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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)

Physical Resource or Software Tool Software

408 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
Kids First Data Resource PortalResource, disease-related portal, topical portal, database, organization portal, service resource, portal, storage service resource, data repository, data or information resourcePortal for analysis and interpretation of pediatric genomic and clinical data to advance personalized medicine for detection, therapy, and management of childhood cancer and structural birth defects. For patients, researchers, and clinicians to create centralized database of well curated clinical and genetic sequence data from patients with childhood cancer or structural birth defects.pediatric, genomic, clinical, disease, data, children, cancer, birth, defect, analysisSCR_016493(Kids First Data Resource Portal, RRID:SCR_016493)pediatric cancer, birth defectNIH, the Common Fund’s Gabriella Miller Kids First Pediatric Research Programrecommended by: National Library of Medicine, BRAIN InitiativeLast checked downSCR_016553https://commonfund.nih.gov/kidsfirst, https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001168.v1.p1, https://commonfund.nih.gov/kidsfirst
Opal ResearchResource, software resource, data processing software, data analysis software, sequence analysis software, software applicationSoftware which integrates a comprehensive, automated genome annotation engine with the VAAST and Phevor disease gene prioritization tools to rank gene variants on the severity of their impact on protein function and likelihood to cause disease. Each variant in a gene is analyzed for its impact on protein function, conservation and frequency. Each gene is ranked rather than filtered in order to ensure critical targets are not prematurely removed.sequence analysis software, genome interpretation, variant prioritization, disease gene prioritization, next-generation sequencing, clinical interpretation, clinical genomics software, genome, protein function, disease, genomic variant, mutationSCR_000405(Opal Research, RRID:SCR_000405)related to: VAASTPMID:23895124Last checked downSciRes_000140
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
University of Washington Nath Research GroupResource, service resource, portal, core facility, access service resource, data or information resourceA University of Washington - affiliated research lab focused on understanding the roles of protein dynamics in health and human disease. They focus on developing methods to characterize and control protein dynamics through utilizing methods like single-molecule fluorescence, computational modeling, and protein engineering. There is an emphasis on proteins involved in degenerative disorders such as Alzheimer's disease, stress responses and drug metabolism.research, protein dynamics, health, disease, alzheimer's disease, computational modeling, stress response, drug metabolism, drug design, protein engineering, university, lab, alzheimersSCR_000180(University of Washington Nath Research Group, RRID:SCR_000180)University of Washington; Seattle; USA listed by: Science ExchangeLast checked upSciEx_2024
OmicsSIMLAResource, software resource, software application, simulation software, software toolkitSoftware tool for generating multi omics data with disease status. Simulates genomics (SNPs and copy number variations), epigenomics ( whole genome bisulphite sequencing), transcriptomics ( RNA seq), and proteomics (normalized reverse phase protein array) data at the whole genome level. Available as desktop and web application version.multi, omics, data, simulator, disease, genomic, epigenomic, transcriptomic, proteomic, genome, sequencing, protein, RNASCR_017011(OmicsSIMLA, RRID:SCR_017011)Ministry of Science and Technology in Taiwanlisted by: OMICtoolsDOI:10.1101/426510Last checked downOMICS_31363
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
KGGSeqResource, software resourceA biological Knowledge-based mining platform for Genomic and Genetic studies using Sequence data. The software platform, constituted of bioinformatics and statistical genetics functions, makes use of valuable biologic resources and knowledge for sequencing-based genetic mapping of variants / genes responsible for human diseases / traits. It facilitates geneticists to fish for the genetic determinants of human diseases / traits in the big sea of DNA sequences. KGGSeq has paid attention to downstream analysis of genetic mapping. The framework was implemented to filter and prioritize genetic variants from whole exome sequencing data.genomic, genetic, sequence, mutation, exome sequencing, disease, gene, variantSCR_005311(KGGSeq, RRID:SCR_005311)University of Hong Kong; Hong Kong; China Monogenic disorder, Cancerlisted by: OMICtoolsPMID:22241780Last checked upOMICS_02260
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
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
