will facilitate the identification of (local) experts on primary immunodeficiency diseases.phenotype, disease, immunodeficiency, biomarker, ontologySCR_005833(PIDFinder, RRID:SCR_005833)Primary Immunodeficiency Diseaserelated to: PIDO - Primary Immunodeficiency Disease OntologyLast checked downnlx_149343
PhenomizerResource, analysis service resource, data analysis service, service resource, production service resourceThe Phenomizer offers three different approaches to find the appropriate term for a phenotypic abnormality, indicated by the three tabs on the left hand side: Feature, Disease and Ontology. The Phenomizer is intended to be used by qualified and licensed physicians in order to provide assistance in reaching the correct diagnosis in patients with hereditary diseases and for use as a teaching aid. The Phenomizer does not make diagnoses. Rather, it produces a ranked list of possibilities that can be used by physicians as a part of the diagnostic workup. The Phenomizer does not contain information about all possible diagnoses or even all possible hereditary diseases. The Phenomizer should not be used to make medical decisions without the advice of a physician.feature, disease, ontology, clinical, differential diagnosesSCR_006157(Phenomizer, RRID:SCR_006157)Charite - Universitatsmedizin Berlin; Berlin; Germany related to: HPO - Human Phenotype Ontology, Human Phenotype Ontology AnnotationsLast checked upnlx_151657
InterSpecies Analysing Application using ContainersResource, analysis service resource, software resource, data analysis service, service resource, production service resourceWeb based tool to enable the analysis of sets of genes, transcripts and proteins under different biological viewpoints and to interactively modify these sets at any point of the analysis. Detailed history and snapshot information allows tracing each action. One can switch back to previous states and perform new analyses. Sets can be viewed in the context of genomes, protein functions, protein interactions, pathways, regulation, diseases and drugs. Additionally, users can switch between species with an automatic, orthology based translation of existing gene sets. Sets as well as results of analyses can be exchanged between members of groups.protein function, protein interaction, pathway, mirna, disease, drug, gene, genome, transcript, protein, regulationSCR_006243(InterSpecies Analysing Application using Containers, RRID:SCR_006243)University of Wurzburg; Bavaria; Germany related to: Gene Ontology, listed by: OMICtoolsPMID:24428905Last checked downOMICS_02237
KOBASResource, analysis service resource, software resource, data analysis service, service resource, production service resourceWeb server to identify statistically enriched pathways, diseases, and GO terms for a set of genes or proteins, using pathway, disease, and GO knowledge from multiple famous databases. It allows for both ID mapping and cross-species sequence similarity mapping. It then performs statistical tests to identify statistically significantly enriched pathways and diseases. KOBAS 2.0 incorporates knowledge across 1327 species from 5 pathway databases (KEGG PATHWAY, PID, BioCyc, Reactome and Panther) and 5 human disease databases (OMIM, KEGG DISEASE, FunDO, GAD and NHGRI GWAS Catalog). A standalone command line version is also availableortholog, pathway, disease, gene, protein, annotation, command lineSCR_006350(KOBAS, RRID:SCR_006350)Peking University; Beijing; China related to: Gene Ontology, KEGG, OMIM, Pathway Interaction Database, BioCarta Pathways, Reactome, BioCyc, PANTHER, FunDO, Genetic Association Database, GWAS: Catalog of Published Genome-Wide Association Studies, listed by: OMICtoolsPMID:21715386Last checked upOMICS_02228
Pig Genome MappingResource, atlas, database, image collection, data or information resourceMap of identifyied genes controlling traits of economic and welfare significance in the pig. The project objectives were to produce a genetic map with markers spaced at approximately 20 centiMorgan intervals over at least 90% of the pig genome; to produce a physical map with at least one distal and one proximal landmark locus mapped on each porcine chromosome arm and also genetically mapped; to develop a flow karyotype for the pig based on FACS sorted chromosomes; to develop PCR based techniques to enable rapid genotyping for polymorphic markers; to evaluate synteny conservation between pigs, man, mice and cattle; to develop and evaluate the statistical techniques required to analyze data from QTL mapping experiments and to plan and initiate the mapping of QTLs in the pig; to map loci affecting traits of economic and biological significance in the pig; and to develop the molecular tools to allow the future identification and cloning of mapped loci. Animal breeders currently assume that economically important traits such as growth, carcass composition and reproductive performance are controlled by an infinite number of genes each of infinitessimal effect. Although this model is known to be unrealistic, it has successfully underpinned the genetic improvement of livestock, including pigs, over recent decades. A map of the pig genome would allow the development of more realistic models of the genetic control of economic traits and the ultimately the identification of the major trait genes. This would allow the development of more efficient marker assisted selection which may be of particular value for traits such as disease resistance and meat quality.gene, genetic, artificial chromosome, bacteriophage, biological, carcass, cattle, cdna, comparative, disease, genome, genotype, growth, human, karyotpe, linkage, livestock, locus, map, mapping, marker, mice, molecular, p1, pig, quality, quantitative, sus scrofa, trait, yeastSCR_012884(Pig Genome Mapping, RRID:SCR_012884)Roslin Institute PMID:7749223Last checked upnif-0000-20987http://www.projects.roslin.ac.uk/pigmap/pigmap.html
Allen InstituteResource, atlas, organization portal, database, portal, data or information resourceNon profit bioscience research organization in Seattle, Washington dedicated to accelerating research globally and sharing that data within the science community. Allen Institute for Brain Science, Allen Institute for Cell Science, Allen Institute for Immunology, and The Paul G. Allen Frontiers Group are four divisions of this Institute with commitment to open science model within its research institutes.organization, brain, health, disease, research, human, mouse, dataset, cell, immunology, data, mapSCR_005435(Allen Institute, RRID:SCR_005435)hosts: Allen Brain AtlasLast checked upnlx_144532
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