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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
FIVA - Functional Information Viewer and AnalyzerResource, software resource, software application, data processing softwareFunctional Information Viewer and Analyzer (FIVA) aids researchers in the prokaryotic community to quickly identify relevant biological processes following transcriptome analysis. Our software is able to assist in functional profiling of large sets of genes and generates a comprehensive overview of affected biological processes. Currently, seven different modules containing functional information have been implemented: (i) gene regulatory interactions, (ii) cluster of orthologous groups (COG) of proteins, (iii) gene ontologies (GO), (iv) metabolic pathways (v) Swiss Prot keywords, (vi) InterPro domains - and (vii) generic functional categories. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatiblegene, gene expression, gene expression pattern, functional profile, statistical analysis, metabolic pathway, gene ontology, function, ortholog, gene regulatory interaction, biological process, transcriptome, visualization, analysisSCR_005776(FIVA - Functional Information Viewer and Analyzer, RRID:SCR_005776)MolGen Center IOP Genomics, European Union, industrial partners in the NWO-BMI project number 050.50.206 on Computational Genomics of Prokaryotes, Netherlands Organization for Scientific Researchrelated to: Gene Ontology, listed by: Gene Ontology ToolsPMID:17237043Last checked downnlx_149245
Expression ProfilerResource, analysis service resource, data analysis service, service resource, production service resourceTHIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The EP:GO browser is built into EBI's Expression Profiler, a set of tools for clustering, analysis and visualization of gene expression and other genomic data. With it, you can search for GO terms and identify gene associations for a node, with or without associated subnodes, for the organism of your choice.other analysis, cluster, analysis, visualization, gene expression, genomic, gene ontology, gene association, microarray, protein-protein interaction, geneSCR_005821(Expression Profiler, RRID:SCR_005821)European Bioinformatics Institute Estonian Science Foundation, European Union, Wellcome Trustrelated to: Gene Ontology, listed by: Gene Ontology ToolsPMID:15215431Last checked downnlx_149323
FunSimMatResource, data analysis service, data access protocol, production service resource, analysis service resource, database, web service, service resource, software resource, data or information resourceFunSimMat is a comprehensive resource of semantic and functional similarity values. It allows ranking disease candidate proteins for OMIM diseases and searching for functional similarity values for proteins (extracted from UniProt), and protein families (Pfam, SMART). FunSimMat provides several different semantic and functional similarity measures for each protein pair using the Gene Ontology annotation from UniProtKB and the Gene Ontology Annotation project at EBI (GOA). There are several search options available: Disease candidate prioritization: * Rank candidate proteins using any OMIM disease entry * Compare a list of proteins to any OMIM disease entry * Compare all human proteins to any OMIM disease entry Functional similarity: * Compare one protein / protein family to a list of proteins / protein families * Compare a list of GO terms to a list of proteins / protein families Semantic similarity: * For a list of GO terms, FunSimMat performs an all-against-all comparison and displays the semantic similarity values. FunSimMat provides an XML-RPC interface for performing automatic queries and processing of the results as well as a RestLike Interface. Platform: Online toolfunctional similarity value, protein family, protein similarity, semantic similarity value, similarity value, functional similarity, disease gene candidate prioritization, disease, protein, protein family, disease candidate prioritization, semantic similarity, gene ontology, visualization, annotation, database or data warehouseSCR_002729(FunSimMat, RRID:SCR_002729)Max-Planck-Institute for Informatics; Saarbrucken; Germany European Union, German National Genome Research Network, Klinische Forschergrupperelated to: Gene Ontology, listed by: Gene Ontology ToolsReferences (2)Last checked upnif-0000-02860
PathbaseResource, ontology, data access protocol, database, web service, image collection, service resource, storage service resource, software resource, image repository, data repository, controlled vocabulary, data or information resourceDatabase of histopathology photomicrographs and macroscopic images derived from mutant or genetically manipulated mice. The database currently holds more than 1000 images of lesions from mutant mice and their inbred backgrounds and further images are being added continuously. Images can be retrieved by searching for specific lesions or class of lesion, by genetic locus, or by a wide set of parameters shown on the Advanced Search Interface. Its two key aims are: * To provide a searchable database of histopathology images derived from experimental manipulation of the mouse genome or experiments conducted on genetically manipulated mice. * A reference / didactic resource covering all aspects of mouse pathology Lesions are described according to the Pathbase pathology ontology developed by the Pathbase European Consortium, and are available at the site or on the Gene Ontology Consortium site - OBO. As this is a community resource, they encourage everyone to upload their own images, contribute comments to images and send them their feedback. Please feel free to use any of the SOAP/WSDL web services. (under development)histopathology, photomicrograph, macroscopic, mutant, genetically manipulated, pathology, transgenic, rodent, mpath ontology, mouse pathology ontology, skinbase, genotype, skin, gene, tissue, hair, mutant mouse strainSCR_006141(Pathbase, RRID:SCR_006141)University of Cambridge; Cambridge; United Kingdom Lesion, Mutant mouse strain, Inbred mouse strainEllison Medical Foundation, European Union, NCI, NCRR, NIH, North American Hair Research Societyrelated to: Gene OntologyReferences (3)Last checked upnlx_151637
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