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GET /api/t/?collectionID=%22Rare+Disease%22
{ "count": 247, "next": "?page=2", "previous": null, "list": [ { "name": "neXtProt", "description": "neXtProt was an innovative knowledge platform dedicated to human proteins. This resource contained a wealth of high-quality data on all the human proteins that are produced by the 20'000 protein-coding genes found in the human genome. The content of neXtProt was continuously extended so as to provide many more carefully selected data sets and analysis tools. neXtProt data and tools have been archived.", "homepage": "https://www.expasy.org/archives/nextprot", "biotoolsID": "nextprot", "biotoolsCURIE": "biotools:nextprot", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_2479", "term": "Protein sequence analysis" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" }, { "uri": "http://edamontology.org/operation_2406", "term": "Protein structure analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_0601", "term": "Protein modifications" }, { "uri": "http://edamontology.org/topic_3120", "term": "Protein variants" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "CC-BY-4.0", "collectionID": [ "Rare Disease", "Proteomics" ], "maturity": "Legacy", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [ "Data" ], "elixirNode": [ "Switzerland" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/calipho-sib/", "type": [ "Repository" ], "note": "neXtProt software repository with issue tracking" }, { "url": "https://twitter.com/nextprot_news", "type": [ "Social media" ], "note": "neXtProt release news, publications, presentations, tips and more. DM us with feedback!" }, { "url": "https://www.expasy.org/resources/nextprot", "type": [ "Software catalogue" ], "note": "neXtProt entry in Expasy" } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkz995", "pmid": "31724716", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The neXtProt knowledgebase in 2020: Data, tools and usability improvements", "abstract": "The neXtProt knowledgebase (https://www.nextprot.org) is an integrative resource providing both data on human protein and the tools to explore these. In order to provide comprehensive and up-to-date data, we evaluate and add new data sets. We describe the incorporation of three new data sets that provide expression, function, protein-protein binary interaction, post-translational modifications (PTM) and variant information. New SPARQL query examples illustrating uses of the new data were added. neXtProt has continued to develop tools for proteomics. We have improved the peptide uniqueness checker and have implemented a new protein digestion tool. Together, these tools make it possible to determine which proteases can be used to identify trypsin-resistant proteins by mass spectrometry. In terms of usability, we have finished revamping our web interface and completely rewritten our API. Our SPARQL endpoint now supports federated queries. All the neXtProt data are available via our user interface, API, SPARQL endpoint and FTP site, including the new PEFF 1.0 format files. Finally, the data on our FTP site is now CC BY 4.0 to promote its reuse.", "date": "2020-01-01T00:00:00Z", "citationCount": 155, "authors": [ { "name": "Zahn-Zabal M." }, { "name": "Michel P.-A." }, { "name": "Gateau A." }, { "name": "Nikitin F." }, { "name": "Schaeffer M." }, { "name": "Audot E." }, { "name": "Gaudet P." }, { "name": "Duek P.D." }, { "name": "Teixeira D." }, { "name": "De Laval V.R." }, { "name": "Samarasinghe K." }, { "name": "Bairoch A." }, { "name": "Lane L." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkr1179", "pmid": "22139911", "pmcid": "PMC3245017", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "NeXtProt: A knowledge platform for human proteins", "abstract": "neXtProt (http://www.nextprot.org/) is a new human protein-centric knowledge platform. Developed at the Swiss Institute of Bioinformatics (SIB), it aims to help researchers answer questions relevant to human proteins. To achieve this goal, neXtProt is built on a corpus containing both curated knowledge originating from the UniProtKB/Swiss-Prot knowledgebase and carefully selected and filtered high-throughput data pertinent to human proteins. This article presents an overview of the database and the data integration process. We also lay out the key future directions of neXtProt that we consider the necessary steps to make neXtProt the one-stop-shop for all research projects focusing on human proteins. © The Author(s) 2011.", "date": "2012-01-01T00:00:00Z", "citationCount": 168, "authors": [ { "name": "Lane L." }, { "name": "Argoud-Puy G." }, { "name": "Britan A." }, { "name": "Cusin I." }, { "name": "Duek P.D." }, { "name": "Evalet O." }, { "name": "Gateau A." }, { "name": "Gaudet P." }, { "name": "Gleizes A." }, { "name": "Masselot A." }, { "name": "Zwahlen C." }, { "name": "Bairoch A." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "SIB Swiss Institute of Bioinformatics", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Support", "email": "support@nextprot.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Pascale Gaudet", "email": null, "url": null, "orcidid": "http://orcid.org/0000-0003-1813-6857", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "owner": "SIB", "additionDate": "2015-01-21T13:30:06Z", "lastUpdate": "2025-04-02T08:05:19.163091Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools", "mzahn", "LanfearJ" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Gen Seeker", "description": "Gen Seeker is the browser of variants detected in the Czech population included in the Czech digital genome map. \nAlthough Slavs are the largest European ethnolinguistic group, Slavic and especially Czech genomes are underrepresented in international genomic databases, which limits the ability to understand and interpret specific slavic gene variations.", "homepage": "https://czechgenome.cz/search", "biotoolsID": "gen_seeker", "biotoolsCURIE": "biotools:gen_seeker", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3918", "term": "Genome analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1027", "term": "Gene ID (NCBI)" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0860", "term": "Sequence signature data" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_2012", "term": "Sequence coordinates" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_3134", "term": "Gene transcript report" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3134", "term": "Gene transcript report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "JavaScript" ], "license": "Not licensed", "collectionID": [ "ELIXIR-CZ", "EATRIS-CZ", "Palacky University", "Rare Disease" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Data" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [ "Human Copy Number Variation", "Federated Human Data", "Rare Diseases" ], "link": [], "download": [], "documentation": [ { "url": "https://czechgenome.cz/data-info", "type": [ "General" ], "note": null } ], "publication": [], "credit": [ { "name": "Institute of Applied Biotechnologies, a.s.", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Developer" ], "note": null }, { "name": "Palacky University Olomouc, Czech Republic", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Maintainer" ], "note": null }, { "name": "Ministry of Industry of the Czech Republic", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [], "note": null } ], "owner": "ELIXIR-CZ", "additionDate": "2024-11-26T07:47:41.489067Z", "lastUpdate": "2024-11-26T08:03:23.603198Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "WikiPathways App", "description": "Easy access to pathway content at WikiPathways.org from Cytoscape.", "homepage": "http://apps.cytoscape.org/apps/wikipathways", "biotoolsID": "wikipathways_app", "biotoolsCURIE": "biotools:wikipathways_app", "version": [ "3.3.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3439", "term": "Pathway or network prediction" }, { "uri": "http://edamontology.org/operation_0277", "term": "Pathway or network comparison" }, { "uri": "http://edamontology.org/operation_3562", "term": "Network simulation" }, { "uri": "http://edamontology.org/operation_3083", "term": "Pathway or network visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Plug-in" ], "topic": [ { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Shell", "Java" ], "license": "Apache-2.0", "collectionID": [ "RD-connect", "Rare Disease", "WikiPathways", "Cytoscape" ], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [ "Netherlands" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/wikipathways/cytoscape-wikipathways-app", "type": [ "Repository" ], "note": null }, { "url": "https://wikipathways.slack.com/?redir=%2Fmessages%2Fwikipathways-helpdesk%2F", "type": [ "Helpdesk" ], "note": null } ], "download": [], "documentation": [ { "url": "http://wikipathways.org/index.php/Help:DataVisualizationInCytoscape", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.12688/F1000RESEARCH.4254.2", "pmid": "25254103", "pmcid": "PMC4168754", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization", "abstract": "In this paper we present the open-source WikiPathways app for Cytoscape ( http://apps.cytoscape.org/apps/wikipathways) that can be used to import biological pathways for data visualization and network analysis. WikiPathways is an open, collaborative biological pathway database that provides fully annotated pathway diagrams for manual download or through web services. The WikiPathways app allows users to load pathways in two different views: as an annotated pathway ideal for data visualization and as a simple network to perform computational analysis. An example pathway and dataset are used to demonstrate the functionality of the WikiPathways app and how they can be combined and used together with other apps. More than 3000 downloads in the first 12 months following its release in August 2013 highlight the importance and adoption of the app in the network biology field.", "date": "2014-09-11T00:00:00Z", "citationCount": 47, "authors": [ { "name": "Kutmon M." }, { "name": "Lotia S." }, { "name": "Evelo C.T." }, { "name": "Pico A.R." } ], "journal": "F1000Research" } }, { "doi": "10.1371/journal.pone.0006447", "pmid": "19649250", "pmcid": "PMC2714472", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Mining biological pathways using WikiPathways web services", "abstract": "WikiPathways is a platform for creating, updating, and sharing biological pathways [1]. Pathways can be edited and downloaded using the wiki-style website. Here we present a SOAP web service that provides programmatic access to WikiPathways that is complementary to the website. We describe the functionality that this web service offers and discuss several use cases in detail. Exposing WikiPathways through a web service opens up new ways of utilizing pathway information and assisting the community curation process. © 2009 Kelder et al.", "date": "2009-07-30T00:00:00Z", "citationCount": 99, "authors": [ { "name": "Kelder T." }, { "name": "Pico A.R." }, { "name": "Hanspers K." }, { "name": "Van Iersel M.P." }, { "name": "Evelo C." }, { "name": "Conklin B.R." } ], "journal": "PLoS ONE" } } ], "credit": [ { "name": "Martina Kutmon", "email": "mkutmon@gmail.com", "url": null, "orcidid": "http://orcid.org/0000-0002-7699-8191", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "aotamendi.1", "additionDate": "2018-09-04T10:24:29Z", "lastUpdate": "2024-11-25T14:08:30.617797Z", "editPermission": { "type": "group", "authors": [ "ChrisEvelo" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "HomozygosityMapper", "description": "A web base approach to homozygosity mapping. Users upload SNP genotype or sequencing files for analysis and detection of long homozygous stretches between affected individuals. Human, rodent and other mammals are mappable.", "homepage": "http://www.homozygositymapper.org", "biotoolsID": "homozygositymapper", "biotoolsCURIE": "biotools:homozygositymapper", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3196", "term": "Genotyping" }, { "uri": "http://edamontology.org/operation_3501", "term": "Over-representation analysis" }, { "uri": "http://edamontology.org/operation_0282", "term": "Genetic mapping" }, { "uri": "http://edamontology.org/operation_0484", "term": "SNP detection" }, { "uri": "http://edamontology.org/operation_2429", "term": "Mapping" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" }, { "uri": "http://edamontology.org/topic_0634", "term": "Pathology" }, { "uri": "http://edamontology.org/topic_3500", "term": "Animals" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "RD-connect", "Rare Disease", "ELIXIR-DE" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.homozygositymapper.org/documentation.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkp369", "pmid": "19465395", "pmcid": "PMC2703915", "type": [], "version": null, "note": null, "metadata": { "title": "HomozygosityMapper - An interactive approach to homozygosity mapping", "abstract": "Homozygosity mapping is a common method for mapping recessive traits in consanguineous families. In most studies, applications for multipoint linkage analyses are applied to determine the genomic region linked to the disease. Unfortunately, these are neither suited for very large families nor for the inclusion of tens of thousands of SNPs. Even if less than 10 000 markers are employed, such an analysis may easily last hours if not days. Here we present a web-based approach to homozygosity mapping. Our application stores marker data in a database into which users can directly upload their own SNP genotype files. Within a few minutes, the database analyses the data, detects homozygous stretches and provides an intuitive graphical interface to the results. The homozygosity in affected individuals is visualized genome-wide with the ability to zoom into single chromosomes and user-defined chromosomal regions. The software also displays the underlying genotypes in all samples. It is integrated with our candidate gene search engine, GeneDistiller, so that users can interactively determine the most promising gene. They can at any point restrict access to their data or make it public, allowing HomozygosityMapper to be used as a data repository for homozygosity-mapping studies. HomozygosityMapper is available at http://www.homozygositymapper.org/.", "date": "2009-08-04T00:00:00Z", "citationCount": 326, "authors": [ { "name": "Seelow D." }, { "name": "Schuelke M." }, { "name": "Hildebrandt F." }, { "name": "Nurnberg P." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gks487", "pmid": "22669902", "pmcid": "PMC3394249", "type": [], "version": null, "note": null, "metadata": { "title": "HomozygosityMapper2012-bridging the gap between homozygosity mapping and deep sequencing", "abstract": "Homozygosity mapping is a common method to map recessive traits in consanguineous families. To facilitate these analyses, we have developed HomozygosityMapper, a web-based approach to homozygosity mapping. HomozygosityMapper allows researchers to directly upload the genotype files produced by the major genotyping platforms as well as deep sequencing data. It detects stretches of homozygosity shared by the affected individuals and displays them graphically. Users can interactively inspect the underlying genotypes, manually refine these regions and eventually submit them to our candidate gene search engine GeneDistiller to identify the most promising candidate genes. Here, we present the new version of HomozygosityMapper. The most striking new feature is the support of Next Generation Sequencing *.vcf files as input. Upon users' requests, we have implemented the analysis of common experimental rodents as well as of important farm animals. Furthermore, we have extended the options for single families and loss of heterozygosity studies. Another new feature is the export of *.bed files for targeted enrichment of the potential disease regions for deep sequencing strategies. HomozygosityMapper also generates files for conventional linkage analyses which are already restricted to the possible disease regions, hence superseding CPU-intensive genome-wide analyses. HomozygosityMapper is freely available at http://www.homozygositymapper.org/. © 2012 The Author(s).", "date": "2012-07-01T00:00:00Z", "citationCount": 61, "authors": [ { "name": "Seelow D." }, { "name": "Schuelke M." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Support", "email": "dominik.seelow@charite.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Dominik", "additionDate": "2017-03-25T12:41:02Z", "lastUpdate": "2024-11-25T14:08:26.490635Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MutationDistiller", "description": "Make the analysis of Next-Generation Sequencing data simple. Depending on your background and interest, it offers various modes with optimised settings: Clinical (HPO), Clinical (Gene Panels), Gene Function and Basic Search.", "homepage": "https://www.mutationdistiller.org/", "biotoolsID": "mutationdistiller", "biotoolsCURIE": "biotools:mutationdistiller", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3501", "term": "Enrichment analysis" }, { "uri": "http://edamontology.org/operation_3227", "term": "Variant calling" }, { "uri": "http://edamontology.org/operation_2495", "term": "Expression analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0850", "term": "Sequence set" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "RD-connect", "Rare Disease", "ELIXIR-DE" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [ "Tools" ], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://www.mutationdistiller.org/MutationDistiller/info/documentation.html", "type": [ "User manual" ], "note": null }, { "url": "https://www.mutationdistiller.org/MutationDistiller/info/tutorial.html", "type": [ "Training material" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkz330", "pmid": "31106342", "pmcid": "PMC6602447", "type": [], "version": null, "note": null, "metadata": { "title": "MutationDistiller: User-driven identification of pathogenic DNA variants", "abstract": "MutationDistiller is a freely available online tool for user-driven analyses of Whole Exome Sequencing data. It offers a user-friendly interface aimed at clinicians and researchers, who are not necessarily bioinformaticians. MutationDistiller combines MutationTaster's pathogenicity predictions with a phenotype-based approach. Phenotypic information is not limited to symptoms included in the Human Phenotype Ontology (HPO), but may also comprise clinical diagnoses and the suspected mode of inheritance. The search can be restricted to lists of candidate genes (e.g. virtual gene panels) and by tissue-specific gene expression. The inclusion of GeneOntology (GO) and metabolic pathways facilitates the discovery of hitherto unknown disease genes. In a novel approach, we trained MutationDistiller's HPO-based prioritization on authentic genotype-phenotype sets obtained from ClinVar and found it to match or outcompete current prioritization tools in terms of accuracy. In the output, the program provides a list of potential disease mutations ordered by the likelihood of the affected genes to cause the phenotype. MutationDistiller provides links to gene-related information from various resources. It has been extensively tested by clinicians and their suggestions have been valued in many iterative cycles of revisions. The tool, a comprehensive documentation and examples are freely available at https://www.mutationdistiller.org/", "date": "2019-07-01T00:00:00Z", "citationCount": 31, "authors": [ { "name": "Hombach D." }, { "name": "Schuelke M." }, { "name": "Knierim E." }, { "name": "Ehmke N." }, { "name": "Schwarz J.M." }, { "name": "Fischer-Zirnsak B." }, { "name": "Seelow D." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": null, "email": "daniela.hombach@charite.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": null, "email": "dominik.seelow@charite.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Dominik", "additionDate": "2018-12-06T12:56:05Z", "lastUpdate": "2024-11-25T14:08:24.923182Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "UMD-Predictor", "description": "A tool that provides a combinatorial approach to identify potential pathogenic variations, that associates the following data: localization within the protein, conservation, biochemical properties of the mutant and wild-type residues, and the potential impact of the variation on mRNA.", "homepage": "http://umd-predictor.eu", "biotoolsID": "umd-predictor", "biotoolsCURIE": "biotools:umd-predictor", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3225", "term": "Variant classification" }, { "uri": "http://edamontology.org/operation_3197", "term": "Genetic variation analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3574", "term": "Human genetics" }, { "uri": "http://edamontology.org/topic_3512", "term": "Gene transcripts" }, { "uri": "http://edamontology.org/topic_0634", "term": "Pathology" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" }, { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "PHP", "JavaScript" ], "license": null, "collectionID": [ "Developed_RD-Connect", "RD-Connect", "Rare Disease", "ELIXIR-FR" ], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1002/humu.22965", "pmid": "26842889", "pmcid": "PMC5067603", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "UMD-Predictor: A High-Throughput Sequencing Compliant System for Pathogenicity Prediction of any Human cDNA Substitution", "abstract": "Whole-exome sequencing (WES) is increasingly applied to research and clinical diagnosis of human diseases. It typically results in large amounts of genetic variations. Depending on the mode of inheritance, only one or two correspond to pathogenic mutations responsible for the disease and present in affected individuals. Therefore, it is crucial to filter out nonpathogenic variants and limit downstream analysis to a handful of candidate mutations. We have developed a new computational combinatorial system UMD-Predictor (http://umd-predictor.eu) to efficiently annotate cDNA substitutions of all human transcripts for their potential pathogenicity. It combines biochemical properties, impact on splicing signals, localization in protein domains, variation frequency in the global population, and conservation through the BLOSUM62 global substitution matrix and a protein-specific conservation among 100 species. We compared its accuracy with the seven most used and reliable prediction tools, using the largest reference variation datasets including more than 140,000 annotated variations. This system consistently demonstrated a better accuracy, specificity, Matthews correlation coefficient, diagnostic odds ratio, speed, and provided the shortest list of candidate mutations for WES. Webservices allow its implementation in any bioinformatics pipeline for next-generation sequencing analysis. It could benefit to a wide range of users and applications varying from gene discovery to clinical diagnosis. UMD-Predictor is a new bionformatics system to predict the pathogenicity of human genes mutations. It is today the most efficient system and it can be integrated in any NGS analysis pipeline. It will benefit to a wide range of users and applications varying from gene discovery to clinical diagnosis.", "date": "2016-05-01T00:00:00Z", "citationCount": 97, "authors": [ { "name": "Salgado D." }, { "name": "Desvignes J.-P." }, { "name": "Rai G." }, { "name": "Blanchard A." }, { "name": "Miltgen M." }, { "name": "Pinard A." }, { "name": "Levy N." }, { "name": "Collod-Beroud G." }, { "name": "Beroud C." } ], "journal": "Human Mutation" } } ], "credit": [ { "name": "Christophe Beroud", "email": "christophe.beroud@univ-amu.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "David Salgado", "email": "david.salgado@univ-amu.