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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
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
pSTIINGResource, data or information resource, databaseA publicly accessible knowledgebase about protein-protein, protein-lipid, protein-small molecules, ligand-receptor interactions, receptor-cell type information, transcriptional regulatory and signal transduction modules relevant to inflammation, cell migration and tumourigenesis. It integrates in-house curated information from the literature, biochemical experiments, functional assays and in vivo studies, with publicly available information from multiple and diverse sources across human, rat, mouse, fly, worm and yeast. The knowledgebase allowing users to search and to dynamically generate visual representations of protein-protein interactions and transcriptional regulatory networks. Signalling and transcriptional modules can also be displayed singly or in combination. This allow users to identify important "cross-talks" between signalling modules via connections with key components or "hubs". The knowledgebase will facilitate a "systems-wide" understanding across many protein, signalling and transcriptional regulatory networks triggered by multiple environmental cues, and also serve as a platform for future efforts to computationally and mathematically model the system behavior of inflammatory processes and tumourigenesis.protein-protein, protein-lipid, protein-small molecule, ligand-receptor interaction, receptor-cell type, transcriptional regulatory module, signal transduction module, inflammation, cell migration, tumorigenesis, protein-protein interaction, transcriptional regulatory network, signalling pathway, interaction, protein interaction, motif, domain, protein, geneSCR_002045(pSTIING, RRID:SCR_002045)University College London; London; United Kingdom Inflammation, Tumor, Cancerrelated to: Gene Ontology, listed by: OMICtoolsPMID:16381926Last checked downOMICS_01916
L2L Microarray Analysis ToolResource, data analysis service, data analysis software, data processing software, production service resource, analysis service resource, software application, database, service resource, storage service resource, software resource, data repository, data or information resourceNO LONGER IN SERVICE. Documented on August 26, 2019.\\n\\nDatabase of published microarray gene expression data, and a software tool for comparing that published data to a user''''s own microarray results. It is very simple to use - all you need is a web browser and a list of the probes that went up or down in your experiment. If you find L2L useful please consider contributing your published data to the L2L Microarray Database in the form of list files. L2L finds true biological patterns in gene expression data by systematically comparing your own list of genes to lists of genes that have been experimentally determined to be co-expressed in response to a particular stimulus - in other words, published lists of microarray results. The patterns it finds can point to the underlying disease process or affected molecular function that actually generated the observed changed in gene expression. Its insights are far more systematic than critical gene analyses, and more biologically relevant than pure Gene Ontology-based analyses. The publications included in the L2L MDB initially reflected topics thought to be related to Cockayne syndrome: aging, cancer, and DNA damage. Since then, the scope of the publications included has expanded considerably, to include chromatin structure, immune and inflammatory mediators, the hypoxic response, adipogenesis, growth factors, hormones, cell cycle regulators, and others. Despite the parochial origins of the database, the wide range of topics covered will make L2L of general interest to any investigator using microarrays to study human biology. In addition to the L2L Microarray Database, L2L contains three sets of lists derived from Gene Ontology categories: Biological Process, Cellular Component, and Molecular Function. As with the L2L MDB, each GO sub-category is represented by a text file that contains annotation information and a list of the HUGO symbols of the genes assigned to that sub-category or any of its descendants. You don''''t need to download L2L to use it to analyze your microarray data. There is an easy-to-use web-based analysis tool, and you have the option of downloading your results so you can view them at any time on your own computer, using any web browser. However, if you prefer, the entire L2L project, and all of its components, can be downloaded from the download page. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatiblemicroarray, gene expression, adipogenesis, biological, biological process, cancer, cell cycle regulator, cellular component, chromatin, cockayne syndrome, dna damage, growth factor, hormone, human biology, hypoxic response, immune mediator, inflammatory mediator, molecular function, molecular neuroanatomy resource, adipocyte, development, hypoxia, immune, inflammation, metabolism, mitogen, neuro, rna, vascular, transcription, tissue, splicing, mouse, human, rat, source code, statistical analysis, gene, chromatin structureSCR_013440(L2L Microarray Analysis Tool, RRID:SCR_013440)University of Washington; Seattle; USA Cockayne syndrome, DNA damage, Other, Aging, CancerCora May Poncin Foundation, NIGMSrelated to: Gene Ontology, listed by: Gene Ontology ToolsPMID:16168088Last checked upnif-0000-10463
