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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
phenomeNETResource, source code, data analysis service, database, analysis service resource, production service resource, service resource, software resource, data or information resourcePhenomeNet is a cross-species phenotype similarity network. It contains the experimentally observed phenotypes of multiple species as well as the phenotypes of human diseases. PhenomeNet provides a measure of phenotypic similarity between the phenotypes it contains. The latest release (from 22 June 2012) contains 124,730 complex phenotype nodes taken from the yeast, fish, worm, fly, rat, slime mold and mouse model organism databases as well as human disease phenotypes from OMIM and OrphaNet. The network is a complete graph in which edge weights represent the degree of phenotypic similarity. Phenotypic similarity can be used to identify and prioritize candidate disease genes, find genes participating in the same pathway and orthologous genes between species. To compute phenotypic similarity between two sets of phenotypes, we use a weighted Jaccard index. First, phenotype ontologies are used to infer all the implications of a phenotype observation using several phenotype ontologies. As a second step, the information content of each phenotype is computed and used as a weight in the Jaccard index. Phenotypic similarity is useful in several ways. Phenotypic similarity between a phenotype resulting from a genetic mutation and a disease can be used to suggest candidate genes for a disease. Phenotypic similarity can also identify genes in a same pathway or orthologous genes. PhenomeNet uses the axioms in multiple species-dependent phenotype ontologies to infer equivalent and related phenotypes across species. For this purpose, phenotype ontologies and phenotype annotations are integrated in a single ontology, and automated reasoning is used to infer equivalences. Specifically, for every phenotype, PhenomeNet infers the related mammalian phenotype and uses the Mammalian Phenotype Ontology for computing phenotypic similarity. Tools: * PhenomeBLAST - A tool for cross-species alignments of phenotypes * PhenomeDrug - method for drug-repurposingphenotype, disease, gene, genotype, allele, model organism, human disease, candidate disease gene, pathway, orthologous gene, ortholog, ontology, semantic similarity, mutant phenotype, disease pathway, alignment, pharmacogenomics, drugSCR_006165(phenomeNET, RRID:SCR_006165)University of Cambridge; Cambridge; United Kingdom BBSRC, European Union 7th FPRICORDO project, NHGRIrelated to: OMIM, Orphanet, PharmGKB, MPOPMID:21737429Last checked downnlx_151667
Genes to Cognition: Neuroscience Research ProgrammeResource, blog, topical portal, software application, narrative resource, portal, software resource, training material, data or information resourceA neuroscience research program that studies genes, the brain and behavior in an integrated manner, established to elucidate the molecular mechanisms of learning and memory, and shed light on the pathogenesis of disorders of cognition. Central to G2C investigations is the NMDA receptor complex (NRC/MASC), that is found at the synapses in the central nervous system which constitute the functional connections between neurons. Changes in the receptor and associated components are thought to be in a large part responsible for the phenomenon of synaptic plasticity, that may underlie learning and memory. G2C is addressing the function of synapse proteins using large scale approaches combining genomics, proteomics and genetic methods with electrophysiological and behavioral studies. This is incorporated with computational models of the organization of molecular networks at the synapse. These combined approaches provide a powerful and unique opportunity to understand the mechanisms of disease genes in behavior and brain pathology as well as provide fundamental insights into the complexity of the human brain. Additionally, Genes to Cognition makes available its biological resources, including gene-targeting vectors, ES cell lines, antibodies, and transgenic mice, generated for its phenotyping pipeline. The resources are freely-available to interested researchers.electrophysiological, es cell, functional, gene, gene-target vector, genetic, 1295s, allele, antibody, behavior, behavioral, brain, c57bl/6j, central nervous system, clone, cognition, computation, connection, deletion, disease, disorder, dlg3, dlg4, domain, genomic, guanylate kinase, hprt gene, hras1, human, knockout, learning, mechanism, memory, model, molecular, mouse, mutation, network, neuron, neuroscience, nmda receptor complex, pathogenesis, phenotyping, protein, proteomics, ptk2, strain, synapse, synaptic plasticity, syngap1, transgenic, modelSCR_007121(Genes to Cognition: Neuroscience Research Programme, RRID:SCR_007121)Wellcome Trust Sanger Institute; Hinxton; United Kingdom BBSRC, EPSRC, European Union, Framework Programme, Gatsby Charitable Foundation, Human Frontiers Science Programme, MRC, NSF, Wellcome Trustlisted by: 3DVCLast checked downnif-0000-10235