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "dsalgado", "additionDate": "2017-03-05T09:42:12Z", "lastUpdate": "2024-11-25T14:07:06.419265Z", "editPermission": { "type": "group", "authors": [ "lmatalonga", "dsalgado" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "GeneCards", "description": "Database of human genes, their products, and involvement in diseases. It automatically integrates gene-centric data from ~150 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information.", "homepage": "http://www.genecards.org/", "biotoolsID": "genecards", "biotoolsCURIE": "biotools:genecards", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3761", "term": "Service discovery" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_3436", "term": "Aggregation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3574", "term": "Human genetics" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_1775", "term": "Function analysis" }, { "uri": "http://edamontology.org/topic_3366", "term": "Data integration and warehousing" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "RD-connect", "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.genecards.org/Guide", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1016/s0168-9525(97)01103-7", "pmid": "9097728", "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "GeneCards: Integrating information about genes, proteins and diseases", "abstract": "", "date": "1997-01-01T00:00:00Z", "citationCount": 538, "authors": [ { "name": "Rebhan M." }, { "name": "Chalifa-Caspi V." }, { "name": "Prilusky J." }, { "name": "Lancet D." } ], "journal": "Trends in Genetics" } }, { "doi": "10.1093/bioinformatics/18.11.1542", "pmid": "12424129", "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "GeneCards™ 2002: Towards a complete, object-oriented, human gene compendium", "abstract": "Motivation: In the post-genomic era, functional analysis of genes requires a sophisticated interdisciplinary arsenal. Comprehensive resources are challenged to provide consistently improving, state-of-the-art tools. Results: GeneCards (Rebhan et al., 1998) has made innovative strides: (a) regular updates and enhancements incorporating new genes enriched with sequences, genomic locations, cDNA assemblies, orthologies, medical information, 3D protein structures, gene expression, and focused SNP summaries; (b) restructured software using object-oriented Perl, migration to schema-driven XML, and (c) pilot studies, introducing methods to produce cards for novel and predicted genes.", "date": "2002-11-01T00:00:00Z", "citationCount": 171, "authors": [ { "name": "Safran M." }, { "name": "Solomon I." }, { "name": "Shmueli O." }, { "name": "Lapidot M." }, { "name": "Shen-Orr S." }, { "name": "Adato A." }, { "name": "Ben-Dor U." }, { "name": "Esterman N." }, { "name": "Rosen N." }, { "name": "Peter I." }, { "name": "Olender T." }, { "name": "Chalifa-Caspi V." }, { "name": "Lancet D." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/bioinformatics/14.8.656", "pmid": "9789091", "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "GeneCards: A novel functional genomics compendium with automated data mining and query reformulation support", "abstract": "Motivation: Modern biology is shifting from the 'one gene one postdoc' approach to genomic analyses that include the simultaneous monitoring of thousands of genes. The importance of efficient access to concise and integrated biomedical information to support data analysis and decision making is therefore increasing rapidly, in both academic and industrial research. However knowledge discovery in the widely scattered resources relevant for biomedical research is often a cumbersome and non-trivial task, one that requires a significant amount of training and effort. Results: To develop a model for a new type of topic-specific overview resource that provides efficient access to distributed information we designed a database called 'GeneCards'. It is a freely accessible Web resource that offers one hypertext (card) for each of the more than 7000 human genes that currently have an approved gene symbol published by the HUGO/GDB nomenclature committee. The presented information aims at giving immediate insight into current knowledge about the respective gene including a focus on its functions in health and disease. It is compiled by Perl scripts that automatically extract relevant information from several databases including SWISS-PROT, OMIM, Genatlas and GDB. Analyses of the interactions of users with the Web interface of GeneCards triggered development of easy-to-scan displays optimized for human browsing. Also, we developed algorithms that offer 'ready-to-click' query reformulation support to facilitate information retrieval and exploration. Many of the long-term users turn to GeneCards to quickly access information about the function of very large sets of genes, for example in the realm of large-scale expression studies using 'DNA chip' technology or two-dimensional protein ebectrophoresis. Availability: Freely available at http://bioinformatics.weizmann.ac.il/cards/ Contact: cards@@@bioinformatics.weizmann.ac.il.", "date": "1998-01-01T00:00:00Z", "citationCount": 347, "authors": [ { "name": "Rebhan M." }, { "name": "Chalifa-Caspi V." }, { "name": "Prilusky J." }, { "name": "Lancet D." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Support", "email": "support@lifemapsc.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-EE", "additionDate": "2017-03-30T21:27:44Z", "lastUpdate": "2024-11-25T13:46:01.243335Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Genatlas", "description": "The Genatlas database provides information on the structure, expression and function of genes, gene mutations and their consequences on diseases.", "homepage": "http://www.genatlas.org", "biotoolsID": "genatlasdb", "biotoolsCURIE": "biotools:genatlasdb", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_2495", "term": "Gene expression analysis" }, { "uri": "http://edamontology.org/operation_3672", "term": "Gene functional annotation" }, { "uri": "http://edamontology.org/operation_3436", "term": "Aggregation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0634", "term": "Pathology" }, { "uri": "http://edamontology.org/topic_3053", "term": "Genetics" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_1775", "term": "Function analysis" }, { "uri": "http://edamontology.org/topic_3366", "term": "Data integration and warehousing" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "Apache-2.0", "collectionID": [ "RD-connect", "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1016/s0764-4469(99)80021-3", "pmid": "9835018", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Genatlas database, genes and development defects", "abstract": "This article aims to illustrate the potentialities of the Genatlas database, taking, as an example, the developmental genes and their associated diseases in man. These genes belong to several categories intervening from the first stages of embryonic life. They operate at all steps of developmental cascades from extracellular signaling to activation of target genes. Quite a number of those genes have been identified in man, which are the orthologs of genes previously described in lower species. These genes are mapped and an increasing number are associated with developmental anomalies. These studies shed light on the mechanisms of congenital malformations. They disclose a large array of genetic and phenotypic heterogeneity and a high degree of complexity.", "date": "1998-10-01T00:00:00Z", "citationCount": 56, "authors": [ { "name": "Frezal J." } ], "journal": "Comptes Rendus de l'Academie des Sciences - Serie III" } } ], "credit": [ { "name": "Claude Mugnier", "email": "claude.mugnier@univ-paris5.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Marie-Liesse Chauvet", "email": "marie-liesse.chauvet@inserm.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Martine Lemerrer", "email": "martine.lemerrer@inserm.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Alexandra Caude", "email": "alexandra.caude@inserm.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-EE", "additionDate": "2017-07-04T12:34:10Z", "lastUpdate": "2024-11-25T13:45:59.920028Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "LOVD", "description": "The Leiden Open Variation Database (LOVD) provides a flexible, freely available tool for gene-centered collection and display of DNA variations. LOVD 3.0 extends this idea to also provide patient-centered data storage and storage of NGS data, even of variants outside of genes.", "homepage": "http://www.lovd.nl/3.0/home", "biotoolsID": "lovd", "biotoolsCURIE": "biotools:lovd", "version": [ "3.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_3197", "term": "Genetic variation analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3574", "term": "Human genetics" }, { "uri": "http://edamontology.org/topic_0085", "term": "Functional genomics" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "PHP" ], "license": "GPL-3.0", "collectionID": [ "NBIC", "Rare Disease", "ELIXIR-NL" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "http://www.lovd.nl/3.0/download", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.lovd.nl/3.0/docs/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1002/humu.21438", "pmid": "21520333", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "LOVD v.2.0: The next generation in gene variant databases", "abstract": "Locus-Specific DataBases (LSDBs) store information on gene sequence variation associated with human phenotypes and are frequently used as a reference by researchers and clinicians. We developed the Leiden Open-source Variation Database (LOVD) as a platform-independent Web-based LSDB-in-a-Box package. LOVD was designed to be easy to set up and maintain and follows the Human Genome Variation Society (HGVS) recommendations. Here we describe LOVD v.2.0, which adds enhanced flexibility and functionality and has the capacity to store sequence variants in multiple genes per patient. To reduce redundancy, patient and sequence variant data are stored in separate tables. Tables are linked to generate connections between sequence variant data for each gene and every patient. The dynamic structure allows database managers to add custom columns. The database structure supports fast queries and allows storage of sequence variants from high-throughput sequence analysis, as demonstrated by the X-chromosomal Mental Retardation LOVD installation. LOVD contains measures to ensure database security from unauthorized access. Currently, the LOVD Website () lists 71 public LOVD installations hosting 3,294 gene variant databases with 199,000 variants in 84,000 patients. To promote LSDB standardization and thereby database interoperability, we offer free server space and help to establish an LSDB on our Leiden server. © 2011 Wiley-Liss, Inc.", "date": "2011-05-01T00:00:00Z", "citationCount": 817, "authors": [ { "name": "Fokkema I.F.A.C." }, { "name": "Taschner P.E.M." }, { "name": "Schaafsma G.C.P." }, { "name": "Celli J." }, { "name": "Laros J.F.J." }, { "name": "den Dunnen J.T." } ], "journal": "Human Mutation" } } ], "credit": [ { "name": "ELIXIR-NL", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": null, "url": "http://www.lovd.nl/3.0/contact", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-NL", "additionDate": "2015-12-01T15:59:44Z", "lastUpdate": "2024-11-24T21:08:42.537394Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MOLGENIS", "description": "A framework for scientific data management, exploration, integration and analysis. It is adaptable to many types of scientific data and data workflows, and there are several pre-configured MOLGENIS systems for specific data types.", "homepage": "https://molgenis.org", "biotoolsID": "molgenis", "biotoolsCURIE": "biotools:molgenis", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_3436", "term": "Aggregation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3071", "term": "Data management" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R", "Java", "SQL" ], "license": "LGPL-3.0", "collectionID": [ "NBIC", "Rare Disease", "BBMRI", "BioMedBridges Tools", "ELIXIR-NL" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Interoperability" ], "elixirNode": [ "Netherlands" ], "elixirCommunity": [], "link": [], "download": [ { "url": "https://github.com/molgenis/molgenis", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://molgenis.gitbooks.io/molgenis/content/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btw155", "pmid": "27153686", "pmcid": "PMC4937195", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "MOLGENIS/connect: A system for semi-automatic integration of heterogeneous phenotype data with applications in biobanks", "abstract": "Motivation: While the size and number of biobanks, patient registries and other data collections are increasing, biomedical researchers still often need to pool data for statistical power, a task that requires time-intensive retrospective integration. Results: To address this challenge, we developed MOLGENIS/connect, a semi-automatic system to find, match and pool data from different sources. The system shortlists relevant source attributes from thousands of candidates using ontology-based query expansion to overcome variations in terminology. Then it generates algorithms that transform source attributes to a common target DataSchema. These include unit conversion, categorical value matching and complex conversion patterns (e.g. calculation of BMI). In comparison to human-experts, MOLGENIS/connect was able to auto-generate 27% of the algorithms perfectly, with an additional 46% needing only minor editing, representing a reduction in the human effort and expertise needed to pool data. Availability and Implementation: Source code, binaries and documentation are available as open-source under LGPLv3 from http://github.com/molgenis/molgenis and www.molgenis.org/connect. Contact: Supplementary information: Supplementary data are available at Bioinformatics online.", "date": "2016-07-15T00:00:00Z", "citationCount": 13, "authors": [ { "name": "Pang C." }, { "name": "Van Enckevort D." }, { "name": "De Haan M." }, { "name": "Kelpin F." }, { "name": "Jetten J." }, { "name": "Hendriksen D." }, { "name": "De Boer T." }, { "name": "Charbon B." }, { "name": "Winder E." }, { "name": "Van Der Velde K.J." }, { "name": "Doiron D." }, { "name": "Fortier I." }, { "name": "Hillege H." }, { "name": "Swertz M.A." } ], "journal": "Bioinformatics" } }, { "doi": "10.1186/1471-2105-11-s12-s12", "pmid": "21210979", "pmcid": "PMC3040526", "type": [], "version": null, "note": null, "metadata": { "title": "The MOLGENIS toolkit: Rapid prototyping of biosoftware at the push of a button", "abstract": "Background: There is a huge demand on bioinformaticians to provide their biologists with user friendly and scalable software infrastructures to capture, exchange, and exploit the unprecedented amounts of new *omics data. We here present MOLGENIS, a generic, open source, software toolkit to quickly produce the bespoke MOLecular GENetics Information Systems needed.Methods: The MOLGENIS toolkit provides bioinformaticians with a simple language to model biological data structures and user interfaces. At the push of a button, MOLGENIS' generator suite automatically translates these models into a feature-rich, ready-to-use web application including database, user interfaces, exchange formats, and scriptable interfaces. Each generator is a template of SQL, JAVA, R, or HTML code that would require much effort to write by hand. This 'model-driven' method ensures reuse of best practices and improves quality because the modeling language and generators are shared between all MOLGENIS applications, so that errors are found quickly and improvements are shared easily by a re-generation. A plug-in mechanism ensures that both the generator suite and generated product can be customized just as much as hand-written software.Results: In recent years we have successfully evaluated the MOLGENIS toolkit for the rapid prototyping of many types of biomedical applications, including next-generation sequencing, GWAS, QTL, proteomics and biobanking. Writing 500 lines of model XML typically replaces 15,000 lines of hand-written programming code, which allows for quick adaptation if the information system is not yet to the biologist's satisfaction. Each application generated with MOLGENIS comes with an optimized database back-end, user interfaces for biologists to manage and exploit their data, programming interfaces for bioinformaticians to script analysis tools in R, Java, SOAP, REST/JSON and RDF, a tab-delimited file format to ease upload and exchange of data, and detailed technical documentation. Existing databases can be quickly enhanced with MOLGENIS generated interfaces using the 'ExtractModel' procedure.Conclusions: The MOLGENIS toolkit provides bioinformaticians with a simple model to quickly generate flexible web platforms for all possible genomic, molecular and phenotypic experiments with a richness of interfaces not provided by other tools. All the software and manuals are available free as LGPLv3 open source at http://www.molgenis.org. © 2010 Swertz et al; licensee BioMed Central Ltd.", "date": "2010-12-21T00:00:00Z", "citationCount": 91, "authors": [ { "name": "Swertz M.A." }, { "name": "Dijkstra M." }, { "name": "Adamusiak T." }, { "name": "van der Velde J.K." }, { "name": "Kanterakis A." }, { "name": "Roos E.T." }, { "name": "Lops J." }, { "name": "Thorisson G.A." }, { "name": "Arends D." }, { "name": "Byelas G." }, { "name": "Muilu J." }, { "name": "Brookes A.J." }, { "name": "De Brock E.O." }, { "name": "Jansen R.C." }, { "name": "Parkinson H." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "UMC Groningen and collaborators", "email": null, "url": "http://www.rug.nl/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "BioMedBridges", "email": null, "url": "http://www.biomedbridges.eu", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Documentor" ], "note": null }, { "name": "ELIXIR-NL", "email": null, "url": "https://www.dtls.nl/elixir-nl/elixir-nl-2/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": null, "email": "molgenis-hackers@googlegroups.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Morris Swertz", "email": "m.a.swertz@rug.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": null, "email": "molgenis-support@umcg.nl", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Support" ], "note": null } ], "owner": "mswertz", "additionDate": "2015-12-02T11:00:49Z", "lastUpdate": "2024-11-24T21:08:40.375468Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "UMD", "description": "Universal Mutation Database (UMD) is a database for mutations. UMD-predictor is a tool that enables functional annotation of variants to find the relevant ones.", "homepage": "http://www.umd.be/", "biotoolsID": "umd", "biotoolsCURIE": "biotools:umd", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3202", "term": "Polymorphism detection" }, { "uri": "http://edamontology.org/operation_3196", "term": "Genotyping" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_3305", "term": "Public health and epidemiology" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "Unlicense", "collectionID": [ "RD-connect", "Rare Disease", "ELIXIR-FR" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Restricted access", "elixirPlatform": [], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.umd.be/UMD_Manual.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1002/(sici)1098-1004(200001)15:1<86::aid-humu16>3.0.co;2-4", "pmid": "10612827", "pmcid": null, "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1002/humu.20210", "pmid": "16086365", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "UMD (Universal Mutation Database): 2005 Update", "abstract": "With the completion of the Human Genome Project, our vision of human genetic diseases has changed. The cloning of new disease-causing genes can now be performed in silico, and thousands of mutations are being identified in diagnostic and research laboratories yearly. Knowledge about these mutations and their association with clinical and biological data is essential for clinicians, geneticists, and researchers. To collect and analyze these data, we developed a generic software called Universal Mutation Databases (UMD ) to create locus-specific databases. Here we report the new release (September 2004) of this freely available tool (www.umd.be), which allows the creation of LSDBs for virtually any gene and includes a large set of new analysis tools. We have implemented new features to integrate noncoding sequences, clinical data, pictures, monoclonal antibodies, and polymorphic markers (SNPs). Today the UMD retains all specifically designed tools to analyze mutations at the molecular level, as well as new sets of routines to search for genotype-phenotype correlations. We also created specific tools for infrequent mutations such as gross deletions and duplications, and deep intronic mutations. A large set of dedicated tools are now available for intronic mutations, including methods to calculate the consensus values (CVs) of potential splice sites and to search for exonic splicing enhancer (ESE) motifs. In addition, we have created specific routines to help researchers design new therapeutic strategies, such as exon skipping, aminoglycoside read-through of stop codons, or monoclonal antibody selection and epitope scanning for gene therapy. © 2005 Wiley-Liss, Inc.", "date": "2005-09-01T00:00:00Z", "citationCount": 92, "authors": [ { "name": "Beroud C." }, { "name": "Hamroun D." }, { "name": "Collod-Beroud G." }, { "name": "Boileau C." }, { "name": "Soussi T." }, { "name": "Claustres M." } ], "journal": "Human Mutation" } } ], "credit": [ { "name": "Christophe Béroud", "email": "christophe.beroud@inserm.fr", "url": "http://rd-connect.eu/contacts/christophe-beroud/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "David Salgado", "email": "david.salgado@univ-amu.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "dsalgado", "additionDate": "2017-09-26T08:01:18Z", "lastUpdate": "2024-11-24T21:05:05.832637Z", "editPermission": { "type": "group", "authors": [ "lmatalonga", "dsalgado" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "RegulationSpotter", "description": "RegulationSpotter is a web-based tool for the user-friendly annotation and interpretation of 'extratranscriptic' DNA variants. It annotates individual variants with underlying regulatory features in an intuitive way by assessing over 100 genome-wide annotations. Additionally, it calculates a score, which reflects the regulatory potential of the variant region.\nPhenotypic data can be used to focus on likely disease genes.", "homepage": "https://www.regulationspotter.org/", "biotoolsID": "RegulationSpotter", "biotoolsCURIE": "biotools:RegulationSpotter", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3225", "term": "Variant classification" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "SQL", "Perl" ], "license": null, "collectionID": [ "Rare Disease", "RD-connect", "ELIXIR-DE" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkz327", "pmid": "31106382", "pmcid": "PMC6602480", "type": [], "version": null, "note": null, "metadata": { "title": "RegulationSpotter: Annotation and interpretation of extratranscriptic DNA variants", "abstract": "RegulationSpotter is a web-based tool for the user-friendly annotation and interpretation of DNA variants located outside of protein-coding transcripts (extratranscriptic variants). It is designed for clinicians and researchers who wish to assess the potential impact of the considerable number of non-coding variants found in Whole Genome Sequencing runs. It annotates individual variants with underlying regulatory features in an intuitive way by assessing over 100 genome-wide annotations. Additionally, it calculates a score, which reflects the regulatory potential of the variant region. Its dichotomous classifications, 'functional' or 'non-functional', and a human-readable presentation of the underlying evidence allow a biologically meaningful interpretation of the score. The output shows key aspects of every variant and allows rapid access to more detailed information about its possible role in gene regulation. RegulationSpotter can either analyse single variants or complete VCF files. Variants located within protein-coding transcripts are automatically assessed by MutationTaster as well as by RegulationSpotter to account for possible intragenic regulatory effects. RegulationSpotter offers the possibility of using phenotypic data to focus on known disease genes or genomic elements interacting with them. RegulationSpotter is freely available at https://www.regulationspotter.org.", "date": "2019-07-01T00:00:00Z", "citationCount": 16, "authors": [ { "name": "Schwarz J.M." }, { "name": "Hombach D." }, { "name": "Kohler S." }, { "name": "Cooper D.N." }, { "name": "Schuelke M." }, { "name": "Seelow D." } ], "journal": "Nucleic Acids Research" } } ], "credit": [], "owner": "Dominik", "additionDate": "2019-07-19T13:24:41Z", "lastUpdate": "2024-11-24T21:04:08.016505Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Mendelian", "description": "R-package for heuristic variant filtering.", "homepage": "https://github.com/BartBroeckx/Mendelian", "biotoolsID": "mendelian", "biotoolsCURIE": "biotools:mendelian", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3227", "term": "Variant calling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0916", "term": "Gene report" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-2.0", "collectionID": [ "BIG N2N", "UGent", "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://github.com/BartBroeckx/Mendelian", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/s12859-015-0822-7", "pmid": "26597515", "pmcid": "PMC4656174", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors", "abstract": "Background: Identification of one or several disease causing variant(s) from the large collection of variants present in an individual is often achieved by the sequential use of heuristic filters. The recent development of whole exome sequencing enrichment designs for several non-model species created the need for a species-independent, fast and versatile analysis tool, capable of tackling a wide variety of standard and more complex inheritance models. With this aim, we developed \"Mendelian\", an R-package that can be used for heuristic variant filtering. Results: The R-package Mendelian offers fast and convenient filters to analyze putative variants for both recessive and dominant models of inheritance, with variable degrees of penetrance and detectance. Analysis of trios is supported. Filtering against variant databases and annotation of variants is also included. This package is not species specific and supports parallel computation. We validated this package by reanalyzing data from a whole exome sequencing experiment on intellectual disability in humans. In a second example, we identified the mutations responsible for coat color in the dog. This is the first example of whole exome sequencing without prior mapping in the dog. Conclusion: We developed an R-package that enables the identification of disease-causing variants from the long list of variants called in sequencing experiments. The software and a detailed manual are available at https://github.com/BartBroeckx/Mendelian.", "date": "2015-11-19T00:00:00Z", "citationCount": 5, "authors": [ { "name": "Broeckx B.J.G." }, { "name": "Coopman F." }, { "name": "Verhoeven G." }, { "name": "Bosmans T." }, { "name": "Gielen I." }, { "name": "Dingemanse W." }, { "name": "Saunders J.H." }, { "name": "Deforce D." }, { "name": "Van Nieuwerburgh F." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "ugent.be", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Bart J. G. Broeckx", "email": "Bart.Broeckx@UGent.be", "url": null, "orcidid": "http://orcid.org/0000-0001-6742-3911", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Filip Van Nieuwerburgh", "email": "Filip.VanNieuwerburgh@UGent.be", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Katrijn.Vannerum@ugent.be", "additionDate": "2016-05-17T10:17:53Z", "lastUpdate": "2024-11-24T20:58:29.067273Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Orphanet", "description": "Information on rare diseases and orphan drugs.", "homepage": "http://www.orpha.net/consor/cgi-bin/index.php", "biotoolsID": "orphanet", "biotoolsCURIE": "biotools:orphanet", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2800", "term": "Orpha number" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1622", "term": "Disease report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0634", "term": "Pathology" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "DRCAT", "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Data" ], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.orpha.net/consor/cgi-bin/Education_EducationTools.php?stapage=HM_BLOC_HEADER_HELP_SITEMAP&lng=EN", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1002/humu.22078", "pmid": "22422702", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Representation of rare diseases in health information systems: The orphanet approach to serve a wide range of end users", "abstract": "Rare disorders are scarcely represented in international classifications and therefore invisible in information systems. One of the major needs in health information systems and for research is to share and/or to integrate data coming from heterogeneous sources with diverse reference terminologies. ORPHANET (www.orpha.net) is a multilingual information portal on rare diseases and orphan drugs. Orphanet information system is supported by a relational database built around the concept of rare disorders. Representation of rare diseases in Orphanet encompasses levels of increasing complexity: lexical (multilingual terminology), nosological (multihierarchical classifications), relational (annotations-epidemiological data-and classes of objects-genes, manifestations, and orphan drugs-integrated in a relational database), and interoperational (semantic interoperability). Rare disorders are mapped to International Classification of Diseases (10th version), SNOMED CT, MeSH, MedDRA, and UMLS. Genes are cross-referenced with HGNC, UniProt, OMIM, and Genatlas. A suite of tools allow for extraction of massive datasets giving different views that can be used in bioinformatics to answer complex questions, intended to serve the needs of researchers and the pharmaceutical industry in developing medicinal products for rare diseases. An ontology is under development. The Orphanet nomenclature is at the crossroads of scientific data repositories and of clinical terminology standards, and is suitable to be used as a standard terminology. © 2012 Wiley Periodicals, Inc.", "date": "2012-05-01T00:00:00Z", "citationCount": 268, "authors": [ { "name": "Rath A." }, { "name": "Olry A." }, { "name": "Dhombres F." }, { "name": "Brandt M.M." }, { "name": "Urbero B." }, { "name": "Ayme S." } ], "journal": "Human Mutation" } } ], "credit": [ { "name": "Inserm US14", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": null, "url": "http://www.orpha.net/consor/cgi-bin/Directory_Contact.php?lng=EN", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "CRodwell", "additionDate": "2015-10-07T18:11:10Z", "lastUpdate": "2024-11-24T20:58:27.798370Z", "editPermission": { "type": "group", "authors": [ "lmatalonga" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ESP", "description": "NHLBI Exome Sequencing Project (ESP): Exome Variant Server (EVS) for browsing single nucleotide variation data from exome sequencing experiments mainly focused on heart, lung and blood disorders.", "homepage": "http://evs.gs.washington.edu/EVS/", "biotoolsID": "esp", "biotoolsCURIE": "biotools:esp", "version": [], "otherID": [ { "value": "RRID:SCR_012761", "type": "rrid", "version": null } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_3675", "term": "Variant filtering" }, { "uri": "http://edamontology.org/operation_3197", "term": "Genetic variation analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3676", "term": "Exome sequencing" }, { "uri": "http://edamontology.org/topic_3408", "term": "Haematology" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_0634", "term": "Pathology" }, { "uri": "http://edamontology.org/topic_3322", "term": "Respiratory medicine" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "RD-connect", "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://evs.gs.washington.edu/EVS/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/hmg/ddt384", "pmid": "23962721", "pmcid": "PMC3782073", "type": [], "version": null, "note": null, "metadata": { "title": "Databases of genomic variation and phenotypes: Existing resources and future needs", "abstract": "Massively parallel sequencing (MPS) has become an important tool for identifyingmedically significant variants in both research and the clinic. Accurate variation and genotype-phenotype databases are critical in our ability tomake sense of the vast amount of information thatMPSgenerates. The purpose of this review is to summarize the state of the art of variation and genotype-phenotype databases, how they can be used, and opportunities to improve these resources. Our working assumption is that the objective of the clinical genomicist is to identify highly penetrant variants that could explain existing disease or predict disease risk for individual patients or research participants. We have detailed how current databases contribute to this goal providing frequency data, literature reviews and predictions of causation for individual variants. For variant annotation, databases vary greatly in their ease of use, the use of standard mutation nomenclature, the comprehensiveness of the variant cataloging and the degree of expert opinion. Ultimately, we need a dynamic and comprehensive reference database of medically important variants that is easily cross referenced to exome and genome sequence data and allows for an accumulation of expert opinion.", "date": "2013-10-01T00:00:00Z", "citationCount": 49, "authors": [ { "name": "Johnston J.J." }, { "name": "Biesecker L.G." } ], "journal": "Human Molecular Genetics" } } ], "credit": [ { "name": null, "email": "evsserver@uw.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-EE", "additionDate": "2017-09-26T07:49:23Z", "lastUpdate": "2024-11-24T20:32:25.053431Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MARRVEL", "description": "Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome.", "homepage": "http://marrvel.org/", "biotoolsID": "marrvel", "biotoolsCURIE": "biotools:marrvel", "version": [], "otherID": [ { "value": "RRID:SCR_016871", "type": "rrid", "version": null } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3077", "term": "Data acquisition" }, { "uri": "http://edamontology.org/topic_3053", "term": "Genetics" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Rare Disease" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://marrvel.org/about", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1016/j.ajhg.2017.04.010", "pmid": "28502612", "pmcid": "PMC5670038", "type": [], "version": null, "note": null, "metadata": { "title": "MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome", "abstract": "One major challenge encountered with interpreting human genetic variants is the limited understanding of the functional impact of genetic alterations on biological processes. Furthermore, there remains an unmet demand for an efficient survey of the wealth of information on human homologs in model organisms across numerous databases. To efficiently assess the large volume of publically available information, it is important to provide a concise summary of the most relevant information in a rapid user-friendly format. To this end, we created MARRVEL (model organism aggregated resources for rare variant exploration). MARRVEL is a publicly available website that integrates information from six human genetic databases and seven model organism databases. For any given variant or gene, MARRVEL displays information from OMIM, ExAC, ClinVar, Geno2MP, DGV, and DECIPHER. Importantly, it curates model organism-specific databases to concurrently display a concise summary regarding the human gene homologs in budding and fission yeast, worm, fly, fish, mouse, and rat on a single webpage. Experiment-based information on tissue expression, protein subcellular localization, biological process, and molecular function for the human gene and homologs in the seven model organisms are arranged into a concise output. Hence, rather than visiting multiple separate databases for variant and gene analysis, users can obtain important information by searching once through MARRVEL. Altogether, MARRVEL dramatically improves efficiency and accessibility to data collection and facilitates analysis of human genes and variants by cross-disciplinary integration of 18 million records available in public databases to facilitate clinical diagnosis and basic research.", "date": "2017-06-01T00:00:00Z", "citationCount": 150, "authors": [ { "name": "Wang J." }, { "name": "Al-Ouran R." }, { "name": "Hu Y." }, { "name": "Kim S.-Y." }, { "name": "Wan Y.-W." }, { "name": "Wangler M.F." }, { "name": "Yamamoto S." }, { "name": "Chao H.-T." }, { "name": "Comjean A." }, { "name": "Mohr S.E." }, { "name": "Adams C.J." }, { "name": "Adams D.R." }, { "name": "Alejandro M.E." }, { "name": "Allard P." }, { "name": "Ashley E.A." }, { "name": "Azamian M.S." }, { "name": "Bacino C.A." }, { "name": "Balasubramanyam A." }, { "name": "Barseghyan H." }, { "name": "Beggs A.H." }, { "name": "Bellen H.J." }, { "name": "Bernstein J.A." }, { "name": "Bican A." }, { "name": "Bick D.P." }, { "name": "Birch C.L." }, { "name": "Boone B.E." }, { "name": "Briere L.C." }, { "name": "Brown D.M." }, { "name": "Brush M." }, { "name": "Burke E.A." }, { "name": "Burrage L.C." }, { "name": "Chao K.R." }, { "name": "Clark G.D." }, { "name": "Cogan J.D." }, { "name": "Cooper C.M." }, { "name": "Craigen W.J." }, { "name": "Davids M." }, { "name": "Dayal J.G." }, { "name": "Dell'Angelica E.C." }, { "name": "Dhar S.U." }, { "name": "Dipple K.M." }, { "name": "Donnell-Fink L.A." }, { "name": "Dorrani N." }, { "name": "Dorset D.C." }, { "name": "Draper D.D." }, { "name": "Dries A.M." }, { "name": "Eckstein D.J." }, { "name": "Emrick L.T." }, { "name": "Eng C.M." }, { "name": "Esteves C." }, { "name": "Estwick T." }, { "name": "Fisher P.G." }, { "name": "Frisby T.S." }, { "name": "Frost K." }, { "name": "Gahl W.A." }, { "name": "Gartner V." }, { "name": "Godfrey R.A." }, { "name": "Goheen M." }, { "name": "Golas G.A." }, { "name": "Goldstein D.B." }, { "name": "Gordon M.G." }, { "name": "Gould S.E." }, { "name": "Gourdine J.-P.F." }, { "name": "Graham B.H." }, { "name": "Groden C.A." }, { "name": "Gropman A.L." }, { "name": "Hackbarth M.E." }, { "name": "Haendel M." }, { "name": "Hamid R." }, { "name": "Hanchard N.A." }, { "name": "Handley L.H." }, { "name": "Hardee I." }, { "name": "Herzog M.R." }, { "name": "Holm I.A." }, { "name": "Howerton E.M." }, { "name": "Jacob H.J." }, { "name": "Jain M." }, { "name": "Jiang Y.-H." }, { "name": "Johnston J.M." }, { "name": "Jones A.L." }, { "name": "Koehler A.E." }, { "name": "Koeller D.M." }, { "name": "Kohane I.S." }, { "name": "Kohler J.N." }, { "name": "Krasnewich D.M." }, { "name": "Krieg E.L." }, { "name": "Krier J.B." }, { "name": "Kyle J.E." }, { "name": "Lalani S.R." }, { "name": "Latham L." }, { "name": "Latour Y.L." }, { "name": "Lau C.C." }, { "name": "Lazar J." }, { "name": "Lee B.H." }, { "name": "Lee H." }, { "name": "Lee P.R." }, { "name": "Levy S.E." }, { "name": "Levy D.J." }, { "name": "Lewis R.A." }, { "name": "Liebendorfer A.P." }, { "name": "Lincoln S.A." }, { "name": "Loomis C.R." }, { "name": "Loscalzo J." }, { "name": "Maas R.L." }, { "name": "Macnamara E.F." }, { "name": "MacRae C.A." }, { "name": "Maduro V.V." }, { "name": "Malicdan M.C.V." }, { "name": "Mamounas L.A." }, { "name": "Manolio T.A." }, { "name": "Markello T.C." }, { "name": "Mazur P." }, { "name": "McCarty A.J." }, { "name": "McConkie-Rosell A." }, { "name": "McCray A.T." }, { "name": "Metz T.O." }, { "name": "Might M." }, { "name": "Moretti P.M." }, { "name": "Mulvihill J.J." }, { "name": "Murphy J.L." }, { "name": "Muzny D.M." }, { "name": "Nehrebecky M.E." }, { "name": "Nelson S.F." }, { "name": "Newberry J.S." }, { "name": "Newman J.H." }, { "name": "Nicholas S.K." }, { "name": "Novacic D." }, { "name": "Orange J.S." }, { "name": "Pallais J.C." }, { "name": "Palmer C.G.S." }, { "name": "Papp J.C." }, { "name": "Pena L.D.M." }, { "name": "Phillips J.A." }, { "name": "Posey J.E." }, { "name": "Postlethwait J.H." }, { "name": "Potocki L." }, { "name": "Pusey B.N." }, { "name": "Ramoni R.B." }, { "name": "Robertson A.K." }, { "name": "Rodan L.H." }, { "name": "Rosenfeld J.A." }, { "name": "Sadozai S." }, { "name": "Schaffer K.E." }, { "name": "Schoch K." }, { "name": "Schroeder M.C." }, { "name": "Scott D.A." }, { "name": "Sharma P." }, { "name": "Shashi V." }, { "name": "Silverman E.K." }, { "name": "Sinsheimer J.S." }, { "name": "Soldatos A.G." }, { "name": "Spillmann R.C." }, { "name": "Splinter K." }, { "name": "Stoler J.M." }, { "name": "Stong N." }, { "name": "Strong K.A." }, { "name": "Sullivan J.A." }, { "name": "Sweetser D.A." }, { "name": "Thomas S.P." }, { "name": "Tifft C.J." }, { "name": "Tolman N.J." }, { "name": "Toro C." }, { "name": "Tran A.A." }, { "name": "Valivullah Z.M." }, { "name": "Vilain E." }, { "name": "Waggott D.M." }, { "name": "Wahl C.E." }, { "name": "Walley N.M." }, { "name": "Walsh C.A." }, { "name": "Wangler M.F." }, { "name": "Warburton M." }, { "name": "Ward P.A." }, { "name": "Waters K.M." }, { "name": "Webb-Robertson B.-J.M." }, { "name": "Weech A.A." }, { "name": "Westerfield M." }, { "name": "Wheeler M.T." }, { "name": "Wise A.L." }, { "name": "Wolfe L.A." }, { "name": "Worthey E.A." }, { "name": "Yamamoto S." }, { "name": "Yang Y." }, { "name": "Yu G." }, { "name": "Zornio P.A." }, { "name": "Perrimon N." }, { "name": "Liu Z." } ], "journal": "American Journal of Human Genetics" } } ], "credit": [ { "name": "Zhandong Liu", "email": "zhandonl@bcm.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "d.gabrielaitis", "additionDate": "2018-08-11T09:29:45Z", "lastUpdate": "2024-11-24T20:29:37.772750Z", "editPermission": { "type": "group", "authors": [ "ChrisEvelo" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "InterMine", "description": "Open source data warehouse built specifically for the integration and analysis of complex biological data. It enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding your own data.", "homepage": "http://www.intermine.org", "biotoolsID": "intermine", "biotoolsCURIE": "biotools:intermine", "version": [ "5.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1255", "term": "Sequence features" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2600", "term": "Pathway or network" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Web application", "Web API", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3366", "term": "Data integration and warehousing" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "R", "Ruby", "Java", "Python", "JavaScript", "Perl" ], "license": "LGPL-2.1", "collectionID": [ "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [ "Tools" ], "elixirNode": [ "UK" ], "elixirCommunity": [], "link": [ { "url": "https://registry.intermine.org", "type": [ "Software catalogue" ], "note": null }, { "url": "http://intermine.org", "type": [ "Other" ], "note": null } ], "download": [ { "url": "http://github.com/intermine/", "type": "Source code", "note": null, "version": null }, { "url": "https://repo1.maven.org/maven2/org/intermine/", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "http://intermine.org/im-docs", "type": [ "General" ], "note": null }, { "url": "http://intermine.org/intermine-user-docs", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bts577", "pmid": "23023984", "pmcid": "PMC3516146", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "InterMine: A flexible data warehouse system for the integration and analysis of heterogeneous biological data", "abstract": "InterMine is an open-source data warehouse system that facilitates the building of databases with complex data integration requirements and a need for a fast customizable query facility. Using InterMine, large biological databases can be created from a range of heterogeneous data sources, and the extensible data model allows for easy integration of new data types. The analysis tools include a flexible query builder, genomic region search and a library of 'widgets' performing various statistical analyses. The results can be exported in many commonly used formats. InterMine is a fully extensible framework where developers can add new tools and functionality. Additionally, there is a comprehensive set of web services, for which client libraries are provided in five commonly used programming languages. © The Author 2012. Published by Oxford University Press. All rights reserved.", "date": "2012-12-01T00:00:00Z", "citationCount": 202, "authors": [ { "name": "Smith R.N." }, { "name": "Aleksic J." }, { "name": "Butano D." }, { "name": "Carr A." }, { "name": "Contrino S." }, { "name": "Hu F." }, { "name": "Lyne M." }, { "name": "Lyne R." }, { "name": "Kalderimis A." }, { "name": "Rutherford K." }, { "name": "Stepan R." }, { "name": "Sullivan J." }, { "name": "Wakeling M." }, { "name": "Watkins X." }, { "name": "Micklem G." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/nar/gku301", "pmid": "24753429", "pmcid": "PMC4086141", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "InterMine: Extensive web services for modern biology", "abstract": "InterMine (www.intermine.org) is a biological data warehousing system providing extensive automatically generated and configurable RESTful web services that underpin the web interface and can be re-used in many other applications: to find and filter data; export it in a flexible and structured way; to upload, use, manipulate and analyze lists; to provide services for flexible retrieval of sequence segments, and for other statistical and analysis tools. Here we describe these features and discuss how they can be used separately or in combinations to support integrative and comparative analysis. © 2014 The Author(s).", "date": "2014-07-01T00:00:00Z", "citationCount": 94, "authors": [ { "name": "Kalderimis A." }, { "name": "Lyne R." }, { "name": "Butano D." }, { "name": "Contrino S." }, { "name": "Lyne M." }, { "name": "Heimbach J." }, { "name": "Hu F." }, { "name": "Smith R." }, { "name": "Stepan R." }, { "name": "Sullivan J." }, { "name": "Micklem G." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "University of Cambridge", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "BBSRC", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "Wellcome Trust", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "NIH", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "gen.cam.ac.uk", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "InterMine", "additionDate": "2016-02-04T15:55:00Z", "lastUpdate": "2024-11-24T20:28:49.677323Z", "editPermission": { "type": "group", "authors": [ "rachelyne" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "TopHat", "description": "Program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is built on the ultrafast short read mapping program Bowtie. A stable SAMtools version is now packaged with the program.", "homepage": "http://ccb.jhu.edu/software/tophat/index.shtml", "biotoolsID": "tophat", "biotoolsCURIE": "biotools:tophat", "version": [ "2.1.1" ], "otherID": [ { "value": "RRID:SCR_013035", "type": "rrid", "version": null } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0433", "term": "Splice site prediction" }, { "uri": "http://edamontology.org/operation_3198", "term": "Read mapping" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2749", "term": "Genome identifier" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1234", "term": "Sequence set (nucleic acid)" }, "format": [ { "uri": "http://edamontology.org/format_1930", "term": "FASTQ" }, { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2573", "term": "SAM" } ] }, { "data": { "uri": "http://edamontology.org/data_3002", "term": "Annotation track" }, "format": [ { "uri": "http://edamontology.org/format_3003", "term": "BED" } ] }, { "data": { "uri": "http://edamontology.org/data_3002", "term": "Annotation track" }, "format": [ { "uri": "http://edamontology.org/format_3003", "term": "BED" } ] } ], "note": "TopHat can find splice junctions without a reference annotation by mapping RNA-Seq reads to a reference genome. The basename of the genome index to be searched. A list of files containing reads. A list of read alignments Track of junctions reported by TopHat. Tracks of insertions and deletions reported by TopHat.", "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" }, { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "C++" ], "license": null, "collectionID": [ "galaxyPasteur", "Rare Disease", "TopHat" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/urgi_tools/tophat_parallel/1.0.0", "type": [ "Galaxy service" ], "note": null }, { "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/tophat/tophat/1.4.1.1", "type": [ "Galaxy service" ], "note": null } ], "download": [], "documentation": [ { "url": "http://ccb.jhu.edu/software/tophat/manual.shtml", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btp120", "pmid": "19289445", "pmcid": "PMC2672628", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "TopHat: Discovering splice junctions with RNA-Seq", "abstract": "Motivation: A new protocol for sequencing the messenger RNA in a cell, known as RNA-Seq, generates millions of short sequence fragments in a single run. These fragments, or 'reads', can be used to measure levels of gene expression and to identify novel splice variants of genes. However, current software for aligning RNA-Seq data to a genome relies on known splice junctions and cannot identify novel ones. TopHat is an efficient read-mapping algorithm designed to align reads from an RNA-Seq experiment to a reference genome without relying on known splice sites. Results: We mapped the RNA-Seq reads from a recent mammalian RNA-Seq experiment and recovered more than 72% of the splice junctions reported by the annotation-based software from that study, along with nearly 20 000 previously unreported junctions. The TopHat pipeline is much faster than previous systems, mapping nearly 2.2 million reads per CPU hour, which is sufficient to process an entire RNA-Seq experiment in less than a day on a standard desktop computer. We describe several challenges unique to ab initio splice site discovery from RNA-Seq reads that will require further algorithm development. © 2009 The Author(s).", "date": "2009-05-07T00:00:00Z", "citationCount": 9574, "authors": [ { "name": "Trapnell C." }, { "name": "Pachter L." }, { "name": "Salzberg S.L." } ], "journal": "Bioinformatics" } }, { "doi": "10.7490/f1000research.1114334.