AutismKBResource, data analysis service, production service resource, analysis service resource, database, service resource, data or information resourceGenetic factors contribute significantly to ASD. AutismKB is an evidence-based knowledgebase of Autism spectrum disorder (ASD) genetics. The current version contains 2193 genes (99 syndromic autism related genes and 2135 non-syndromic autism related genes), 4617 Copy Number Variations (CNVs) and 158 linkage regions associated with ASD by one or more of the following six experimental methods: # Genome-Wide Association Studies (GWAS); # Genome-wide CNV studies; # Linkage analysis; # Low-scale genetic association studies; # Expression profiling; # Other low-scale gene studies. Based on a scoring and ranking system, 99 syndromic autism related genes and 383 non-syndromic autism related genes (434 genes in total) were designated as having high confidence. Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental disorder with a prevalence of 1.0-2.6%. The three core symptoms of ASD are: # impairments in reciprocal social interaction; # communication impairments; # presence of restricted, repetitive and stereotyped patterns of behavior, interests and activities.gene, copy number variation, linkage region, genome-wide association study, family-based association study, case-control association study, expression profile, blast, syndromic, non-syndromic, snp, vntrSCR_006937(AutismKB, RRID:SCR_006937)Peking University; Beijing; China Autism spectrum disorder, AutismJohnson and Johnson, Merck, Natural Science Foundation of Chinarelated to: Gene OntologyPMID:22139918Last checked upnlx_151318
AgingDBResource, service resource, data or information resource, data repository, storage service resource, databaseA database that stores information on the biomolecules which are modulated during aging and by caloric restriction (CR). To enhance its usefulness, data collected from studies of CR''''s anti-oxidative action on gene expression, oxidative stress, and many chronic age-related diseases are included. AgingDB is organized into two sections A) apoptosis and the various mitochondrial biomolecules that play a role in aging; B) nuclear transcription factors known to be_sensitive to oxidative environment. AgingDB features an imagemap of biomolecular signal pathways and visualized information that includes protein-protein interactions of biomolecules. Authorized users can submit a new biomolecule or edit an existing biomolecule to reflect latest developments.oxidative stress, calorie restriction, pathway, biomolecule, signal pathway, interaction, gene, protein, protein-protein interaction, apoptosis, mitochondrial, nuclear transcription factorSCR_010226(AgingDB, RRID:SCR_010226)Pusan National University; Busan; South Korea Agingrelated to: Gene OntologyPMID:23604914Last checked upnlx_156773
UBERONResource, ontology, data or information resource, controlled vocabularyAn integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. Uberon consists of over 10000 classes (March 2014) representing structures that are shared across a variety of metazoans. The majority of these classes are chordate specific, and there is large bias towards model organisms and human.anatomy, comparative, evolution, organ system, anatomical structure, body part, organ, tissue, body, vertebrate, function, phenotype, expression, model organism, oboSCR_010668(UBERON, RRID:SCR_010668)OBO ARRA, DOE, NCRR, NHGRI, NSFrelated to: Gene Ontology, used by: Monarch Initiative, Neuroscience Information Framework, listed by: BioPortalPMID:22293552Last checked upnlx_74404
gsGatorResource, analysis service resource, data analysis service, service resource, production service resourceA web-based platform for functional interpretation of gene sets with features such as cross-species Gene Set Analysis (GSA), Flexible and Interactive GSA, simultaneous GSA for multiple gene set, and and a fully integrated network viewer for both visualizing GSA results and molecular networks.linux, windows, gene, orthology, pathway, phenotype, mirna target, molecular network, genomic annotation, functionSCR_012035(gsGator, RRID:SCR_012035)Ewha Womans University; Seoul; South Korea related to: Gene Ontology, listed by: OMICtoolsPMID:24423189Last checked upOMICS_02233