SNP Function PortalResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceDatabase for exploring the function implication of single nucleotide polymorphism (SNP) alleles. It is designed to be a clearing house for all public domain SNP functional annotation data, as well as in-house functional annotations derived from different data sources. It currently contains SNP functional annotations in six major categories including genomic elements, transcription regulation, protein function, pathway, disease and population genetics. Besides extensive SNP functional annotations, it includes a search engine that accepts different types of genetic markers as input and identifies all genetically related SNPs based on the HapMap Phase II data as well as the relationship of different markers to known genes. As a result, the system allows users to identify the potential biological impact of genetic markers and complex relationships among genetic markers and genes, and it greatly facilitates knowledge discovery in genome-wide SNP scanning experiments.single nucleotide polymorphism, linkage disequibrilium, functional annotation, function, annotation, genomic element, transcription regulation, protein function, pathway, disease, population geneticsSCR_001954(SNP Function Portal, RRID:SCR_001954)University of Michigan; Michigan; USA listed by: OMICtoolsPMID:16873516Last checked upOMICS_01928
GEUVADISResource, organization portal, portal, consortium, data or information resourceA European Medical Sequencing Consortium committed to gaining insights into the human genome and its role in health and medicine by sharing data, experience and expertise in high-throughput sequencing.genetic, variation, health, disease, medical, sequencing, high-throughput sequencing, human genome, genome, genomics, personalized medicine, genomic medicineSCR_000684(GEUVADIS, RRID:SCR_000684)European Union, FP7, HEALTHlisted by: OMICtoolsLast checked upOMICS_01779
Cancer Gene IndexResource, data or information resource, databaseTHIS RESOURCE IS NO LONGER SUPPORTED, documented on November 17, 2016. A database of genes that have been experimentally associated with human cancer diseases and/or pharmacological compounds, the evidence of these associations, and relevant annotations on the data.gene, cancer, genetics, pharmacology, disease, database, dataSCR_001117(Cancer Gene Index, RRID:SCR_001117)National Cancer Institute Cancerlisted by: OMICtoolsLast checked upOMICS_01575
My Cancer GenomeResource, data or information resource, databaseA freely available online personalized cancer medicine knowledge resource for physicians, patients, caregivers and researchers that gives up-to-date information on what mutations make cancers grow and related therapeutic implications, including available clinical trials. It is a one-stop tool that matches tumor mutations to therapies, making information accessible and convenient for busy clinicians.genome, disease, genome, medicine, clinical trial, mutation, therapySCR_004140(My Cancer Genome, RRID:SCR_004140)Vanderbilt University; Tennessee; USA Cancer, Tumorlisted by: OMICtoolsLast checked upOMICS_01552
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
MuGeXResource, service resourceService that automatically extracts mutation-gene pairs from MEDLINE abstracts for a given disease.disease, gene, mutationSCR_005306(MuGeX, RRID:SCR_005306)Sabanci University; Istanbul; Turkey related to: MEDLINE, listed by: OMICtoolsPMID:18172928Last checked upOMICS_01189
Coremine MedicalResource, service resourceService to access comprehensive information on diseases, drugs, treatments and medical biology. It is ideal for those seeking an overview of a complex subject while allowing the possibility to drill down to specific details. Search results are presented in a dashboard format comprized of panels containing various categories of information ranging from introductory sources to the latest scientific articles.disease, drug, treatment, medical biology, text mining, health, medicine, biology, network, databaseSCR_005323(Coremine Medical, RRID:SCR_005323)PubGene European Union FP7, Innovation Norway, NLM, Research Council of Norwayrelated to: MeSH, Entrez Gene, MEDLINE, PubMed, DrugBank, Gene Ontology, Universal Protein Resource, listed by: OMICtoolsLast checked upOMICS_01179
CoINResource, service resourceA web-based system that assess articles according to their term correlations among sentences. It employs the co-occurrence relations and their network centralities to evaluate the influence of biomedical terms from Comparative Toxicogenomics Database (CTD).gene, disease, chemical, biomedical, association, document triage, databaseSCR_005332(CoIN, RRID:SCR_005332)National Cheng Kung University; Tainan; Taiwan listed by: OMICtoolsLast checked downOMICS_01177
CistromeFinderResource, data set, data or information resourceData portal that can help query, evaluate and visualize publicly available Chromatin immunoprecipitation and DNase I hypersensitivity assays with high-throughput sequencing data in human and mouse. The database currently contains 6378 samples over 4391 datasets, 313 factors and 102 cell lines or cell populations (May 2013). Each dataset has gone through a consistent analysis and quality control pipeline; therefore, users could evaluate the overall quality of each dataset before examining binding sites near their genes of interest. CistromeFinder is integrated with UCSC genome browser for visualization, Primer3Plus for ChIP-qPCR primer design and CistromeMap for submitting newly available datasets. It also allows users to leave comments to facilitate data evaluation and update.chip-seq, dnase-seq, cell, tissue, disease, histone modification, transcription factor, chromatin regulator, dnase, binding site, gene, transcription regulationSCR_005405(CistromeFinder, RRID:SCR_005405)Dana-Farber Cancer Institute related to: UCSC Genome Browser, CistromeMap, listed by: OMICtoolsPMID:23508969Last checked downOMICS_00528
NECTARResource, service resource, data or information resource, databaseA database and web application to annotate disease-related and functionally important amino acids in human proteins.annotation, protein, disease, amino acid, gene, functionSCR_007757(NECTAR, RRID:SCR_007757)listed by: OMICtoolsPMID:24297257Last checked upOMICS_00276
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