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Daehwan Kim", "email": "infphilo@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "seqwiki_import", "additionDate": "2017-01-13T13:16:53Z", "lastUpdate": "2024-11-24T20:26:57.822012Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "OncoVar", "description": "An integrated database and analysis platform for oncogenic driver variants in cancers.\n\nOncoVar is a platform to systematically prioritize the oncogenic ability of somatic mutations and cancer genes.", "homepage": "https://oncovar.org/", "biotoolsID": "oncovar", "biotoolsCURIE": "biotools:oncovar", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3227", "term": "Variant calling" }, { "uri": "http://edamontology.org/operation_3226", "term": "Variant prioritisation" }, { "uri": "http://edamontology.org/operation_0331", "term": "Variant effect prediction" }, { "uri": "http://edamontology.org/operation_3196", "term": "Genotyping" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_3676", "term": "Exome sequencing" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "Rare Disease" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://oncovar.org/welcome/links", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkaa1033", "pmid": "33179738", "pmcid": "PMC7778899", "type": [], "version": null, "note": null, "metadata": { "title": "OncoVar: An integrated database and analysis platform for oncogenic driver variants in cancers", "abstract": "The prevalence of neutral mutations in cancer cell population impedes the distinguishing of cancer-causing driver mutations from passenger mutations. To systematically prioritize the oncogenic ability of somatic mutations and cancer genes, we constructed a useful platform, OncoVar (https://oncovar.org/), which employed published bioinformatics algorithms and incorporated known driver events to identify driver mutations and driver genes. We identified 20 162 cancer driver mutations, 814 driver genes and 2360 pathogenic pathways with high-confidence by reanalyzing 10 769 exomes from 33 cancer types in The Cancer Genome Atlas (TCGA) and 1942 genomes from 18 cancer types in International Cancer Genome Consortium (ICGC). OncoVar provides four points of view, 'Mutation', 'Gene', 'Pathway' and 'Cancer', to help researchers to visualize the relationships between cancers and driver variants. Importantly, identification of actionable driver alterations provides promising druggable targets and repurposing opportunities of combinational therapies. OncoVar provides a user-friendly interface for browsing, searching and downloading somatic driver mutations, driver genes and pathogenic pathways in various cancer types. This platform will facilitate the identification of cancer drivers across individual cancer cohorts and helps to rank mutations or genes for better decision-making among clinical oncologists, cancer researchers and the broad scientific community interested in cancer precision medicine.", "date": "2021-01-08T00:00:00Z", "citationCount": 56, "authors": [ { "name": "Wang T." }, { "name": "Ruan S." }, { "name": "Zhao X." }, { "name": "Shi X." }, { "name": "Teng H." }, { "name": "Zhong J." }, { "name": "You M." }, { "name": "Xia K." }, { "name": "Sun Z." }, { "name": "Mao F." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Kun Xia", "email": "xiakun@sklmg.edu.cn", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Zhongsheng Sun", "email": "sunzs@biols.ac.cn", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Fengbiao Mao", "email": "maofengbiao08@163.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "owner": "Niclaskn", "additionDate": "2021-01-18T11:45:16Z", "lastUpdate": "2024-11-24T20:24:06.547174Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "PredictSNP2", "description": "A consensus classifier that combines five of the top performing tools (CADD, DANN, FATHMM, FunSeq2 and GWAVA) for the evaluation of pathogenic effect of SNPs within the human genome. The obtained results are provided together with annotations extracted from dbSNP, GenBank, Clinvar, OMIM, RegulomeDB, HaploReg, UCSC and Ensembl databases.", "homepage": "https://loschmidt.chemi.muni.cz/predictsnp2", "biotoolsID": "predictsnp2", "biotoolsCURIE": "biotools:predictsnp2", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3672", "term": "Gene functional annotation" }, { "uri": "http://edamontology.org/operation_3225", "term": "Variant classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3019", "term": "GVF" }, { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" }, { "uri": "http://edamontology.org/format_3508", "term": "PDF" } ] } ], "note": "VCF file containing scores and PDF file containing scores and database links", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" }, { "uri": "http://edamontology.org/topic_2533", "term": "DNA mutation" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "JavaScript", "Java" ], "license": "Proprietary", "collectionID": [ "Czech Republic", "Rare Disease", "ELIXIR-CZ" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [], "link": [], "download": [ { "url": "https://loschmidt.chemi.muni.cz/peg/software/predictsnp2-standalone/", "type": "Downloads page", "note": null, "version": "1.0" } ], "documentation": [ { "url": "https://loschmidt.chemi.muni.cz/predictsnp2/docs/userguide.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pcbi.1004962", "pmid": "27224906", "pmcid": "PMC4880439", "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions", "abstract": "An important message taken from human genome sequencing projects is that the human population exhibits approximately 99.9% genetic similarity. Variations in the remaining parts of the genome determine our identity, trace our history and reveal our heritage. The precise delineation of phenotypically causal variants plays a key role in providing accurate personalized diagnosis, prognosis, and treatment of inherited diseases. Several computational methods for achieving such delineation have been reported recently. However, their ability to pinpoint potentially deleterious variants is limited by the fact that their mechanisms of prediction do not account for the existence of different categories of variants. Consequently, their output is biased towards the variant categories that are most strongly represented in the variant databases. Moreover, most such methods provide numeric scores but not binary predictions of the deleteriousness of variants or confidence scores that would be more easily understood by users. We have constructed three datasets covering different types of disease-related variants, which were divided across five categories: (i) regulatory, (ii) splicing, (iii) missense, (iv) synonymous, and (v) nonsense variants. These datasets were used to develop category-optimal decision thresholds and to evaluate six tools for variant prioritization: CADD, DANN, FATHMM, FitCons, FunSeq2 and GWAVA. This evaluation revealed some important advantages of the category-based approach. The results obtained with the five best-performing tools were then combined into a consensus score. Additional comparative analyses showed that in the case of missense variations, protein-based predictors perform better than DNA sequence-based predictors. A user-friendly web interface was developed that provides easy access to the five tools’ predictions, and their consensus scores, in a user-understandable format tailored to the specific features of different categories of variations. To enable comprehensive evaluation of variants, the predictions are complemented with annotations from eight databases. The web server is freely available to the community at http://loschmidt.chemi.muni.cz/predictsnp2.", "date": "2016-05-01T00:00:00Z", "citationCount": 143, "authors": [ { "name": "Bendl J." }, { "name": "Musil M." }, { "name": "Stourac J." }, { "name": "Zendulka J." }, { "name": "Damborsky J." }, { "name": "Brezovsky J." } ], "journal": "PLoS Computational Biology" } } ], "credit": [ { "name": "Jaroslav Bendl", "email": "jaroslav.bendl@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0001-9989-2720", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Jan Stourac", "email": "stourac.jan@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0003-3139-3700", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Support" ], "note": null }, { "name": "Milos Musil", "email": "xmusil46@stud.fit.vutbr.cz", "url": null, "orcidid": "https://orcid.org/0000-0001-9373-7930", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Jan Brezovsky", "email": "brezovsky@mail.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0001-9677-5078", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Jiri Damborsky", "email": "1441@mail.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0002-7848-8216", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Eric D. Wieben", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Jaroslav Zendulka", "email": "zendulka@fit.vut.cz", "url": null, "orcidid": "https://orcid.org/0000-0001-8718-7493", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Antonin Pavelka", "email": "99207@mail.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Loschmidt Laboratories", "email": null, "url": "https://loschmidt.chemi.muni.cz/peg/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Masaryk University, Brno, Czech Republic", "email": null, "url": "https://www.muni.cz/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "International Centre for Clinical Research, Brno, Czech Republic", "email": null, "url": "https://www.fnusa-icrc.org/en/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Brno University of Technology, Brno, Czech Republic", "email": null, "url": "https://www.vutbr.cz/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "ELIXIR-CZ", "email": null, "url": "https://www.elixir-czech.cz/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [ "Provider" ], "note": null }, { "name": "PredictSNP team", "email": "predictsnp@sci.muni.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "European Regional Development Fund", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "European Social Fund", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "Grant Agency of the Czech Republic", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "Ministry of Education of the Czech Republic", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null }, { "name": "Brno University of Technology", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": null } ], "owner": "Loschmidt Laboratories", "additionDate": "2016-06-30T09:32:44Z", "lastUpdate": "2024-11-24T20:23:08.475881Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PredictSNP", "description": "A consensus classifier that combines six of the top performing tools for the prediction of the effects of mutation on protein function. The obtained results are provided together with annotations extracted from the Protein Mutant Database and the UniProt database.", "homepage": "https://loschmidt.chemi.muni.cz/predictsnp1", "biotoolsID": "predictsnp", "biotoolsCURIE": "biotools:predictsnp", "version": [ "1.0" ], "otherID": [], "relation": [ { "biotoolsID": "mapp", "type": "uses" }, { "biotoolsID": "nssnpanalyzer", "type": "uses" }, { "biotoolsID": "panther", "type": "uses" }, { "biotoolsID": "phd-snp", "type": "uses" }, { "biotoolsID": "polyphen", "type": "uses" }, { "biotoolsID": "polyphen-2", "type": "uses" }, { "biotoolsID": "sift", "type": "uses" }, { "biotoolsID": "snap", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0331", "term": "Variant effect prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2974", "term": "Protein sequence (raw)" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1277", "term": "Protein features" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_2291", "term": "UniProt ID" }, "format": [] } ], "note": "Prediction of the effect of amino acid substitution on protein function", "cmd": null } ], "toolType": [ "Command-line tool", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" }, { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" }, { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_3053", "term": "Genetics" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "JavaScript", "Java", "Python" ], "license": "Proprietary", "collectionID": [ "Czech Republic", "Rare Disease", "ELIXIR-CZ" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Czech Republic" ], "elixirCommunity": [], "link": [], "download": [ { "url": "https://loschmidt.chemi.muni.cz/predictsnp1/docs/predictsnp-1.0.tar.gz", "type": "Binaries", "note": null, "version": null } ], "documentation": [ { "url": "https://loschmidt.chemi.muni.cz/predictsnp1/docs/USER_GUIDE.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1371/journal.pcbi.1003440", "pmid": "24453961", "pmcid": "PMC3894168", "type": [ "Primary" ], "version": "1.0", "note": null, "metadata": { "title": "PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations", "abstract": "Single nucleotide variants represent a prevalent form of genetic variation. Mutations in the coding regions are frequently associated with the development of various genetic diseases. Computational tools for the prediction of the effects of mutations on protein function are very important for analysis of single nucleotide variants and their prioritization for experimental characterization. Many computational tools are already widely employed for this purpose. Unfortunately, their comparison and further improvement is hindered by large overlaps between the training datasets and benchmark datasets, which lead to biased and overly optimistic reported performances. In this study, we have constructed three independent datasets by removing all duplicities, inconsistencies and mutations previously used in the training of evaluated tools. The benchmark dataset containing over 43,000 mutations was employed for the unbiased evaluation of eight established prediction tools: MAPP, nsSNPAnalyzer, PANTHER, PhD-SNP, PolyPhen-1, PolyPhen-2, SIFT and SNAP. The six best performing tools were combined into a consensus classifier PredictSNP, resulting into significantly improved prediction performance, and at the same time returned results for all mutations, confirming that consensus prediction represents an accurate and robust alternative to the predictions delivered by individual tools. A user-friendly web interface enables easy access to all eight prediction tools, the consensus classifier PredictSNP and annotations from the Protein Mutant Database and the UniProt database. The web server and the datasets are freely available to the academic community at http://loschmidt.chemi.muni.cz/predictsnp. © 2014 Bendl et al.", "date": "2014-01-01T00:00:00Z", "citationCount": 595, "authors": [ { "name": "Bendl J." }, { "name": "Stourac J." }, { "name": "Salanda O." }, { "name": "Pavelka A." }, { "name": "Wieben E.D." }, { "name": "Zendulka J." }, { "name": "Brezovsky J." }, { "name": "Damborsky J." } ], "journal": "PLoS Computational Biology" } } ], "credit": [ { "name": "Jaroslav Bendl", "email": "jaroslav.bendl@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0001-9989-2720", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Jan Stourac", "email": "stourac.jan@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0003-3139-3700", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Support" ], "note": null }, { "name": "Ondrej Salanda", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Jan Brezovsky", "email": "brezovsky@mail.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0001-9677-5078", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Jiri Damborsky", "email": "1441@mail.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0002-7848-8216", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Eric D. 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"elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/jielab/pageant/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/nar/gkab1245", "pmid": "34928375", "pmcid": "PMC9023285", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "PAGEANT: Personal access to genome and analysis of natural traits", "abstract": "GWASs have identified numerous genetic variants associated with a wide variety of diseases, yet despite the wide availability of genetic testing the insights that would enhance the interpretability of these results are not widely available to members of the public. As a proof of concept and demonstration of technological feasibility, we developed PAGEANT (Personal Access to Genome & Analysis of Natural Traits), usable through Graphical User Interface or command line-based version, aiming to serve as a protocol and prototype that guides the overarching design of genetic reporting tools. PAGEANT is structured across five core modules, summarized by five Qs: (i) quality assurance of the genetic data; (ii) qualitative assessment of genetic characteristics; (iii) quantitative assessment of health risk susceptibility based on polygenic risk scores and population reference; (iv) query of third-party variant databases (e.g. ClinVAR and PharmGKB) and (v) quick Response code of genetic variants of interest. Literature review was conducted to compare PAGEANT with academic and industry tools. For 2504 genomes made publicly available through the 1000 Genomes Project, we derived their genomic characteristics for a suite of qualitative and quantitative traits. One exemplary trait is susceptibility to COVID-19, based on the most up-to-date scientific findings reported.", "date": "2022-04-22T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Huang J." }, { "name": "Liang Z.-S." }, { "name": "Pallotti S." }, { "name": "Ranson J.M." }, { "name": "Llewellyn D.J." }, { "name": "Zheng Z.-J." }, { "name": "King D.A." }, { "name": "Zhou Q." }, { "name": "Zheng H." }, { "name": "Napolioni V." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "valerio.napolioni@unicam.it", "email": "valerio.napolioni@unicam.it", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Jie Huang", "email": "jiehuang001@pku.edu.cn", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Kigaard", "additionDate": "2022-01-17T09:10:55.154485Z", "lastUpdate": "2024-11-24T20:12:59.248495Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "WaveQTL", "description": "Wavelet-based genetic association analysis of functional phenotypes arising from high-throughput sequencing assays", "homepage": "https://github.com/heejungshim/WaveQTL", "biotoolsID": "waveqtl", "biotoolsCURIE": "biotools:waveqtl", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0282", "term": "Genetic mapping" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3169", "term": "ChIP-seq" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" }, { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" } ], "operatingSystem": [ "Linux" ], "language": [ "R", "C++" ], "license": "GPL-3.0", "collectionID": [ "Animal and Crop Genomics", "Rare Disease" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://github.com/heejungshim/WaveQTL", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1214/14-aoas776", "pmid": "29399242", "pmcid": "PMC5795621", "type": [], "version": null, "note": null, "metadata": { "title": "Wavelet-based genetic association analysis of functional phenotypes arising from high-throughput sequencing assays", "abstract": "Understanding how genetic variants influence cellular-level processes is an important step toward understanding how they influence important organismal-level traits, or “phenotypes,” including human disease susceptibility. To this end, scientists are undertaking large-scale genetic association studies that aim to identify genetic variants associated with molecular and cellular phenotypes, such as gene expression, transcription factor binding, or chromatin accessibility. These studies use high-throughput sequencing assays (e.g., RNA-seq, ChIP-seq, DNase-seq) to obtain high-resolution data on how the traits vary along the genome in each sample. However, typical association analyses fail to exploit these high-resolution measurements, instead aggregating the data at coarser resolutions, such as genes, or windows of fixed length. Here we develop and apply statistical methods that better exploit the high-resolution data. The key idea is to treat the sequence data as measuring an underlying “function” that varies along the genome, and then, building on wavelet-based methods for functional data analysis, test for association between genetic variants and the underlying function. Applying these methods to identify genetic variants associated with chromatin accessibility (dsQTLs), we find that they identify substantially more associations than a simpler window-based analysis, and in total we identify 772 novel dsQTLs not identified by the original analysis.", "date": "2015-06-01T00:00:00Z", "citationCount": 18, "authors": [ { "name": "Shim H." }, { "name": "Stephens M." } ], "journal": "Annals of Applied Statistics" } }, { "doi": "10.1186/s12864-021-07582-6", "pmid": "33932983", "pmcid": "PMC8088671", "type": [], "version": null, "note": null, "metadata": { "title": "A fast wavelet-based functional association analysis replicates several susceptibility loci for birth weight in a Norwegian population", "abstract": "Background: Birth weight (BW) is one of the most widely studied anthropometric traits in humans because of its role in various adult-onset diseases. The number of loci associated with BW has increased dramatically since the advent of whole-genome screening approaches such as genome-wide association studies (GWASes) and meta-analyses of GWASes (GWAMAs). To further contribute to elucidating the genetic architecture of BW, we analyzed a genotyped Norwegian dataset with information on child’s BW (N=9,063) using a slightly modified version of a wavelet-based method by Shim and Stephens (2015) called WaveQTL. Results: WaveQTL uses wavelet regression for regional testing and offers a more flexible functional modeling framework compared to conventional GWAS methods. To further improve WaveQTL, we added a novel feature termed “zooming strategy” to enhance the detection of associations in typically small regions. The modified WaveQTL replicated five out of the 133 loci previously identified by the largest GWAMA of BW to date by Warrington et al. (2019), even though our sample size was 26 times smaller than that study and 18 times smaller than the second largest GWAMA of BW by Horikoshi et al. (2016). In addition, the modified WaveQTL performed better in regions of high LD between SNPs. Conclusions: This study is the first adaptation of the original WaveQTL method to the analysis of genome-wide genotypic data. Our results highlight the utility of the modified WaveQTL as a complementary tool for identifying loci that might escape detection by conventional genome-wide screening methods due to power issues. An attractive application of the modified WaveQTL would be to select traits from various public GWAS repositories to investigate whether they might benefit from a second analysis.", "date": "2021-12-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Denault W.R.P." }, { "name": "Romanowska J." }, { "name": "Helgeland O." }, { "name": "Jacobsson B." }, { "name": "Gjessing H.K." }, { "name": "Jugessur A." } ], "journal": "BMC Genomics" } } ], "credit": [ { "name": null, "email": null, "url": "https://groups.google.com/forum/?hl=en#!forum/waveqtlusers", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "admin", "additionDate": "2017-08-20T15:59:18Z", "lastUpdate": "2024-11-24T20:12:56.535070Z", "editPermission": { "type": "group", "authors": [ "animalandcropgenomics" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BridgeDbR", "description": "Use BridgeDb functions and load identifier mapping databases in R.", "homepage": "http://bioconductor.org/packages/release/bioc/html/BridgeDbR.html", "biotoolsID": "bridgedbr", "biotoolsCURIE": "biotools:bridgedbr", "version": [ "1.8.0", "2.4.