Automated Microarray PipelineResource, analysis service resource, data analysis service, service resource, production service resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented November 4, 2015. Web application based on the TM4 Microarray Software Suite to provide a means of normalization and analysis of microarray data. Users can upload data in the form of Affymetrix CEL files, and define an analysis pipeline by selecting several intuitive options. It performs data normalization (eg RMA), basic statistical analysis (eg t-test, ANOVA), and analysis of annotation using gene classification (eg Gene Ontology term assignment). The analysis are performed without user intervention and the results are presented in a web-based summary that allows data to be downloaded in a variety of formats compatible with further directed analysis.microarray, normalizationSCR_001219(Automated Microarray Pipeline, RRID:SCR_001219)TM4 NLMrelated to: Gene Ontology, listed by: OMICtoolsLast checked upOMICS_02125
globaltestResource, software resource, data processing software, data analysis software, sequence analysis software, software applicationA software package that tests groups of covariates (or features) for association with a response variable. The package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms.differential expression, go, microarray, one channel, pathwaySCR_001256(globaltest, RRID:SCR_001256)Bioconductor related to: Gene Ontology, uses: KEGG, listed by: OMICtoolsLast checked upOMICS_02084
Flash GviewerResource, software resourceFlash GViewer is a customizable Flash movie that can be easily inserted into a web page to display each chromosome in a genome along with the locations of individual features on the chromosomes. It is intended to provide an overview of the genomic locations of a specific set of features - eg. genes and QTLs associated with a specific phenotype, etc. rather than as a way to view all features on the genome. The features can hyperlink out to a detail page to enable to GViewer to be used as a navigation tool. In addition the bands on the chromosomes can link to defineable URL and new region selection sliders can be used to select a specific chromosome region and then link out to a genome browser for higher resolution information. Genome maps for Rat, Mouse, Human and C. elegans are provided but other genome maps can be easily created. Annotation data can be provided as static text files or produced as XML via server scripts. This tool is not GO-specific, but was built for the purpose of viewing GO annotation data. Platform: Online toolvisualization, chromosome, video, gene, qtl, genome, navitgation, phenotype, ontology or annotation visualizationSCR_012870(Flash Gviewer, RRID:SCR_012870)Medical College of Wisconsin; Wisconsin; USA related to: Gene Ontology, listed by: Gene Ontology ToolsLast checked upnlx_149333
EASE: the Expression Analysis Systematic ExplorerResource, software resource, software application, data processing softwareWindows(c) desktop software application, customizable and standalone, that facilitates the biological interpretation of gene lists derived from the results of microarray, proteomic, and SAGE experiments. Provides statistical methods for discovering enriched biological themes within gene lists, generates gene annotation tables, and enables automated linking to online analysis tools. Offers statistical models to deal with multi-test comparison problem. Platform: Windows compatiblegene, microarray, genome, gene ontology, statistical analysis, enrichment analysisSCR_013361(EASE: the Expression Analysis Systematic Explorer, RRID:SCR_013361)Database for Annotation Visualization and Integrated Discovery NIAIDrelated to: Gene Ontology, listed by: 3DVC, Gene Ontology ToolsReferences (3)Last checked upnlx_149218
Semantic Measures LibraryResource, software resource, software toolkit, software libraryOpen source Java library dedicated to semantic measures computation and analysis. Tools based on the SML are also provided through the SML-Toolkit, a command line software giving access to some of the functionalities of the library. The SML and the toolkit can be used to compute semantic similarity and semantic relatedness between semantic elements (e.g. concepts, terms) or entities semantically characterized (e.g. entities defined in a semantic graph, documents annotated by concepts defined in an ontology).semantic measure, semantic similarity, semantic relatedness, functional similarity, gene ontology, annotation, parse, gene, disease ontology, mesh, rdf, owl, umls, snomed-ct, java, semantic, command lineSCR_001383(Semantic Measures Library, RRID:SCR_001383)Ecole des Mines d'Ales; Ales; France Ecole des Mines d'Ales; Ales; France, LGI2P Research Centerrelated to: Gene Ontology, listed by: FORCE11, Gene Ontology ToolsLast checked downnlx_152555