GWAS: Catalog of Published Genome-Wide Association StudiesResource, catalog, data or information resource, databaseCatalog of published genome-wide association studies. Genome-wide set of genetic variants in different individuals to see if any variant is associated with trait and disease. Database of genome-wide association study (GWAS) publications including only those attempting to assay single nucleotide polymorphisms (SNPs). Publications are organized from most to least recent date of publication. Studies are identified through weekly PubMed literature searches, daily NIH-distributed compilations of news and media reports, and occasional comparisons with an existing database of GWAS literature (HuGE Navigator).gene-wide association study, adult, genome, genome-wide association study, single nucleotide polymorphism, publication, literature, phenotype, trait, disease, loci, genetic variant, disorder, snp trait associationSCR_012745(GWAS: Catalog of Published Genome-Wide Association Studies, RRID:SCR_012745)National Human Genome Research Institute BBSRC, NHGRIrelated to: PheWAS Catalog, Psychiatric Genomics Consortium, KOBAS, used by: NIF Data Federation, Monarch Initiative, Schizo-PiPMID:19474294Last checked upnif-0000-06666
Eukaryotic Linear MotifResource, data analysis service, database, analysis service resource, production service resource, service resource, data or information resourceComputational biology resource for investigating candidate functional sites in eukarytic proteins. Functional sites which fit to the description linear motif are currently specified as patterns using Regular Expression rules. To improve the predictive power, context-based rules and logical filters are being developed and applied to reduce the amount of false positives. The current version of the ELM server provides core functionality including filtering by cell compartment, phylogeny, globular domain clash (using the SMART/Pfam databases) and structure. In addition, both the known ELM instances and any positionally conserved matches in sequences similar to ELM instance sequences are identified and displayed (see ELM instance mapper). Although the ELM resource contains a large collection of functional site motifs, the current set of motifs is not exhaustive.linear motif, regulatory protein, motif, protein sequence, functional site, prediction, disease, virus, cell compartment, phylogeny, globular domain clash, structure, proteinSCR_003085(Eukaryotic Linear Motif, RRID:SCR_003085)European Molecular Biology Laboratory BBSRC, Biotechnology and Biological Sciences Research Council, EMBL Interdisciplinary PostDoc fellowship, EMBL international PhD program, European Community Seventh Framework Programme FP7/2009, Federal Government Department of Education and Science, German Research Foundation, Polish Ministry of Science and Higher Education, Region Alsace and College Doctoral Europeen, Science Foundation Ireland, Swiss National Science Foundationrelated to: SMART, PfamPMID:22110040Last checked upnif-0000-30486
PHI-baseResource, data or information resource, databaseDatabase that catalogs experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts. It is an invaluable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. In collaboration with the FRAC team, it also includes antifungal compounds and their target genes. Each entry is curated by domain experts and is supported by strong experimental evidence (gene disruption experiments, STM etc), as well as literature references in which the original experiments are described. Each gene is presented with its nucleotide and deduced amino acid sequence, as well as a detailed description of the predicted protein's function during the host infection process. To facilitate data interoperability, genes have been annotated using controlled vocabularies and links to external sources (Gene Ontology terms, EC Numbers, NCBI taxonomy, EMBL, PubMed and FRAC).gene expression, pathogenic bacteria, virulence, infection, target site, gene, pathogen-host interaction, interaction, phenotype, pathogen, disease, host, anti-infective, nucleotide sequence, amino acid sequenceSCR_003331(PHI-base, RRID:SCR_003331)BBSRClisted by: re3data.orgReferences (3)Last checked upnif-0000-03276
PIDO - Primary Immunodeficiency Disease OntologyResource, ontology, data or information resource, controlled vocabularyThe Primary Immunodeficiency Disease Ontology Project is developing an ontology for the phenotypic description of Primary Immunodeficiency Diseases. The ontology can be used for integrative research in both biomedical and clinical research. Primary Immunodeficiency Diseases (PIDs) are Mendelian diseases, caused by defects or deletions of genes involved in the development, regulation and maintenance of the immune system. They usually affect newborns and toddlers, but can also manifest much later in life. Information about PIDs is often widely scattered across the research literature and a number of databases. PIDO is an attempt to develop both a machine- as well as a human-comprehensible representation of these diseases, starting with a phenotypic descriptions of disease.phenotype, disease, young human, childSCR_005834(PIDO - Primary Immunodeficiency Disease Ontology, RRID:SCR_005834)Google Project Hosting , Hannover Medical School; Lower Saxony; Germany Primary Immunodeficiency DiseaseBBSRC, DFG, European Union FP7, Hannover Medical School; Lower Saxony; Germanyrelated to: PIDFinderPMID:21949270Last checked upnlx_149345
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