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_1812", "term": "Loading" }, { "uri": "http://edamontology.org/operation_3282", "term": "ID mapping" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1025", "term": "Gene identifier" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_2108", "term": "Reaction ID" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0989", "term": "Protein identifier" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_1086", "term": "Compound identifier" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1025", "term": "Gene identifier" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_2108", "term": "Reaction ID" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_0989", "term": "Protein identifier" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_1086", "term": "Compound identifier" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_3345", "term": "Data identity and mapping" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "R" ], "license": "GPL-3.0", "collectionID": [ "Rare Disease", "BridgeDb", "BioConductor" ], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [ "Interoperability" ], "elixirNode": [ "Netherlands" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/bridgedb/BridgeDb", "type": [ "Mirror" ], "note": null }, { "url": "https://github.com/BiGCAT-UM/bridgedb-r", "type": [ "Mirror" ], "note": null } ], "download": [ { "url": "http://bioconductor/packages/release/bioc/src/contrib/BridgeDbR_1.8.0.tar.gz", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://bioconductor.org/packages/release/bioc/html/BridgeDbR.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1186/s12859-015-0708-8", "pmid": "26298294", "pmcid": "PMC4546821", "type": [ "Review" ], "version": null, "note": null, "metadata": { "title": "Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment", "abstract": "Background: Biological pathways are descriptive diagrams of biological processes widely used for functional analysis of differentially expressed genes or proteins. Primary data analysis, such as quality control, normalisation, and statistical analysis, is often performed in scripting languages like R, Perl, and Python. Subsequent pathway analysis is usually performed using dedicated external applications. Workflows involving manual use of multiple environments are time consuming and error prone. Therefore, tools are needed that enable pathway analysis directly within the same scripting languages used for primary data analyses. Existing tools have limited capability in terms of available pathway content, pathway editing and visualisation options, and export file formats. Consequently, making the full-fledged pathway analysis tool PathVisio available from various scripting languages will benefit researchers. Results: We developed PathVisioRPC, an XMLRPC interface for the pathway analysis software PathVisio. PathVisioRPC enables creating and editing biological pathways, visualising data on pathways, performing pathway statistics, and exporting results in several image formats in multiple programming environments. We demonstrate PathVisioRPC functionalities using examples in Python. Subsequently, we analyse a publicly available NCBI GEO gene expression dataset studying tumour bearing mice treated with cyclophosphamide in R. The R scripts demonstrate how calls to existing R packages for data processing and calls to PathVisioRPC can directly work together. To further support R users, we have created RPathVisio simplifying the use of PathVisioRPC in this environment. We have also created a pathway module for the microarray data analysis portal ArrayAnalysis.org that calls the PathVisioRPC interface to perform pathway analysis. This module allows users to use PathVisio functionality online without having to download and install the software and exemplifies how the PathVisioRPC interface can be used by data analysis pipelines for functional analysis of processed genomics data. Conclusions: PathVisioRPC enables data visualisation and pathway analysis directly from within various analytical environments used for preliminary analyses. It supports the use of existing pathways from WikiPathways or pathways created using the RPC itself. It also enables automation of tasks performed using PathVisio, making it useful to PathVisio users performing repeated visualisation and analysis tasks. PathVisioRPC is freely available for academic and commercial use at http://projects.bigcat.unimaas.nl/pathvisiorpc.", "date": "2015-08-23T00:00:00Z", "citationCount": 13, "authors": [ { "name": "Bohler A." }, { "name": "Eijssen L.M.T." }, { "name": "van Iersel M.P." }, { "name": "Leemans C." }, { "name": "Willighagen E.L." }, { "name": "Kutmon M." }, { "name": "Jaillard M." }, { "name": "Evelo C.T." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Egon Willighagen", "email": "egon.willighagen@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "egonw", "additionDate": "2017-01-17T14:55:09Z", "lastUpdate": "2024-11-24T20:10:32.370453Z", "editPermission": { "type": "group", "authors": [ "ChrisEvelo", "LanfearJ" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "WikiPathways", "description": "WikiPathways is a database of biological pathways maintained by and for the scientific community.", "homepage": "http://www.wikipathways.org", "biotoolsID": "wikipathways", "biotoolsCURIE": "biotools:wikipathways", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_2497", "term": "Pathway or network analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0842", "term": "Identifier" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": "getPathway", "cmd": null } ], "toolType": [ "Web API", "Web application", "Database portal", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "JavaScript" ], "license": "Apache-2.0", "collectionID": [ "RD-connect", "Rare Disease", "WikiPathways", "BIGCAT-UM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Netherlands" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/wikipathways/pvjs", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://www.wikipathways.org/index.php/WikiPathways", "type": [ "General" ], "note": null }, { "url": "http://www.wikipathways.org/index.php/Help:WikiPathways_Webservice", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkv1024", "pmid": "26481357", "pmcid": "PMC4702772", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "WikiPathways: Capturing the full diversity of pathway knowledge", "abstract": "WikiPathways (http://www.wikipathways.org) is an open, collaborative platform for capturing and disseminating models of biological pathways for data visualization and analysis. Since our last NAR update, 4 years ago, WikiPathways has experienced massive growth in content, which continues to be contributed by hundreds of individuals each year. New aspects of the diversity and depth of the collected pathways are described from the perspective of researchers interested in using pathway information in their studies. We provide updates on extensions and services to support pathway analysis and visualization via popular standalone tools, i.e. PathVisio and Cytoscape, web applications and common programming environments. We introduce the Quick Edit feature for pathway authors and curators, in addition to new means of publishing pathways and maintaining custom pathway collections to serve specific research topics and communities. In addition to the latest milestones in our pathway collection and curation effort, we also highlight the latest means to access the content as publishable figures, as standard data files, and as linked data, including bulk and programmatic access.", "date": "2016-01-01T00:00:00Z", "citationCount": 325, "authors": [ { "name": "Kutmon M." }, { "name": "Riutta A." }, { "name": "Nunes N." }, { "name": "Hanspers K." }, { "name": "Willighagen E.L." }, { "name": "Bohler A." }, { "name": "Melius J." }, { "name": "Waagmeester A." }, { "name": "Sinha S.R." }, { "name": "Miller R." }, { "name": "Coort S.L." }, { "name": "Cirillo E." }, { "name": "Smeets B." }, { "name": "Evelo C.T." }, { "name": "Pico A.R." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1371/journal.pone.0006447", "pmid": "19649250", "pmcid": "PMC2714472", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Mining biological pathways using WikiPathways web services", "abstract": "WikiPathways is a platform for creating, updating, and sharing biological pathways [1]. Pathways can be edited and downloaded using the wiki-style website. Here we present a SOAP web service that provides programmatic access to WikiPathways that is complementary to the website. We describe the functionality that this web service offers and discuss several use cases in detail. Exposing WikiPathways through a web service opens up new ways of utilizing pathway information and assisting the community curation process. © 2009 Kelder et al.", "date": "2009-07-30T00:00:00Z", "citationCount": 99, "authors": [ { "name": "Kelder T." }, { "name": "Pico A.R." }, { "name": "Hanspers K." }, { "name": "Van Iersel M.P." }, { "name": "Evelo C." }, { "name": "Conklin B.R." } ], "journal": "PLoS ONE" } }, { "doi": "10.1093/nar/gkaa1024", "pmid": "33211851", "pmcid": "PMC7779061", "type": [], "version": null, "note": null, "metadata": { "title": "WikiPathways: Connecting communities", "abstract": "WikiPathways (https://www.wikipathways.org) is a biological pathway database known for its collaborative nature and open science approaches. With the core idea of the scientific community developing and curating biological knowledge in pathway models, WikiPathways lowers all barriers for accessing and using its content. Increasingly more content creators, initiatives, projects and tools have started using WikiPathways. Central in this growth and increased use of WikiPathways are the various communities that focus on particular subsets of molecular pathways such as for rare diseases and lipid metabolism. Knowledge from published pathway figures helps prioritize pathway development, using optical character and named entity recognition. We show the growth of WikiPathways over the last three years, highlight the new communities and collaborations of pathway authors and curators, and describe various technologies to connect to external resources and initiatives. The road toward a sustainable, community-driven pathway database goes through integration with other resources such as Wikidata and allowing more use, curation and redistribution of WikiPathways content.", "date": "2021-01-08T00:00:00Z", "citationCount": 492, "authors": [ { "name": "Martens M." }, { "name": "Ammar A." }, { "name": "Riutta A." }, { "name": "Waagmeester A." }, { "name": "Slenter D.N." }, { "name": "Hanspers K." }, { "name": "Miller R.A." }, { "name": "Digles D." }, { "name": "Lopes E.N." }, { "name": "Ehrhart F." }, { "name": "Dupuis L.J." }, { "name": "Winckers L.A." }, { "name": "Coort S.L." }, { "name": "Willighagen E.L." }, { "name": "Evelo C.T." }, { "name": "Pico A.R." }, { "name": "Kutmon M." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkx1064", "pmid": "29136241", "pmcid": "PMC5753270", "type": [], "version": null, "note": null, "metadata": { "title": "WikiPathways: A multifaceted pathway database bridging metabolomics to other omics research", "abstract": "WikiPathways (wikipathways.org) captures the collective knowledge represented in biological pathways. By providing a database in a curated, machine readable way, omics data analysis and visualization is enabled. WikiPathways and other pathway databases are used to analyze experimental data by research groups in many fields. Due to the open and collaborative nature of the WikiPathways platform, our content keeps growing and is getting more accurate, making WikiPathways a reliable and rich pathway database. Previously, however, the focus was primarily on genes and proteins, leaving many metabolites with only limited annotation. Recent curation efforts focused on improving the annotation of metabolism and metabolic pathways by associating unmapped metabolites with database identifiers and providing more detailed interaction knowledge. Here, we report the outcomes of the continued growth and curation efforts, such as a doubling of the number of annotated metabolite nodes in WikiPathways. Furthermore, we introduce an OpenAPI documentation of our web services and the FAIR (Findable, Accessible, Interoperable and Reusable) annotation of resources to increase the interoperability of the knowledge encoded in these pathways and experimental omics data. New search options, monthly downloads, more links to metabolite databases, and new portals make pathway knowledge more effortlessly accessible to individual researchers and research communities.", "date": "2018-01-01T00:00:00Z", "citationCount": 620, "authors": [ { "name": "Slenter D.N." }, { "name": "Kutmon M." }, { "name": "Hanspers K." }, { "name": "Riutta A." }, { "name": "Windsor J." }, { "name": "Nunes N." }, { "name": "Melius J." }, { "name": "Cirillo E." }, { "name": "Coort S.L." }, { "name": "DIgles D." }, { "name": "Ehrhart F." }, { "name": "Giesbertz P." }, { "name": "Kalafati M." }, { "name": "Martens M." }, { "name": "Miller R." }, { "name": "Nishida K." }, { "name": "Rieswijk L." }, { "name": "Waagmeester A." }, { "name": "Eijssen L.M.T." }, { "name": "Evelo C.T." }, { "name": "Pico A.R." }, { "name": "Willighagen E.L." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Martina Kutmon", "email": "martina.kutmon@maastrichtuniversity.nl", "url": "http://www.wikipathways.org/index.php/WikiPathways:About", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Alexander R. Pico", "email": "apico@gladstone.ucsf.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ChrisEvelo", "additionDate": "2017-07-20T18:33:51Z", "lastUpdate": "2024-11-24T20:10:27.500076Z", "editPermission": { "type": "group", "authors": [ "ChrisEvelo", "egonw" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "StrVCTVRE", "description": "Method that predicts the pathogenicity of deletions and duplications that affect one or more exons.", "homepage": "https://strvctvre.berkeley.edu/", "biotoolsID": "strvctvre", "biotoolsCURIE": "biotools:strvctvre", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3226", "term": "Variant prioritisation" }, { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" }, { "uri": "http://edamontology.org/format_3003", "term": "BED" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3175", "term": "Structural variation" }, { "uri": "http://edamontology.org/topic_3958", "term": "Copy number variation" }, { "uri": "http://edamontology.org/topic_3574", "term": "Human genetics" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" }, { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "MIT", "collectionID": [ "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/andrewSharo/StrVCTVRE", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/andrewSharo/StrVCTVRE", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://strvctvre.berkeley.edu/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1016/j.ajhg.2021.12.007", "pmid": "35032432", "pmcid": "PMC8874149", "type": [], "version": null, "note": null, "metadata": { "title": "StrVCTVRE: A supervised learning method to predict the pathogenicity of human genome structural variants", "abstract": "Whole-genome sequencing resolves many clinical cases where standard diagnostic methods have failed. However, at least half of these cases remain unresolved after whole-genome sequencing. Structural variants (SVs; genomic variants larger than 50 base pairs) of uncertain significance are the genetic cause of a portion of these unresolved cases. As sequencing methods using long or linked reads become more accessible and SV detection algorithms improve, clinicians and researchers are gaining access to thousands of reliable SVs of unknown disease relevance. Methods to predict the pathogenicity of these SVs are required to realize the full diagnostic potential of long-read sequencing. To address this emerging need, we developed StrVCTVRE to distinguish pathogenic SVs from benign SVs that overlap exons. In a random forest classifier, we integrated features that capture gene importance, coding region, conservation, expression, and exon structure. We found that features such as expression and conservation are important but are absent from SV classification guidelines. We leveraged multiple resources to construct a size-matched training set of rare, putatively benign and pathogenic SVs. StrVCTVRE performs accurately across a wide SV size range on independent test sets, which will allow clinicians and researchers to eliminate about half of SVs from consideration while retaining a 90% sensitivity. We anticipate clinicians and researchers will use StrVCTVRE to prioritize SVs in probands where no SV is immediately compelling, empowering deeper investigation into novel SVs to resolve cases and understand new mechanisms of disease. StrVCTVRE runs rapidly and is publicly available.", "date": "2022-02-03T00:00:00Z", "citationCount": 23, "authors": [ { "name": "Sharo A.G." }, { "name": "Hu Z." }, { "name": "Sunyaev S.R." }, { "name": "Brenner S.E." } ], "journal": "American Journal of Human Genetics" } } ], "credit": [ { "name": "Andrew Sharo", "email": "sharo@compbio.berkeley.edu", "url": "https://andrewsharo.com/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "andrewSharo", "additionDate": "2022-04-12T23:41:24.255364Z", "lastUpdate": "2024-11-24T20:10:20.152356Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CADD", "description": "Combined Annotation Dependent Depletion (CADD) - tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome.", "homepage": "http://cadd.gs.washington.edu/", "biotoolsID": "cadd_phred", "biotoolsCURIE": "biotools:cadd_phred", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3226", "term": "Variant prioritisation" }, { "uri": "http://edamontology.org/operation_2436", "term": "Gene-set enrichment analysis" }, { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_2269", "term": "Statistics and probability" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3574", "term": "Human genetics" }, { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "Unlicense", "collectionID": [ "RD-connect", "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://cadd.gs.washington.edu/download", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://cadd.gs.washington.edu/info", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1038/ng.2892", "pmid": "24487276", "pmcid": "PMC3992975", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "A general framework for estimating the relative pathogenicity of human genetic variants", "abstract": "Current methods for annotating and interpreting human genetic variation tend to exploit a single information type (for example, conservation) and/or are restricted in scope (for example, to missense changes). Here we describe Combined Annotation-Dependent Depletion (CADD), a method for objectively integrating many diverse annotations into a single measure (C score) for each variant. We implement CADD as a support vector machine trained to differentiate 14.7 million high-frequency human-derived alleles from 14.7 million simulated variants. We precompute C scores for all 8.6 billion possible human single-nucleotide variants and enable scoring of short insertions-deletions. C scores correlate with allelic diversity, annotations of functionality, pathogenicity, disease severity, experimentally measured regulatory effects and complex trait associations, and they highly rank known pathogenic variants within individual genomes. The ability of CADD to prioritize functional, deleterious and pathogenic variants across many functional categories, effect sizes and genetic architectures is unmatched by any current single-annotation method. © 2014 Nature America, Inc. © 2014 Nature America, Inc.", "date": "2014-01-01T00:00:00Z", "citationCount": 4423, "authors": [ { "name": "Kircher M." }, { "name": "Witten D.M." }, { "name": "Jain P." }, { "name": "O'roak B.J." }, { "name": "Cooper G.M." }, { "name": "Shendure J." } ], "journal": "Nature Genetics" } }, { "doi": "10.1093/nar/gky1016", "pmid": "30371827", "pmcid": "PMC6323892", "type": [], "version": null, "note": null, "metadata": { "title": "CADD: Predicting the deleteriousness of variants throughout the human genome", "abstract": "Combined Annotation-Dependent Depletion (CADD) is a widely used measure of variant deleteriousness that can effectively prioritize causal variants in genetic analyses, particularly highly penetrant contributors to severe Mendelian disorders. CADD is an integrative annotation built from more than 60 genomic features, and can score human single nucleotide variants and short insertion and deletions anywhere in the reference assembly. CADD uses a machine learning model trained on a binary distinction between simulated de novo variants and variants that have arisen and become fixed in human populations since the split between humans and chimpanzees; the former are free of selective pressure and may thus include both neutral and deleterious alleles, while the latter are overwhelmingly neutral (or, at most, weakly deleterious) by virtue of having survived millions of years of purifying selection. Here we review the latest updates to CADD, including the most recent version, 1.4, which supports the human genome build GRCh38. We also present updates to our website that include simplified variant lookup, extended documentation, an Application Program Interface and improved mechanisms for integrating CADD scores into other tools or applications. CADD scores, software and documentation are available at https://cadd.gs.washington.edu.", "date": "2019-01-08T00:00:00Z", "citationCount": 2122, "authors": [ { "name": "Rentzsch P." }, { "name": "Witten D." }, { "name": "Cooper G.M." }, { "name": "Shendure J." }, { "name": "Kircher M." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1186/s13073-021-00835-9", "pmid": "33618777", "pmcid": "PMC7901104", "type": [], "version": null, "note": null, "metadata": { "title": "CADD-Splice—improving genome-wide variant effect prediction using deep learning-derived splice scores", "abstract": "Background: Splicing of genomic exons into mRNAs is a critical prerequisite for the accurate synthesis of human proteins. Genetic variants impacting splicing underlie a substantial proportion of genetic disease, but are challenging to identify beyond those occurring at donor and acceptor dinucleotides. To address this, various methods aim to predict variant effects on splicing. Recently, deep neural networks (DNNs) have been shown to achieve better results in predicting splice variants than other strategies. Methods: It has been unclear how best to integrate such process-specific scores into genome-wide variant effect predictors. Here, we use a recently published experimental data set to compare several machine learning methods that score variant effects on splicing. We integrate the best of those approaches into general variant effect prediction models and observe the effect on classification of known pathogenic variants. Results: We integrate two specialized splicing scores into CADD (Combined Annotation Dependent Depletion; cadd.gs.washington.edu), a widely used tool for genome-wide variant effect prediction that we previously developed to weight and integrate diverse collections of genomic annotations. With this new model, CADD-Splice, we show that inclusion of splicing DNN effect scores substantially improves predictions across multiple variant categories, without compromising overall performance. Conclusions: While splice effect scores show superior performance on splice variants, specialized predictors cannot compete with other variant scores in general variant interpretation, as the latter account for nonsense and missense effects that do not alter splicing. Although only shown here for splice scores, we believe that the applied approach will generalize to other specific molecular processes, providing a path for the further improvement of genome-wide variant effect prediction.", "date": "2021-12-01T00:00:00Z", "citationCount": 376, "authors": [ { "name": "Rentzsch P." }, { "name": "Schubach M." }, { "name": "Shendure J." }, { "name": "Kircher M." } ], "journal": "Genome Medicine" } } ], "credit": [ { "name": "CADD support", "email": "cadd-support@uw.