WegoLocResource, analysis service resource, data analysis service, service resource, production service resourceData analysis service that predicts protein subcellular localizations of animal, fungal, plant, and human proteins based on sequence similarity and gene ontology information.subcellular localization, proteinSCR_001402(WegoLoc, RRID:SCR_001402)related to: Gene Ontology, listed by: OMICtoolsLast checked upOMICS_01636
GenNavResource, analysis service resource, data analysis service, service resource, production service resourceGenNav searches GO terms and annotated gene products, and provides a graphical display of a term's position in the GO DAG. Platform: Online toolimage, gene, ontology or annotation browserSCR_000147(GenNav, RRID:SCR_000147)National Library of Medicine related to: Gene Ontology, listed by: Gene Ontology ToolsLast checked downnlx_149123
SynaptomeDBResource, data or information resource, databaseOntology-based knowledgebase for synaptic genes. These genes encode components of the synapse including neurotransmitters and their receptors, adhesion / cytoskeletal proteins, scaffold proteins, transporters, and others. It integrates various and complex data sources for synaptic genes and proteins.gene, protein, pathway, synaptome, protein-protein interaction, synaptic gene, synapse, motif, presynaptic, postsynaptic, vesicleSCR_000157(SynaptomeDB, RRID:SCR_000157)Johns Hopkins University; Maryland; USA related to: Gene OntologyPMID:22285564Last checked downnlx_157656
Arabidopsis Hormone DatabaseResource, data repository, ontology, database, service resource, storage service resource, controlled vocabulary, data or information resourceDatabase providing a systematic and comprehensive view of morphological phenotypes regulated by plant hormones, as well as regulatory genes participating in numerous plant hormone responses. By integrating the data from mutant studies, transgenic analysis and gene ontology annotation, genes related to the stimulus of eight plant hormones were identified, including abscisic acid, auxin, brassinosteroid, cytokinin, ethylene, gibberellin, jasmonic acid and salicylic acid. Another pronounced characteristics of this database is that a phenotype ontology was developed to precisely describe all kinds of morphological processes regulated by plant hormones with standardized vocabularies. To increase the coverage of phytohormone related genes, the database has been updated from AHD to AHD2.0 adding and integrating several pronounced features: (1) added 291 newly published Arabidopsis hormone related genes as well as corrected information (e.g. the arguable ABA receptors) based on the recent 2-year literature; (2) integrated orthologues of sequenced plants in OrthoMCLDB into each gene in the database; (3) integrated predicted miRNA splicing site in each gene in the database; (4) provided genetic relationship of these phytohormone related genes mining from literature, which represents the first effort to construct a relatively comprehensive and complex network of hormone related genes as shown in the home page of our database; (5) In convenience to in-time bioinformatics analysis, they also provided links to a powerful online analysis platform Weblab that they have recently developed, which will allow users to readily perform various sequence analysis with these phytohormone related genes retrieved from AHD2.0; (6) provided links to other protein databases as well as more expression profiling information that would facilitate users for a more systematic analysis related to phytohormone research. Please help to improve the database with your contributions.arabidopsis thaliana, hormone, hormone function, hormone gene, phytohormone, abscisic acid, auxin, brassinosteroid, cytokinin, ethylene, gibberellin, jasmonic acid, salicylic acid, microarray, phenotype, gene, mirna prediction, expression, mutant, blast, orthologue, mirna splicing site, root, cotyledon, leaf, hypocotyl, stem, flower, silique, seed, embryo, stress, morphology, plant, hormone, regulatory gene, mutant, transgenic, annotation, data analysis serviceSCR_001792(Arabidopsis Hormone Database, RRID:SCR_001792)Peking University; Beijing; China Ministry of Education of China, Ministry of Science and Technology of China, National Natural Science Foundation of Chinarelated to: Gene OntologyReferences (2)Last checked upnif-0000-02559
Arabidopsis thaliana Protein Interactome DatabaseResource, service resource, data or information resource, data repository, storage service resource, databaseCentralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome. The Protein-protein interaction pairs are predicted by integrating several methods with the Naive Baysian Classifier. All other related information curated is manually extracted from published literature and other resources from some expert biologists. You are welcomed to upload your PPI or subcellular localization information or report data errors. Arabidopsis proteins is annotated with information (e.g. functional annotation, subcellular localization, tissue-specific expression, phosphorylation information, SNP phenotype and mutant phenotype, etc.) and interaction qualifications (e.g. transcriptional regulation, complex assembly, functional collaboration, etc.) via further literature text mining and integration of other resources. Meanwhile, the related information is vividly displayed to users through a comprehensive and newly developed display and analytical tools. The system allows the construction of tissue-specific interaction networks with display of canonical pathways.gene, gene expression, domain, annotation, ineractome, metabolic pathway, phylogenetic, protein, protein-protein interaction, signaling pathway, proteome, protein subcellular location, ortholog, gene regulation, pathway, phenotypeSCR_001896(Arabidopsis thaliana Protein Interactome Database, RRID:SCR_001896)Northeast Forest University; Harbin; China National Basic Research Program of China, National High Technology Research and Development Program of China, National Natural Science Foundation of China, Science and Technology Commission of Shanghai Municipalityrelated to: Gene Ontology, listed by: OMICtoolsReferences (2)Last checked upnif-0000-02585, OMICS_01898
TM4 Microarray Software Suite - TIGR MultiExperiment ViewerResource, data analysis software, data processing software, software application, data visualization software, software resource, software toolkitA desktop application for the analysis, visualization and data-mining of large-scale genomic data. It is a versatile microarray tool, incorporating sophisticated algorithms for clustering, visualization, classification, statistical analysis and biological theme discovery. MeV generates informative and interrelated displays of expression and annotation data from single or multiple experiments. A huge array of alrogithms are included in MeV modules, and are available at a button-click, such as K-means clustering, Hierarchical clustering, t-Tests, Significance Analysis of Microarrays, Gene Set Enrichment Analysis, and EASE. Extensive documentation is available for helping new users get started with MeV. A Quickstart Guide provides the tutorial a brand new person will need to get their first dataset loaded and displayed in the program. Returning MEV users will want to check out the release notes to see what new features are available in the latest versions of the program. Tutorials have been written about several of its more involved features.gene expression, analysis, annotation, classification, microarray, visualization, statistical analysis, clustering, biological theme, graphic, annotation, data miningSCR_001915(TM4 Microarray Software Suite - TIGR MultiExperiment Viewer, RRID:SCR_001915)Dana-Farber Cancer Institute , J. Craig Venter Institute , University of Washington; Seattle; USA NCRRrelated to: Gene Ontology, listed by: Gene Ontology ToolsReferences (2)Last checked upnif-0000-10486, SCR_005576, OMICS_00781
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
Patterns of Gene Expression in Drosophila EmbryogenesisResource, software resource, source code, database, image collection, data or information resourceDatabase of embryonic expression patterns using a high throughput RNA in situ hybridization of the protein-coding genes identified in the Drosophila melanogaster genome with images and controlled vocabulary annotations. At the end of production pipeline gene expression patterns are documented by taking a large number of digital images of individual embryos. The quality and identity of the captured image data are verified by independently derived microarray time-course analysis of gene expression using Affymetrix GeneChip technology. Gene expression patterns are annotated with controlled vocabulary for developmental anatomy of Drosophila embryogenesis. Image, microarray and annotation data are stored in a modified version of Gene Ontology database and the entire dataset is available on the web in browsable and searchable form or MySQL dump can be downloaded. So far, they have examined expression of 7507 genes and documented them with 111184 digital photographs.embryo, embryogenesis, gene, anatomy, microarray, pattern, protocol, rna, gene expression, expression pattern, embryonic drosophila, in situ hybridization, annotation, estSCR_002868(Patterns of Gene Expression in Drosophila Embryogenesis, RRID:SCR_002868)Berkeley Drosophila Genome Project Howard Hughes Medical Institute, NHGRI, NIGMS, NIHrelated to: Gene OntologyReferences (2)Last checked upnif-0000-25550
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