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-EE", "additionDate": "2017-07-04T12:32:38Z", "lastUpdate": "2024-11-24T15:59:00.549338Z", "editPermission": { "type": "group", "authors": [ "sergitobara" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "UCSC Genome Browser", "description": "Large database of publicly available sequence and annotation data along with an integrated tool set for examining and comparing the genomes of organisms, aligning sequence to genomes, and displaying and sharing users own annotation data.", "homepage": "https://genome.ucsc.edu/", "biotoolsID": "ucsc_genome_browser", "biotoolsCURIE": "biotools:ucsc_genome_browser", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_3197", "term": "Genetic variation analysis" }, { "uri": "http://edamontology.org/operation_3208", "term": "Genome visualisation" }, { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" }, { "uri": "http://edamontology.org/operation_0308", "term": "PCR primer design" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_3366", "term": "Data integration and warehousing" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "Apache-2.0", "collectionID": [ "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkp939", "pmid": "19906737", "pmcid": "PMC2808870", "type": [], "version": null, "note": null, "metadata": { "title": "The UCSC genome browser database: Update 2010", "abstract": "The University of California, Santa Cruz (UCSC) Genome Browser website (http://genome.ucsc.edu/) provides a large database of publicly available sequence and annotation data along with an integrated tool set for examining and comparing the genomes of organisms, aligning sequence to genomes, and displaying and sharing users' own annotation data. As of September 2009, genomic sequence and a basic set of annotation 'tracks' are provided for 47 organisms, including 14 mammals, 10 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms and a yeast. New data highlights this year include an updated human genome browser, a 44-species multiple sequence alignment track, improved variation and phenotype tracks and 16 new genome-wide ENCODE tracks. New features include drag-and-zoom navigation, a Wiki track for user-added annotations, new custom track formats for large datasets (bigBed and bigWig), a new multiple alignment output tool, links to variation and protein structure tools, in silico PCR utility enhancements, and improved track configuration tools. © The Author(s) 2009. Published by Oxford University Press.", "date": "2009-11-10T00:00:00Z", "citationCount": 522, "authors": [ { "name": "Rhead B." }, { "name": "Karolchik D." }, { "name": "Kuhn R.M." }, { "name": "Hinrichs A.S." }, { "name": "Zweig A.S." }, { "name": "Fujita P.A." }, { "name": "Diekhans M." }, { "name": "Smith K.E." }, { "name": "Rosenbloom K.R." }, { "name": "Raney B.J." }, { "name": "Pohl A." }, { "name": "Pheasant M." }, { "name": "Meyer L.R." }, { "name": "Learned K." }, { "name": "Hsu F." }, { "name": "Hillman-Jackson J." }, { "name": "Harte R.A." }, { "name": "Giardine B." }, { "name": "Dreszer T.R." }, { "name": "Clawson H." }, { "name": "Barber G.P." }, { "name": "Haussler D." }, { "name": "Kent W.J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkr1012", "pmid": "22075998", "pmcid": "PMC3245183", "type": [], "version": null, "note": null, "metadata": { "title": "ENCODE whole-genome data in the UCSC Genome Browser: Update 2012", "abstract": "The Encyclopedia of DNA Elements (ENCODE) Consortium is entering its 5th year of productionlevel effort generating high-quality whole-genome functional annotations of the human genome. The past year has brought the ENCODE compendium of functional elements to critical mass, with a diverse set of 27 biochemical assays now covering 200 distinct human cell types. Within the mouse genome, which has been under study by ENCODE groups for the past 2 years, 37 cell types have been assayed. Over 2000 individual experiments have been completed and submitted to the Data Coordination Center for public use. UCSC makes this data available on the quality-reviewed public Genome Browser (http://genome.ucsc.edu) and on an early-access Preview Browser (http://genomepreview. ucsc.edu). Visual browsing, data mining and download of raw and processed data files are all supported. An ENCODE portal (http:// encodeproject.org) provides specialized tools and information about the ENCODE data sets. © The Author(s) 2011.", "date": "2012-01-01T00:00:00Z", "citationCount": 211, "authors": [ { "name": "Rosenbloom K.R." }, { "name": "Dreszer T.R." }, { "name": "Long J.C." }, { "name": "Malladi V.S." }, { "name": "Sloan C.A." }, { "name": "Raney B.J." }, { "name": "Cline M.S." }, { "name": "Karolchik D." }, { "name": "Barber G.P." }, { "name": "Clawson H." }, { "name": "Diekhans M." }, { "name": "Fujita P.A." }, { "name": "Goldman M." }, { "name": "Gravell R.C." }, { "name": "Harte R.A." }, { "name": "Hinrichs A.S." }, { "name": "Kirkup V.M." }, { "name": "Kuhn R.M." }, { "name": "Learned K." }, { "name": "Maddren M." }, { "name": "Meyer L.R." }, { "name": "Pohl A." }, { "name": "Rhead B." }, { "name": "Wong M.C." }, { "name": "Zweig A.S." }, { "name": "Haussler D." }, { "name": "Kent W.J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkr1055", "pmid": "22086951", "pmcid": "PMC3245018", "type": [], "version": null, "note": null, "metadata": { "title": "The UCSC Genome Browser database: Extensions and updates 2011", "abstract": "The University of California Santa Cruz Genome Browser (http://genome.ucsc. edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms. The Browser is an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic data sets. In the past year, the local database has been updated with four new species assemblies, and we anticipate another four will be released by the end of 2011. Further, a large number of annotation tracks have been either added, updated by contributors, or remapped to the latest human reference genome. Among these are new phenotype and disease annotations, UCSC genes, and a major dbSNP update, which required new visualization methods. Growing beyond the local database, this year we have introduced 'track data hubs', which allow the Genome Browser to provide access to remotely located sets of annotations. This feature is designed to significantly extend the number and variety of annotation tracks that are publicly available for visualization and analysis from within our site. We have also introduced several usability features including track search and a context-sensitive menu of options available with a right-click anywhere on the Browser's image. © The Author(s) 2011. Published by Oxford University Press.", "date": "2012-01-01T00:00:00Z", "citationCount": 268, "authors": [ { "name": "Dreszer T.R." }, { "name": "Karolchik D." }, { "name": "Zweig A.S." }, { "name": "Hinrichs A.S." }, { "name": "Raney B.J." }, { "name": "Kuhn R.M." }, { "name": "Meyer L.R." }, { "name": "Wong M." }, { "name": "Sloan C.A." }, { "name": "Rosenbloom K.R." }, { "name": "Roe G." }, { "name": "Rhead B." }, { "name": "Pohl A." }, { "name": "Malladi V.S." }, { "name": "Li C.H." }, { "name": "Learned K." }, { "name": "Kirkup V." }, { "name": "Hsu F." }, { "name": "Harte R.A." }, { "name": "Guruvadoo L." }, { "name": "Goldman M." }, { "name": "Giardine B.M." }, { "name": "Fujita P.A." }, { "name": "Diekhans M." }, { "name": "Cline M.S." }, { "name": "Clawson H." }, { "name": "Barber G.P." }, { "name": "Haussler D." }, { "name": "Kent W.J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1101/gr.229102", "pmid": "12045153", "pmcid": "PMC186604", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The human genome browser at UCSC", "abstract": "As vertebrate genome sequences near completion and research refocuses to their analysis, the issue of effective genome annotation display becomes critical. A mature web tool for rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks, is provided at http://genome.ucsc.edu. This browser displays assembly contigs and gaps, mRNA and expressed sequence tag alignments, multiple gene predictions, cross-species homologies, single nucleotide polymorphisms, sequence-tagged sites, radiation hybrid data, transposon repeats, and more as a stack of coregistered tracks. Text and sequence-based searches provide quick and precise access to any region of specific interest. Secondary links from individual features lead to sequence details and supplementary off-site databases. One-half of the annotation tracks are computed at the University of California, Santa Cruz from publicly available sequence data; collaborators worldwide provide the rest. Users can stably add their own custom tracks to the browser for educational or research purposes. The conceptual and technical framework of the browser, its underlying MYSQL database, and overall use are described. The web site currently serves over 50,000 pages per day to over 3000 different users.", "date": "2002-01-01T00:00:00Z", "citationCount": 7662, "authors": [ { "name": "James Kent W." }, { "name": "Sugnet C.W." }, { "name": "Furey T.S." }, { "name": "Roskin K.M." }, { "name": "Pringle T.H." }, { "name": "Zahler A.M." }, { "name": "Haussler D." } ], "journal": "Genome Research" } }, { "doi": "10.1093/nar/gkg129", "pmid": "12519945", "pmcid": "PMC165576", "type": [], "version": null, "note": null, "metadata": { "title": "The UCSC Genome Browser Database", "abstract": "The University of California Santa Cruz (UCSC) Genome Browser Database is an up to date source for genome sequence data integrated with a large collection of related annotations. The database is optimized to support fast interactive performance with the web-based UCSC Genome Browser, a tool built on top of the database for rapid visualization and querying of the data at many levels. The annotations for a given genome are displayed in the browser as a series of tracks aligned with the genomic sequence. Sequence data and annotations may also be viewed in a text-based tabular format or downloaded as tab-delimited flat files. The Genome Browser Database, browsing tools and downloadable data files can all be found on the UCSC Genome Bioinformatics website (http://genome.ucsc.edu), which also contains links to documentation and related technical information.", "date": "2003-01-01T00:00:00Z", "citationCount": 1273, "authors": [ { "name": "Karolchik D." }, { "name": "Baertsch R." }, { "name": "Diekhans M." }, { "name": "Furey T.S." }, { "name": "Hinrichs A." }, { "name": "Lu Y.T." }, { "name": "Roskin K.M." }, { "name": "Schwartz M." }, { "name": "Sugnet C.W." }, { "name": "Thomas D.J." }, { "name": "Weber R.J." }, { "name": "Haussler D." }, { "name": "Kent W.J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkm966", "pmid": "18086701", "pmcid": "PMC2238835", "type": [], "version": null, "note": null, "metadata": { "title": "The UCSC genome browser database: 2008 update", "abstract": "The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrate and 21 invertebrate species as of September 2007. For each assembly, the GBD contains a collection of annotation data aligned to the genomic sequence. Highlights of this year's additions include a 28-species human-based vertebrate conservation annotation, an enhanced UCSC Genes set, and more human variation, MGC, and ENCODE data. The database is optimized for fast interactive performance with a set of web-based tools that may be used to view, manipulate, filter and download the annotation data. New toolset features include the Genome Graphs tool for displaying genome-wide data sets, session saving and sharing, better custom track management, expanded Genome Browser configuration options and a Genome Browser wiki site. © 2007 The Author(s).", "date": "2008-01-01T00:00:00Z", "citationCount": 431, "authors": [ { "name": "Karolchik D." }, { "name": "Kuhn R.M." }, { "name": "Baertsch R." }, { "name": "Barber G.P." }, { "name": "Clawson H." }, { "name": "Diekhans M." }, { "name": "Giardine B." }, { "name": "Harte R.A." }, { "name": "Hinrichs A.S." }, { "name": "Hsu F." }, { "name": "Kober K.M." }, { "name": "Miller W." }, { "name": "Pedersen J.S." }, { "name": "Pohl A." }, { "name": "Raney B.J." }, { "name": "Rhead B." }, { "name": "Rosenbloom K.R." }, { "name": "Smith K.E." }, { "name": "Stanke M." }, { "name": "Thakkapallayil A." }, { "name": "Trumbower H." }, { "name": "Wang T." }, { "name": "Zweig A.S." }, { "name": "Haussler D." }, { "name": "Kent W.J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkj144", "pmid": "16381938", "pmcid": "PMC1347506", "type": [], "version": null, "note": null, "metadata": { "title": "The UCSC Genome Browser Database: update 2006.", "abstract": "The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, mRNA and expressed sequence tag evidence, comparative genomics, regulation, expression and variation data. The database is optimized to support fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. The Genome Browser displays a wide variety of annotations at all scales from single nucleotide level up to a full chromosome. The Table Browser provides direct access to the database tables and sequence data, enabling complex queries on genome-wide datasets. The Proteome Browser graphically displays protein properties. The Gene Sorter allows filtering and comparison of genes by several metrics including expression data and several gene properties. BLAT and In Silico PCR search for sequences in entire genomes in seconds. These tools are highly integrated and provide many hyperlinks to other databases and websites. The GBD, browsing tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/.", "date": "2006-01-01T00:00:00Z", "citationCount": 893, "authors": [ { "name": "Hinrichs A.S." }, { "name": "Karolchik D." }, { "name": "Baertsch R." }, { "name": "Barber G.P." }, { "name": "Bejerano G." }, { "name": "Clawson H." }, { "name": "Diekhans M." }, { "name": "Furey T.S." }, { "name": "Harte R.A." }, { "name": "Hsu F." }, { "name": "Hillman-Jackson J." }, { "name": "Kuhn R.M." }, { "name": "Pedersen J.S." }, { "name": "Pohl A." }, { "name": "Raney B.J." }, { "name": "Rosenbloom K.R." }, { "name": "Siepel A." }, { "name": "Smith K.E." }, { "name": "Sugnet C.W." }, { "name": "Sultan-Qurraie A." }, { "name": "Thomas D.J." }, { "name": "Trumbower H." }, { "name": "Weber R.J." }, { "name": "Weirauch M." }, { "name": "Zweig A.S." }, { "name": "Haussler D." }, { "name": "Kent W.J." } ], "journal": "Nucleic acids research" } }, { "doi": "10.1093/nar/gkn875", "pmid": "18996895", "pmcid": "PMC2686463", "type": [], "version": null, "note": null, "metadata": { "title": "The UCSC Genome Browser Database: Update 2009", "abstract": "The UCSC Genome Browser Database (GBD, http://genome.ucsc.edu) is a publicly available collection of genome assembly sequence data and integrated annotations for a large number of organisms, including extensive comparative-genomic resources. In the past year, 13 new genome assemblies have been added, including two important primate species, orangutan and marmoset, bringing the total to 46 assemblies for 24 different vertebrates and 39 assemblies for 22 different invertebrate animals. The GBD datasets may be viewed graphically with the UCSC Genome Browser, which uses a coordinate-based display system allowing users to juxtapose a wide variety of data. These data include all mRNAs from GenBank mapped to all organisms, RefSeq alignments, gene predictions, regulatory elements, gene expression data, repeats, SNPs and other variation data, as well as pairwise and multiple-genome alignments. A variety of other bioinformatics tools are also provided, including BLAT, the Table Browser, the Gene Sorter, the Proteome Browser, VisiGene and Genome Graphs. © 2008 The Author(s).", "date": "2009-01-09T00:00:00Z", "citationCount": 305, "authors": [ { "name": "Kuhn R.M." }, { "name": "Karolchik D." }, { "name": "Zweig A.S." }, { "name": "Wang T." }, { "name": "Smith K.E." }, { "name": "Rosenbloom K.R." }, { "name": "Rhead B." }, { "name": "Raney B.J." }, { "name": "Pohl A." }, { "name": "Pheasant M." }, { "name": "Meyer L." }, { "name": "Hsu F." }, { "name": "Hinrichs A.S." }, { "name": "Harte R.A." }, { "name": "Giardine B." }, { "name": "Fujita P." }, { "name": "Diekhans M." }, { "name": "Dreszer T." }, { "name": "Clawson H." }, { "name": "Barber G.P." }, { "name": "Haussler D." }, { "name": "Kent W.J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkt1168", "pmid": "24270787", "pmcid": "PMC3964947", "type": [], "version": null, "note": null, "metadata": { "title": "The UCSC Genome Browser database: 2014 update", "abstract": "The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a large collection of organisms, primarily vertebrates, with an emphasis on the human and mouse genomes. The Browser's web-based tools provide an integrated environment for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic data sets. As of September 2013, the database contained genomic sequence and a basic set of annotation 'tracks' for ∼90 organisms. Significant new annotations include a 60-species multiple alignment conservation track on the mouse, updated UCSC Genes tracks for human and mouse, and several new sets of variation and ENCODE data. New software tools include a Variant Annotation Integrator that returns predicted functional effects of a set of variants uploaded as a custom track, an extension to UCSC Genes that displays haplotype alleles for protein-coding genes and an expansion of data hubs that includes the capability to display remotely hosted user-provided assembly sequence in addition to annotation data. To improve European access, we have added a Genome Browser mirror (http://genome-euro.ucsc.edu) hosted at Bielefeld University in Germany. © 2013 The Author(s). Published by Oxford University Press.", "date": "2014-01-01T00:00:00Z", "citationCount": 528, "authors": [ { "name": "Karolchik D." }, { "name": "Barber G.P." }, { "name": "Casper J." }, { "name": "Clawson H." }, { "name": "Cline M.S." }, { "name": "Diekhans M." }, { "name": "Dreszer T.R." }, { "name": "Fujita P.A." }, { "name": "Guruvadoo L." }, { "name": "Haeussler M." }, { "name": "Harte R.A." }, { "name": "Heitner S." }, { "name": "Hinrichs A.S." }, { "name": "Learned K." }, { "name": "Lee B.T." }, { "name": "Li C.H." }, { "name": "Raney B.J." }, { "name": "Rhead B." }, { "name": "Rosenbloom K.R." }, { "name": "Sloan C.A." }, { "name": "Speir M.L." }, { "name": "Zweig A.S." }, { "name": "Haussler D." }, { "name": "Kuhn R.M." }, { "name": "Kent W.J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gku1177", "pmid": "25428374", "pmcid": "PMC4383971", "type": [], "version": null, "note": null, "metadata": { "title": "The UCSC Genome Browser database: 2015 update", "abstract": "Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome assemblies and annotations to scientists and students worldwide. Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation (100-species multiple alignment and conservation) and a novel distribution mechanism for the browser (GBiB: Genome Browser in a Box). We created browsers for new species (Chinese hamster, elephant shark, minke whale), 'mined the web' for DNA sequences and expanded the browser display with stacked color graphs and region highlighting. As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled.", "date": "2015-01-28T00:00:00Z", "citationCount": 709, "authors": [ { "name": "Rosenbloom K.R." }, { "name": "Armstrong J." }, { "name": "Barber G.P." }, { "name": "Casper J." }, { "name": "Clawson H." }, { "name": "Diekhans M." }, { "name": "Dreszer T.R." }, { "name": "Fujita P.A." }, { "name": "Guruvadoo L." }, { "name": "Haeussler M." }, { "name": "Harte R.A." }, { "name": "Heitner S." }, { "name": "Hickey G." }, { "name": "Hinrichs A.S." }, { "name": "Hubley R." }, { "name": "Karolchik D." }, { "name": "Learned K." }, { "name": "Lee B.T." }, { "name": "Li C.H." }, { "name": "Miga K.H." }, { "name": "Nguyen N." }, { "name": "Paten B." }, { "name": "Raney B.J." }, { "name": "Smit A.F.A." }, { "name": "Speir M.L." }, { "name": "Zweig A.S." }, { "name": "Haussler D." }, { "name": "Kuhn R.M." }, { "name": "Kent W.J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkv1275", "pmid": "26590259", "pmcid": "PMC4702902", "type": [], "version": null, "note": null, "metadata": { "title": "The UCSC Genome Browser database: 2016 update", "abstract": "For the past 15 years, the UCSC Genome Browser (http://genome.ucsc.edu/) has served the international research community by offering an integrated platform for viewing and analyzing information from a large database of genome assemblies and their associated annotations. The UCSC Genome Browser has been under continuous development since its inception with new data sets and software features added frequently. Some release highlights of this year include new and updated genome browsers for various assemblies, including bonobo and zebrafish; new gene annotation sets; improvements to track and assembly hub support; and a new interactive tool, the \"Data Integrator\", for intersecting data from multiple tracks. We have greatly expanded the data sets available on the most recent human assembly, hg38/GRCh38, to include updated gene prediction sets from GENCODE, more phenotype - and disease associated variants from ClinVar and ClinGen, more genomic regulatory data, and a new multiple genome alignment.", "date": "2016-01-01T00:00:00Z", "citationCount": 319, "authors": [ { "name": "Speir M.L." }, { "name": "Zweig A.S." }, { "name": "Rosenbloom K.R." }, { "name": "Raney B.J." }, { "name": "Paten B." }, { "name": "Nejad P." }, { "name": "Lee B.T." }, { "name": "Learned K." }, { "name": "Karolchik D." }, { "name": "Hinrichs A.S." }, { "name": "Heitner S." }, { "name": "Harte R.A." }, { "name": "Haeussler M." }, { "name": "Guruvadoo L." }, { "name": "Fujita P.A." }, { "name": "Eisenhart C." }, { "name": "Diekhans M." }, { "name": "Clawson H." }, { "name": "Casper J." }, { "name": "Barber G.P." }, { "name": "Haussler D." }, { "name": "Kuhn R.M." }, { "name": "Kent W.J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkw1134", "pmid": "27899642", "pmcid": "PMC5210591", "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gky1095", "pmid": "30407534", "pmcid": "PMC6323953", "type": [], "version": null, "note": null, "metadata": { "title": "The UCSC Genome Browser database: 2019 update", "abstract": "The UCSC Genome Browser (https://genome.ucsc.edu) is a graphical viewer for exploring genome annotations. For almost two decades, the Browser has provided visualization tools for genetics and molecular biology and continues to add new data and features. This year, we added a new tool that lets users interactively arrange existing graphing tracks into new groups. Other software additions include new formats for chromosome interactions, a ChIP-Seq peak display for track hubs and improved support for HGVS. On the annotation side, we have added gnomAD, TCGA expression, RefSeq Functional elements, GTEx eQTLs, CRISPR Guides, SNPpedia and created a 30-way primate alignment on the human genome. Nine assemblies now have RefSeq-mapped gene models.", "date": "2019-01-08T00:00:00Z", "citationCount": 534, "authors": [ { "name": "Haeussler M." }, { "name": "Zweig A.S." }, { "name": "Tyner C." }, { "name": "Speir M.L." }, { "name": "Rosenbloom K.R." }, { "name": "Raney B.J." }, { "name": "Lee C.M." }, { "name": "Lee B.T." }, { "name": "Hinrichs A.S." }, { "name": "Gonzalez J.N." }, { "name": "Gibson D." }, { "name": "Diekhans M." }, { "name": "Clawson H." }, { "name": "Casper J." }, { "name": "Barber G.P." }, { "name": "Haussler D." }, { "name": "Kuhn R.M." }, { "name": "Kent W.J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gks1048", "pmid": "23155063", "pmcid": "PMC3531082", "type": [], "version": null, "note": null, "metadata": { "title": "The UCSC Genome Browser database: Extensions and updates 2013", "abstract": "The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms. The Browser is an integrated tool set for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic datasets. As of September 2012, genomic sequence and a basic set of annotation 'tracks' are provided for 63 organisms, including 26 mammals, 13 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms, yeast and sea hare. In the past year 19 new genome assemblies have been added, and we anticipate releasing another 28 in early 2013. Further, a large number of annotation tracks have been either added, updated by contributors or remapped to the latest human reference genome. Among these are an updated UCSC Genes track for human and mouse assemblies. We have also introduced several features to improve usability, including new navigation menus. This article provides an update to the UCSC Genome Browser database, which has been previously featured in the Database issue of this journal. © The Author(s) 2012.", "date": "2013-01-01T00:00:00Z", "citationCount": 623, "authors": [ { "name": "Meyer L.R." }, { "name": "Zweig A.S." }, { "name": "Hinrichs A.S." }, { "name": "Karolchik D." }, { "name": "Kuhn R.M." }, { "name": "Wong M." }, { "name": "Sloan C.A." }, { "name": "Rosenbloom K.R." }, { "name": "Roe G." }, { "name": "Rhead B." }, { "name": "Raney B.J." }, { "name": "Pohl A." }, { "name": "Malladi V.S." }, { "name": "Li C.H." }, { "name": "Lee B.T." }, { "name": "Learned K." }, { "name": "Kirkup V." }, { "name": "Hsu F." }, { "name": "Heitner S." }, { "name": "Harte R.A." }, { "name": "Haeussler M." }, { "name": "Guruvadoo L." }, { "name": "Goldman M." }, { "name": "Giardine B.M." }, { "name": "Fujita P.A." }, { "name": "Dreszer T.R." }, { "name": "Diekhans M." }, { "name": "Cline M.S." }, { "name": "Clawson H." }, { "name": "Barber G.P." }, { "name": "Haussler D." }, { "name": "Kent W.J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkq963", "pmid": "20959295", "pmcid": "PMC3242726", "type": [], "version": null, "note": null, "metadata": { "title": "The UCSC genome browser database: Update 2011", "abstract": "The University of California, Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online access to a database of genomic sequence and annotation data for a wide variety of organisms. The Browser also has many tools for visualizing, comparing and analyzing both publicly available and user-generated genomic data sets, aligning sequences and uploading user data. Among the features released this year are a gene search tool and annotation track drag-reorder functionality as well as support for BAM and BigWig/BigBed file formats. New display enhancements include overlay of multiple wiggle tracks through use of transparent coloring, options for displaying transformed wiggle data, a 'mean+whiskers' windowing function for display of wiggle data at high zoom levels, and more color schemes for microarray data. New data highlights include seven new genome assemblies, a Neandertal genome data portal, phenotype and disease association data, a human RNA editing track, and a zebrafish Conservation track. We also describe updates to existing tracks. © The Author(s) 2010.", "date": "2011-01-01T00:00:00Z", "citationCount": 853, "authors": [ { "name": "Fujita P.A." }, { "name": "Rhead B." }, { "name": "Zweig A.S." }, { "name": "Hinrichs A.S." }, { "name": "Karolchik D." }, { "name": "Cline M.S." }, { "name": "Goldman M." }, { "name": "Barber G.P." }, { "name": "Clawson H." }, { "name": "Coelho A." }, { "name": "Diekhans M." }, { "name": "Dreszer T.R." }, { "name": "Giardine B.M." }, { "name": "Harte R.A." }, { "name": "Hillman-Jackson J." }, { "name": "Hsu F." }, { "name": "Kirkup V." }, { "name": "Kuhn R.M." }, { "name": "Learned K." }, { "name": "Li C.H." }, { "name": "Meyer L.R." }, { "name": "Pohl A." }, { "name": "Raney B.J." }, { "name": "Rosenbloom K.R." }, { "name": "Smith K.E." }, { "name": "Haussler D." }, { "name": "Kent W.J." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Brooke Rhead", "email": "rhead@soe.ucsc.edu", "url": "https://genome.ucsc.edu/contacts.html", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-EE", "additionDate": "2017-03-27T07:56:24Z", "lastUpdate": "2024-11-24T15:58:33.301729Z", "editPermission": { "type": "group", "authors": [ "sergitobara" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "OMIM", "description": "Online Mendelian inheritance in Man (OMIM) - catalog of human genes and genetic disorders with descriptive text, references, and links to many NCBI resources including GenBank and PubMed.", "homepage": "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM", "biotoolsID": "omim", "biotoolsCURIE": "biotools:omim", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3763", "term": "Service invocation" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" }, { "uri": "http://edamontology.org/operation_0282", "term": "Genetic mapping" }, { "uri": "http://edamontology.org/operation_3436", "term": "Aggregation" }, { "uri": "http://edamontology.org/operation_3197", "term": "Genetic variation analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web API", "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_3053", "term": "Genetics" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3574", "term": "Human genetics" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "Unlicense", "collectionID": [ "RD-connect", "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://omim.org/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gki033", "pmid": "15608251", "pmcid": "PMC539987", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders", "abstract": "Online Mendelian Inheritance in Man (OMIM™) is a comprehensive, authoritative and timely knowledgebase of human genes and genetic disorders compiled to support human genetics research and education and the practice of clinical genetics. Started by Dr Victor A. McKusick as the definitive reference Mendelian Inheritance in Man, OMIM (http://www.ncbi.nlm.nih.gov/omim/) is now distributed electronically by the National Center for Biotechnology Information, where it is integrated with the Entrez suite of databases. Derived from the biomedical literature, OMIM is written and edited at Johns Hopkins University with input from scientists and physicians around the world. Each OMIM entry has a full-text summary of a genetically determined phenotype and/or gene and has numerous links to other genetic databases such as DNA and protein sequence, PubMed references, general and locus-specific mutation databases, HUGO nomenclature, MapViewer, GeneTests, patient support groups and many others. OMIM is an easy and straightforward portal to the burgeoning information in human genetics. © Oxford University Press 2005; all rights reserved.", "date": "2005-01-01T00:00:00Z", "citationCount": 2237, "authors": [ { "name": "Hamosh A." }, { "name": "Scott A.F." }, { "name": "Amberger J.S." }, { "name": "Bocchini C.A." }, { "name": "McKusick V.A." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gku1205", "pmid": "25428349", "pmcid": "PMC4383985", "type": [], "version": null, "note": null, "metadata": { "title": "OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an Online catalog of human genes and genetic disorders", "abstract": "Online Mendelian Inheritance in Man, OMIM®, is a comprehensive, authoritative and timely research resource of curated descriptions of human genes and phenotypes and the relationships between them. The new official website for OMIM, OMIM.org (http://omim.org), was launched in January 2011. OMIM is based on the published peer-reviewed biomedical literature and is used by overlapping and diverse communities of clinicians, molecular biologists and genome scientists, as well as by students and teachers of these disciplines. Genes and phenotypes are described in separate entries and are given unique, stable six-digit identifiers (MIM numbers). OMIM entries have a structured free-text format that provides the flexibility necessary to describe the complex and nuanced relationships between genes and genetic phenotypes in an efficient manner. OMIM also has a derivative table of genes and genetic phenotypes, the Morbid Map. OMIM.org has enhanced search capabilities such as genome coordinate searching and thesaurus-enhanced search term options. Phenotypic series have been created to facilitate viewing genetic heterogeneity of phenotypes. Clinical synopsis features are enhanced with UMLS, Human Phenotype Ontology and Elements of Morphology terms and image links. All OMIM data are available for FTP download and through an API. MIMmatch is a novel outreach feature to disseminate updates and encourage collaboration.", "date": "2015-01-28T00:00:00Z", "citationCount": 1642, "authors": [ { "name": "Amberger J.S." }, { "name": "Bocchini C.A." }, { "name": "Schiettecatte F." }, { "name": "Scott A.F." }, { "name": "Hamosh A." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gky1151", "pmid": "30445645", "pmcid": "PMC6323937", "type": [], "version": null, "note": null, "metadata": { "title": "OMIM.org: Leveraging knowledge across phenotype-gene relationships", "abstract": "For over 50 years Mendelian Inheritance in Man has chronicled the collective knowledge of the field of medical genetics. It initially cataloged the known X-linked, autosomal recessive and autosomal dominant inherited disorders, but grew to be the primary repository of curated information on both genes and genetic phenotypes and the relationships between them. Each phenotype and gene is given a separate entry assigned a stable, unique identifier. The entries contain structured summaries of new and important information based on expert review of the biomedical literature. OMIM.org provides interactive access to the knowledge repository, including genomic coordinate searches of the gene map, views of genetic heterogeneity of phenotypes in Phenotypic Series, and side-by-side comparisons of clinical synopses. OMIM.org also supports computational queries via a robust API. All entries have extensive targeted links to other genomic resources and additional references. Updates to OMIM can be found on the update list or followed through the MIMmatch service. Updated user guides and tutorials are available on the website. As of September 2018, OMIM had over 24,600 entries, and the OMIM Morbid Map Scorecard had 6,259 molecularized phenotypes connected to 3,961 genes.", "date": "2019-01-08T00:00:00Z", "citationCount": 550, "authors": [ { "name": "Amberger J.S." }, { "name": "Bocchini C.A." }, { "name": "Scott A.F." }, { "name": "Hamosh A." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkn665", "pmid": "18842627", "pmcid": "PMC2686440", "type": [], "version": null, "note": null, "metadata": { "title": "McKusick's Online Mendelian Inheritance in Man (OMIM®)", "abstract": "McKusick's Online Mendelian Inheritance in Man (OMIM® http://www.ncbi.nlm.nih.gov/omim), a knowledgebase of human genes and phenotypes, was originally published as a book, Mendelian Inheritance in Man, in 1966. The content of OMIM is derived exclusively from the published biomedical literature and is updated daily. It currently contains 18 961 full-text entries describing phenotypes and genes. To date, 2239 genes have mutations causing disease, and 3770 diseases have a molecular basis. Approximately 70 new entries are added and 700 entries are updated per month. OMIM® is expanding content and organization in response to shifting biological paradigms and advancing biotechnology. © 2008 The Author(s).", "date": "2009-01-09T00:00:00Z", "citationCount": 565, "authors": [ { "name": "Amberger J." }, { "name": "Bocchini C.A." }, { "name": "Scott A.F." }, { "name": "Hamosh A." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Ada Hamosh", "email": "ahamosh@jhmi.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-EE", "additionDate": "2017-03-30T22:04:37Z", "lastUpdate": "2024-11-24T15:58:17.550443Z", "editPermission": { "type": "group", "authors": [ "sergitobara" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "GWAS catalog", "description": "A catalogue that provides a publicly available manually curated collection of published GWAS assaying at least 100 000 single-nucleotide polymorphisms (SNPs) and all SNP-trait associations with P <1 × 10−5.", "homepage": "https://www.ebi.ac.uk/gwas/", "biotoolsID": "gwas_catalog", "biotoolsCURIE": "biotools:gwas_catalog", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_0484", "term": "SNP detection" }, { "uri": "http://edamontology.org/operation_3459", "term": "Functional clustering" }, { "uri": "http://edamontology.org/operation_2429", "term": "Mapping" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web API", "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3517", "term": "GWAS study" }, { "uri": "http://edamontology.org/topic_2885", "term": "DNA polymorphism" }, { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_3366", "term": "Data integration and warehousing" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "Apache-2.0", "collectionID": [ "RD-connect", "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://www.ebi.ac.uk/gwas/downloads", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "https://www.ebi.ac.uk/gwas/docs", "type": [ "General" ], "note": null }, { "url": "https://github.com/EBISPOT/goci", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkt1229", "pmid": "24316577", "pmcid": "PMC3965119", "type": [], "version": null, "note": null, "metadata": { "title": "The NHGRI GWAS Catalog, a curated resource of SNP-trait associations", "abstract": "The National Human Genome Research Institute (NHGRI) Catalog of Published Genome-Wide Association Studies (GWAS) Catalog provides a publicly available manually curated collection of published GWAS assaying at least 100 000 single-nucleotide polymorphisms (SNPs) and all SNP-trait associations with P <1 × 10 -5. The Catalog includes 1751 curated publications of 11 912 SNPs. In addition to the SNP-trait association data, the Catalog also publishes a quarterly diagram of all SNP-trait associations mapped to the SNPs' chromosomal locations. The Catalog can be accessed via a tabular web interface, via a dynamic visualization on the human karyotype, as a downloadable tab-delimited file and as an OWL knowledge base. This article presents a number of recent improvements to the Catalog, including novel ways for users to interact with the Catalog and changes to the curation infrastructure. © 2013 The Author(s). Published by Oxford University Press.", "date": "2014-01-01T00:00:00Z", "citationCount": 2139, "authors": [ { "name": "Welter D." }, { "name": "MacArthur J." }, { "name": "Morales J." }, { "name": "Burdett T." }, { "name": "Hall P." }, { "name": "Junkins H." }, { "name": "Klemm A." }, { "name": "Flicek P." }, { "name": "Manolio T." }, { "name": "Hindorff L." }, { "name": "Parkinson H." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkw1133", "pmid": "27899670", "pmcid": "PMC5210590", "type": [], "version": null, "note": null, "metadata": { "title": "The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)", "abstract": "The NHGRI-EBI GWAS Catalog has provided data from published genome-wide association studies since 2008. In 2015, the database was redesigned and relocated to EMBL-EBI. The new infrastructure includes a new graphical user interface (www.ebi. ac.uk/gwas/), ontology supported search functionality and an improved curation interface. These developments have improved the data release frequency by increasing automation of curation and providing scaling improvements. The range of available Catalog data has also been extended with structured ancestry and recruitment information added for all studies. The infrastructure improvements also support scaling for larger arrays, exome and sequencing studies, allowing the Catalog to adapt to the needs of evolving study design, genotyping technologies and user needs in the future.", "date": "2017-01-01T00:00:00Z", "citationCount": 1503, "authors": [ { "name": "MacArthur J." }, { "name": "Bowler E." }, { "name": "Cerezo M." }, { "name": "Gil L." }, { "name": "Hall P." }, { "name": "Hastings E." }, { "name": "Junkins H." }, { "name": "McMahon A." }, { "name": "Milano A." }, { "name": "Morales J." }, { "name": "MayPendlington Z." }, { "name": "Welter D." }, { "name": "Burdett T." }, { "name": "Hindorff L." }, { "name": "Flicek P." }, { "name": "Cunningham F." }, { "name": "Parkinson H." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gky1120", "pmid": "30445434", "pmcid": "PMC6323933", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019", "abstract": "The GWAS Catalog delivers a high-quality curated collection of all published genome-wide association studies enabling investigations to identify causal variants, understand disease mechanisms, and establish targets for novel therapies. The scope of the Catalog has also expanded to targeted and exome arrays with 1000 new associations added for these technologies. As of September 2018, the Catalog contains 5687 GWAS comprising 71673 variant-trait associations from 3567 publications. New content includes 284 full P-value summary statistics datasets for genome-wide and new targeted array studies, representing 6 × 10 9 individual variant-trait statistics. In the last 12 months, the Catalog's user interface was accessed by 1/490000 unique users who viewed >1 million pages. We have improved data access with the release of a new RESTful API to support high-throughput programmatic access, an improved web interface and a new summary statistics database. Summary statistics provision is supported by a new format proposed as a community standard for summary statistics data representation. This format was derived from our experience in standardizing heterogeneous submissions, mapping formats and in harmonizing content. Availability: https://www.ebi.ac.uk/gwas/.", "date": "2019-01-08T00:00:00Z", "citationCount": 2549, "authors": [ { "name": "Buniello A." }, { "name": "Macarthur J.A.L." }, { "name": "Cerezo M." }, { "name": "Harris L.W." }, { "name": "Hayhurst J." }, { "name": "Malangone C." }, { "name": "McMahon A." }, { "name": "Morales J." }, { "name": "Mountjoy E." }, { "name": "Sollis E." }, { "name": "Suveges D." }, { "name": "Vrousgou O." }, { "name": "Whetzel P.L." }, { "name": "Amode R." }, { "name": "Guillen J.A." }, { "name": "Riat H.S." }, { "name": "Trevanion S.J." }, { "name": "Hall P." }, { "name": "Junkins H." }, { "name": "Flicek P." }, { "name": "Burdett T." }, { "name": "Hindorff L.A." }, { "name": "Cunningham F." }, { "name": "Parkinson H." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "GWAS Catalog Support", "email": "gwas-info@ebi.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-EE", "additionDate": "2017-07-04T12:28:58Z", "lastUpdate": "2024-11-24T15:58:13.753841Z", "editPermission": { "type": "group", "authors": [ "sergitobara" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ANNOVAR", "description": "A tool for finding relevant genetic variants from high-throughput sequencing data based on functional annotation.", "homepage": "http://annovar.openbioinformatics.org/en/latest/", "biotoolsID": "annovar", "biotoolsCURIE": "biotools:annovar", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/operation_3226", "term": "Variant prioritisation" }, { "uri": "http://edamontology.org/operation_3672", "term": "Gene functional annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0085", "term": "Functional genomics" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Perl" ], "license": null, "collectionID": [ "Rare Disease", "ANNOVAR" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://annovar.openbioinformatics.org/en/latest/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkq603", "pmid": "20601685", "pmcid": "PMC2938201", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data", "abstract": "High-throughput sequencing platforms are generating massive amounts of genetic variation data for diverse genomes, but it remains a challenge to pinpoint a small subset of functionally important variants. To fill these unmet needs, we developed the ANNOVAR tool to annotate single nucleotide variants (SNVs) and insertions/deletions, such as examining their functional consequence on genes, inferring cytogenetic bands, reporting functional importance scores, finding variants in conserved regions, or identifying variants reported in the 1000 Genomes Project and dbSNP. ANNOVAR can utilize annotation databases from the UCSC Genome Browser or any annotation data set conforming to Generic Feature Format version 3 (GFF3). We also illustrate a 'variants reduction' protocol on 4.7 million SNVs and indels from a human genome, including two causal mutations for Miller syndrome, a rare recessive disease. Through a stepwise procedure, we excluded variants that are unlikely to be causal, and identified 20 candidate genes including the causal gene. Using a desktop computer, ANNOVAR requires ~4 min to perform gene-based annotation and ~15 min to perform variants reduction on 4.7 million variants, making it practical to handle hundreds of human genomes in a day. ANNOVAR is freely available at http://www.openbioinformatics.org/annovar/. © The Author(s) 2010. Published by Oxford University Press.", "date": "2010-07-03T00:00:00Z", "citationCount": 9994, "authors": [ { "name": "Wang K." }, { "name": "Li M." }, { "name": "Hakonarson H." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1038/nprot.2015.105", "pmid": "26379229", "pmcid": "PMC4718734", "type": [], "version": null, "note": null, "metadata": { "title": "Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR", "abstract": "Recent developments in sequencing techniques have enabled rapid and high-throughput generation of sequence data, democratizing the ability to compile information on large amounts of genetic variations in individual laboratories. However, there is a growing gap between the generation of raw sequencing data and the extraction of meaningful biological information. Here, we describe a protocol to use the ANNOVAR (ANNOtate VARiation) software to facilitate fast and easy variant annotations, including gene-based, region-based and filter-based annotations on a variant call format (VCF) file generated from human genomes. We further describe a protocol for gene-based annotation of a newly sequenced nonhuman species. Finally, we describe how to use a user-friendly and easily accessible web server called wANNOVAR to prioritize candidate genes for a Mendelian disease. The variant annotation protocols take 5-30 min of computer time, depending on the size of the variant file, and 5-10 min of hands-on time. In summary, through the command-line tool and the web server, these protocols provide a convenient means to analyze genetic variants generated in humans and other species.", "date": "2015-10-29T00:00:00Z", "citationCount": 658, "authors": [ { "name": "Yang H." }, { "name": "Wang K." } ], "journal": "Nature Protocols" } }, { "doi": "10.1136/jmedgenet-2012-100918", "pmid": "22717648", "pmcid": "PMC3556337", "type": [], "version": null, "note": null, "metadata": { "title": "Wannovar: Annotating genetic variants for personal genomes via the web", "abstract": "Background High-throughput DNA sequencing platforms have become widely available. As a result, personal genomes are increasingly being sequenced in research and clinical settings. However, the resulting massive amounts of variants data pose significant challenges to the average biologists and clinicians without bioinformatics skills. Methods and results We developed a web server called wANNOVAR to address the critical needs for functional annotation of genetic variants from personal genomes. The server provides simple and intuitive interface to help users determine the functional significance of variants. These include annotating single nucleotide variants and insertions/deletions for their effects on genes, reporting their conservation levels (such as PhyloP and GERP++ scores), calculating their predicted functional importance scores (such as SIFT and PolyPhen scores), retrieving allele frequencies in public databases (such as the 1000 Genomes Project and NHLBI-ESP 5400 exomes), and implementing a 'variants reduction' protocol to identify a subset of potentially deleterious variants/genes. We illustrated how wANNOVAR can help draw biological insights from sequencing data, by analysing genetic variants generated on two Mendelian diseases. Conclusions We conclude that wANNOVAR will help biologists and clinicians take advantage of the personal genome information to expedite scientific discoveries. The wANNOVAR server is available at http://wannovar. usc.edu, and will be continuously updated to reflect the latest annotation information.", "date": "2012-07-01T00:00:00Z", "citationCount": 335, "authors": [ { "name": "Chang X." }, { "name": "Wang K." } ], "journal": "Journal of Medical Genetics" } } ], "credit": [ { "name": "Kai Wang", "email": "kai@openbioinformatics.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "seqwiki_import", "additionDate": "2017-01-13T13:13:33Z", "lastUpdate": "2024-11-24T15:58:06.017046Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE", "sergitobara" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ReMM score", "description": "ReMM score is a tool that scores the positions in the human genome in terms of their regulatory probability.\n\nWe use curated regulatory variants involved in Mendelian disease and contrast them with proxy-neutral variants that survived natural selection in a machine learning framework. We use an algorithm for highly imbalanced data, called hyperSMURF, to differentiate deleterious from neutral variants.", "homepage": "https://remm.bihealth.org/", "biotoolsID": "remm_score", "biotoolsCURIE": "biotools:remm_score", "version": [ "v0.3.1.post1", "v0.4" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application", "Workflow", "Web API", "Bioinformatics portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3173", "term": "Epigenomics" }, { "uri": "http://edamontology.org/topic_3574", "term": "Human genetics" }, { "uri": "http://edamontology.org/topic_0160", "term": "Sequence sites, features and motifs" }, { "uri": "http://edamontology.org/topic_0085", "term": "Functional genomics" } ], "operatingSystem": [ "Linux" ], "language": [], "license": "MIT", "collectionID": [ "Rare Disease" ], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/kircherlab/ReMM", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://doi.org/10.5281/zenodo.6576087", "type": "Downloads page", "note": null, "version": "v0.4" } ], "documentation": [ { "url": "https://remm.bihealth.org/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1016/j.ajhg.2016.07.005", "pmid": "27569544", "pmcid": "PMC5011059", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease", "abstract": "The interpretation of non-coding variants still constitutes a major challenge in the application of whole-genome sequencing in Mendelian disease, especially for single-nucleotide and other small non-coding variants. Here we present Genomiser, an analysis framework that is able not only to score the relevance of variation in the non-coding genome, but also to associate regulatory variants to specific Mendelian diseases. Genomiser scores variants through either existing methods such as CADD or a bespoke machine learning method and combines these with allele frequency, regulatory sequences, chromosomal topological domains, and phenotypic relevance to discover variants associated to specific Mendelian disorders. Overall, Genomiser is able to identify causal regulatory variants as the top candidate in 77% of simulated whole genomes, allowing effective detection and discovery of regulatory variants in Mendelian disease.", "date": "2016-09-01T00:00:00Z", "citationCount": 181, "authors": [ { "name": "Smedley D." }, { "name": "Schubach M." }, { "name": "Jacobsen J.O.B." }, { "name": "Kohler S." }, { "name": "Zemojtel T." }, { "name": "Spielmann M." }, { "name": "Jager M." }, { "name": "Hochheiser H." }, { "name": "Washington N.L." }, { "name": "McMurry J.A." }, { "name": "Haendel M.A." }, { "name": "Mungall C.J." }, { "name": "Lewis S.E." }, { "name": "Groza T." }, { "name": "Valentini G." }, { "name": "Robinson P.N." } ], "journal": "American Journal of Human Genetics" } }, { "doi": "10.1101/2022.03.14.484240", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Max Schubach", "email": "max.schubach@bih-charite.de", "url": null, "orcidid": "https://orcid.org/0000-0002-2032-6679", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Martin Kircher", "email": "martin.kircher@bih-charite.de", "url": null, "orcidid": "https://orcid.org/0000-0001-9278-5471", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Lusiné Nazaretyan", "email": "lusine.nazaretyan@bih-charite.de", "url": null, "orcidid": "https://orcid.org/0000-0001-5820-4143", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "visze", "additionDate": "2023-01-03T14:28:36.818779Z", "lastUpdate": "2024-11-24T15:14:10.168821Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "RD-Connect Genome-Phenome Analysis Platform (GPAP)", "description": "An online tool for diagnosis and gene discovery in rare disease research. The platform features allow identifying disease-causing mutations in rare disease patients and linking them with detailed clinical information.", "homepage": "https://platform.rd-connect.eu/", "biotoolsID": "rd-connect_platform", "biotoolsCURIE": "biotools:rd-connect_platform", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/operation_3197", "term": "Genetic variation analysis" }, { "uri": "http://edamontology.org/operation_0361", "term": "Sequence annotation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" }, { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" }, { "uri": "http://edamontology.org/topic_3473", "term": "Data mining" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "RD-connect", "Rare Disease", "ELIXIR-ES", "INB", "RIS3CAT VEIS" ], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": "Restricted access", "elixirPlatform": [], "elixirNode": [ "Spain" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1002/humu.24353", "pmid": "35178824", "pmcid": "PMC9324157", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The RD-Connect Genome-Phenome Analysis Platform: Accelerating diagnosis, research, and gene discovery for rare diseases", "abstract": "Rare disease patients are more likely to receive a rapid molecular diagnosis nowadays thanks to the wide adoption of next-generation sequencing. However, many cases remain undiagnosed even after exome or genome analysis, because the methods used missed the molecular cause in a known gene, or a novel causative gene could not be identified and/or confirmed. To address these challenges, the RD-Connect Genome-Phenome Analysis Platform (GPAP) facilitates the collation, discovery, sharing, and analysis of standardized genome-phenome data within a collaborative environment. Authorized clinicians and researchers submit pseudonymised phenotypic profiles encoded using the Human Phenotype Ontology, and raw genomic data which is processed through a standardized pipeline. After an optional embargo period, the data are shared with other platform users, with the objective that similar cases in the system and queries from peers may help diagnose the case. Additionally, the platform enables bidirectional discovery of similar cases in other databases from the Matchmaker Exchange network. To facilitate genome-phenome analysis and interpretation by clinical researchers, the RD-Connect GPAP provides a powerful user-friendly interface and leverages tens of information sources. As a result, the resource has already helped diagnose hundreds of rare disease patients and discover new disease causing genes.", "date": "2022-06-01T00:00:00Z", "citationCount": 29, "authors": [ { "name": "Laurie S." }, { "name": "Piscia D." }, { "name": "Matalonga L." }, { "name": "Corvo A." }, { "name": "Fernandez-Callejo M." }, { "name": "Garcia-Linares C." }, { "name": "Hernandez-Ferrer C." }, { "name": "Luengo C." }, { "name": "Martinez I." }, { "name": "Papakonstantinou A." }, { "name": "Pico-Amador D." }, { "name": "Protasio J." }, { "name": "Thompson R." }, { "name": "Tonda R." }, { "name": "Bayes M." }, { "name": "Bullich G." }, { "name": "Camps-Puchadas J." }, { "name": "Paramonov I." }, { "name": "Trotta J.-R." }, { "name": "Alonso A." }, { "name": "Attimonelli M." }, { "name": "Beroud C." }, { "name": "Bros-Facer V." }, { "name": "Buske O.J." }, { "name": "Canada-Pallares A." }, { "name": "Fernandez J.M." }, { "name": "Hansson M.G." }, { "name": "Horvath R." }, { "name": "Jacobsen J.O.B." }, { "name": "Kaliyaperumal R." }, { "name": "Lair-Preterre S." }, { "name": "Licata L." }, { "name": "Lopes P." }, { "name": "Lopez-Martin E." }, { "name": "Mascalzoni D." }, { "name": "Monaco L." }, { "name": "Perez-Jurado L.A." }, { "name": "Posada de la Paz M." }, { "name": "Rambla J." }, { "name": "Rath A." }, { "name": "Riess O." }, { "name": "Robinson P.N." }, { "name": "Salgado D." }, { "name": "Smedley D." }, { "name": "Spalding D." }, { "name": "'t Hoen P.A.C." }, { "name": "Topf A." }, { "name": "Zaharieva I." }, { "name": "Graessner H." }, { "name": "Gut I.G." }, { "name": "Lochmuller H." }, { "name": "Beltran S." } ], "journal": "Human Mutation" } }, { "doi": "10.1007/s11606-014-2908-8", "pmid": "25029978", "pmcid": "PMC4124112", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "RD-connect: An integrated platform connecting databases, registries, biobanks and clinical bioinformatics for rare disease research", "abstract": "Research into rare diseases is typically fragmented by data type and disease. Individual efforts often have poor interoperability and do not systematically connect data across clinical phenotype, genomic data, biomaterial availability, and research/trial data sets. Such data must be linked at both an individual-patient and whole-cohort level to enable researchers to gain a complete view of their disease and patient population of interest. Data access and authorization procedures are required to allow researchers in multiple institutions to securely compare results and gain new insights. Funded by the European Union's Seventh Framework Programme under the International Rare Diseases Research Consortium (IRDiRC), RD-Connect is a global infrastructure project initiated in November 2012 that links genomic data with registries, biobanks, and clinical bioinformatics tools to produce a central research resource for rare diseases. © 2014 Society of General Internal Medicine.", "date": "2014-01-01T00:00:00Z", "citationCount": 146, "authors": [ { "name": "Thompson R." }, { "name": "Johnston L." }, { "name": "Taruscio D." }, { "name": "Monaco L." }, { "name": "Beroud C." }, { "name": "Gut I.G." }, { "name": "Hansson M.G." }, { "name": "T Hoen P.-B.A." }, { "name": "Patrinos G.P." }, { "name": "Dawkins H." }, { "name": "Ensini M." }, { "name": "Zatloukal K." }, { "name": "Koubi D." }, { "name": "Heslop E." }, { "name": "Paschall J.E." }, { "name": "Posada M." }, { "name": "Robinson P.N." }, { "name": "Bushby K." }, { "name": "Lochmuller H." } ], "journal": "Journal of General Internal Medicine" } } ], "credit": [ { "name": "Steven Laurie", "email": "steven.laurie@cnag.crg.eu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Davide Piscia", "email": "davide.piscia@cnag.crg.eu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Leslie Matalonga", "email": "leslie.matalonga@cnag.crg.eu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Alberto Corvó", "email": "alberto.corvo@cnag.crg.eu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Marcos Fernández-Callejo", "email": "marcos.fernandez@cnag.crg.eu", "url": 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Many putative EDs are widely used in commercial products regulated by the Food and Drug Administration (FDA) such as food packaging materials, ingredients of cosmetics, medical and dental devices, and drugs. The Endocrine Disruptor Knowledge Base (EDKB) project was initiated in the mid 1990's by the FDA as a resource for the study of EDs. The EDKB database, a component of the project, contains data across multiple assay types for chemicals across a broad structural diversity. This paper demonstrates the utility of EDKB database, an integral part of the EDKB project, for understanding and prioritizing EDs for testing.Results: The EDKB database currently contains 3,257 records of over 1,800 EDs from different assays including estrogen receptor binding, androgen receptor binding, uterotropic activity, cell proliferation, and reporter gene assays. Information for each compound such as chemical structure, assay type, potency, etc. is organized to enable efficient searching. A user-friendly interface provides rapid navigation, Boolean searches on EDs, and both spreadsheet and graphical displays for viewing results. The search engine implemented in the EDKB database enables searching by one or more of the following fields: chemical structure (including exact search and similarity search), name, molecular formula, CAS registration number, experiment source, molecular weight, etc. The data can be cross-linked to other publicly available and related databases including TOXNET, Cactus, ChemIDplus, ChemACX, Chem Finder, and NCI DTP. . Conclusion: The EDKB database enables scientists and regulatory reviewers to quickly access ED data from multiple assays for specific or similar compounds. The data have been used to categorize chemicals according to potential risks for endocrine activity, thus providing a basis for prioritizing chemicals for more definitive but expensive testing. The EDKB database is publicly available and can be found online at http://edkb.fda.gov/webstart/edkb/index.html.Disclaimer:The views presented in this article do not necessarily reflect those of the US Food and Drug Administration. © 2010 Tong et al; licensee BioMed Central Ltd.", "date": "2010-10-07T00:00:00Z", "citationCount": 80, "authors": [ { "name": "Ding D." }, { "name": "Xu L." }, { "name": "Fang H." }, { "name": "Hong H." }, { "name": "Perkins R." }, { "name": "Harris S." }, { "name": "Bearden E.D." }, { "name": "Shi L." }, { "name": "Tong W." } ], "journal": "BMC Bioinformatics" } }, { "doi": "10.3897/rio.8.e83031", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Gladstone Institutes", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Maastricht University", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Manchester University", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Heroit Watt University", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "maastrichtuniversity.nl", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": null, "url": "https://groups.google.com/forum/#!forum/bridgedb-discuss", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "egonw", "additionDate": "2015-12-01T16:27:10Z", "lastUpdate": "2024-11-24T14:49:46.902984Z", "editPermission": { "type": "group", "authors": [ "proteomics.bio.tools", "ChrisEvelo" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Variant Combination Pathogenicity Predictor (VarCoPP) 2.0", "description": "VarCoPP is a machine learning method that predicts the potential pathogenicity of variant combinations in gene pairs. It is based on digenic data present in OLIDA and it was trained against variants from the 1000 Genomes Project. VarCoPP2.0 is a Balanced Random Forest predictor consisting of 400 decision trees. \nA variant combination can be either predicted as disease-causing (i.e. candidate or probably pathogenic) or neutral (i.e. probably neutral). \n\nVarCoPP can be applied for Single Nucleotide Variants (SNVs) and small insertions/deletions from a single individual. It is highly recommended to perform beforehand an initial variant filtering procedure and generally restrict the analysis to variants from up to 150 genes. \n\nVarCoPP was developed in the Interuniversity Institute of Bioinformatics in Brussels, under the collaboration of Université libre de Bruxelles and Vrije Universiteit Brussel.\n\nYou can use it through the online tool ORVAL: https://orval.ibsquare.be.", "homepage": "http://varcopp.ibsquare.be", "biotoolsID": "Variant_Combinaton_Pathogenicity_Predictor", "biotoolsCURIE": "biotools:Variant_Combinaton_Pathogenicity_Predictor", "version": [ "1.0", "2.0" ], "otherID": [], "relation": [ { "biotoolsID": "oligogenic_resource_for_variant_analysis", "type": "includedIn" }, { "biotoolsID": "olida", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2423", "term": "Prediction and recognition" }, { "uri": "http://edamontology.org/operation_3225", "term": "Variant classification" }, { "uri": "http://edamontology.org/operation_3197", "term": "Genetic variation analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Plug-in" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0634", "term": "Pathology" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "GPL-3.0", "collectionID": [ "ELIXIR-BE", "RD-Connect", "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Belgium" ], "elixirCommunity": [ "Rare Diseases" ], "link": [ { "url": "https://github.com/oligogenic/VarCoPP2.0", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/sofiapapad90/VarCoPP/", "type": [ "Repository" ], "note": null }, { "url": "https://orval.ibsquare.be", "type": [ "Service" ], "note": "Web app integrating VarCoPP2.0" } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1073/pnas.1815601116", "pmid": "31127050", "pmcid": "PMC6575632", "type": [], "version": "1.0", "note": null, "metadata": { "title": "Predicting disease-causing variant combinations", "abstract": "Notwithstanding important advances in the context of single-variant pathogenicity identification, novel breakthroughs in discerning the origins of many rare diseases require methods able to identify more complex genetic models. We present here the Variant Combinations Pathogenicity Predictor (VarCoPP), a machine-learning approach that identifies pathogenic variant combinations in gene pairs (called digenic or bilocus variant combinations). We show that the results produced by this method are highly accurate and precise, an efficacy that is endorsed when validating the method on recently published independent disease-causing data. Confidence labels of 95% and 99% are identified, representing the probability of a bilocus combination being a true pathogenic result, providing geneticists with rational markers to evaluate the most relevant pathogenic combinations and limit the search space and time. Finally, the VarCoPP has been designed to act as an interpretable method that can provide explanations on why a bilocus combination is predicted as pathogenic and which biological information is important for that prediction. This work provides an important step toward the genetic understanding of rare diseases, paving the way to clinical knowledge and improved patient care.", "date": "2019-06-11T00:00:00Z", "citationCount": 67, "authors": [ { "name": "Papadimitriou S." }, { "name": "Gazzo A." }, { "name": "Versbraegen N." }, { "name": "Nachtegael C." }, { "name": "Aerts J." }, { "name": "Moreau Y." }, { "name": "Van Dooren S." }, { "name": "Nowe A." }, { "name": "Smits G." }, { "name": "Lenaerts T." } ], "journal": "Proceedings of the National Academy of Sciences of the United States of America" } }, { "doi": "10.1186/s12859-023-05291-3", "pmid": "37127601", "pmcid": "PMC10152795", "type": [], "version": "2.0", "note": null, "metadata": { "title": "Faster and more accurate pathogenic combination predictions with VarCoPP2.0", "abstract": "Background: The prediction of potentially pathogenic variant combinations in patients remains a key task in the field of medical genetics for the understanding and detection of oligogenic/multilocus diseases. Models tailored towards such cases can help shorten the gap of missing diagnoses and can aid researchers in dealing with the high complexity of the derived data. The predictor VarCoPP (Variant Combinations Pathogenicity Predictor) that was published in 2019 and identified potentially pathogenic variant combinations in gene pairs (bilocus variant combinations), was the first important step in this direction. Despite its usefulness and applicability, several issues still remained that hindered a better performance, such as its False Positive (FP) rate, the quality of its training set and its complex architecture. Results: We present VarCoPP2.0: the successor of VarCoPP that is a simplified, faster and more accurate predictive model identifying potentially pathogenic bilocus variant combinations. Results from cross-validation and on independent data sets reveal that VarCoPP2.0 has improved in terms of both sensitivity (95% in cross-validation and 98% during testing) and specificity (5% FP rate). At the same time, its running time shows a significant 150-fold decrease due to the selection of a simpler Balanced Random Forest model. Its positive training set now consists of variant combinations that are more confidently linked with evidence of pathogenicity, based on the confidence scores present in OLIDA, the Oligogenic Diseases Database (https://olida.ibsquare.be). The improvement of its performance is also attributed to a more careful selection of up-to-date features identified via an original wrapper method. We show that the combination of different variant and gene pair features together is important for predictions, highlighting the usefulness of integrating biological information at different levels. Conclusions: Through its improved performance and faster execution time, VarCoPP2.0 enables a more accurate analysis of larger data sets linked to oligogenic diseases. Users can access the ORVAL platform (https://orval.ibsquare.be) to apply VarCoPP2.0 on their data.", "date": "2023-12-01T00:00:00Z", "citationCount": 7, "authors": [ { "name": "Versbraegen N." }, { "name": "Gravel B." }, { "name": "Nachtegael C." }, { "name": "Renaux A." }, { "name": "Verkinderen E." }, { "name": "Nowe A." }, { "name": "Lenaerts T." }, { "name": "Papadimitriou S." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Tom Lenaerts", "email": "tlenaert@ulb.ac.be", "url": "http://www.ibsquare.be", "orcidid": "https://orcid.org/0000-0003-3645-1455", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Sofia Papadomitriou", "email": "sofiapapad.bio@gmail.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Interuniversity Institute of Bioinformatics in Brussels", "email": null, "url": "https://ibsquare.be", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "tlenaert@ulb.ac.be", "additionDate": "2019-07-03T15:13:23Z", "lastUpdate": "2024-11-24T14:45:34.041241Z", "editPermission": { "type": "group", "authors": [ "emmaver" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Digenic Diseases Database (DIDA)", "description": "Digenic Diseases Database (DiDA) provides detailed information on genes and associated genetic variants involved in digenic diseases, the simplest form of oligogenic inheritance.", "homepage": "http://dida.ibsquare.be", "biotoolsID": "dida", "biotoolsCURIE": "biotools:dida", "version": [], "otherID": [], "relation": [ { "biotoolsID": "olida", "type": "hasNewVersion" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_3661", "term": "SNP annotation" }, { "uri": "http://edamontology.org/operation_3197", "term": "Genetic variation analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_0634", "term": "Pathology" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "CC-BY-NC-4.0", "collectionID": [ "ELIXIR-BE", "RD-Connect", "Rare Disease" ], "maturity": "Legacy", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Belgium" ], "elixirCommunity": [ "Rare Diseases" ], "link": [], "download": [], "documentation": [ { "url": "http://dida.ibsquare.be/help/", "type": [ "General" ], "note": null }, { "url": "http://dida.ibsquare.be/documentation/", "type": [ "General" ], "note": "More detailed documentation." } ], "publication": [ { "doi": "10.1093/nar/gkv1068", "pmid": "26481352", "pmcid": "PMC4702791", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "DIDA: A curated and annotated digenic diseases database", "abstract": "DIDA (DIgenic diseases DAtabase) is a novel database that provides for the first time detailed information on genes and associated genetic variants involved in digenic diseases, the simplest form of oligogenic inheritance. The database is accessible via http://dida.ibsquare.be and currently includes 213 digenic combinations involved in 44 different digenic diseases. These combinations are composed of 364 distinct variants, which are distributed over 136 distinct genes. The web interface provides browsing and search functionalities, as well as documentation and help pages, general database statistics and references to the original publications from which the data have been collected. The possibility to submit novel digenic data to DIDA is also provided. Creating this new repository was essential as current databases do not allow one to retrieve detailed records regarding digenic combinations. Genes, variants, diseases and digenic combinations in DIDA are annotated with manually curated information and information mined from other online resources. Next to providing a unique resource for the development of new analysis methods, DIDA gives clinical and molecular geneticists a tool to find the most comprehensive information on the digenic nature of their diseases of interest.", "date": "2016-01-01T00:00:00Z", "citationCount": 78, "authors": [ { "name": "Gazzo A.M." }, { "name": "Daneels D." }, { "name": "Cilia E." }, { "name": "Bonduelle M." }, { "name": "Abramowicz M." }, { "name": "Van Dooren S." }, { "name": "Smits G." }, { "name": "Lenaerts T." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Interuniversity Institute of Bioinformatics in Brussels", "email": null, "url": "https://www.ibsquare.be", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Tom Lenaerts", "email": "tlenaert@ulb.ac.be", "url": "http://www.ibsquare.be", "orcidid": "https://orcid.org/0000-0003-3645-1455", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Charlotte Nachtegael", "email": "Charlotte.Nachtegael@ulb.ac.be", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null } ], "owner": "tlenaert@ulb.ac.be", "additionDate": "2016-06-24T14:08:44Z", "lastUpdate": "2024-11-24T14:45:32.345721Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE", "emmaver" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Oligogenic resource for variant analysis (ORVAL)", "description": "ORVAL is the first web bioinformatics platform for the exploration of predicted candidate disease-causing variant combinations, aiming to aid in uncovering the causes of oligogenic diseases (i.e. diseases caused by variants in a small number of genes). This tool integrates innovative machine learning methods for combinatorial variant pathogenicity prediction, further external annotations and interactive and exploratory visualisation techniques.", "homepage": "https://orval.ibsquare.be", "biotoolsID": "Oligogenic_resource_for_variant_analysis", "biotoolsCURIE": "biotools:Oligogenic_resource_for_variant_analysis", "version": [ "3.0.0" ], "otherID": [], "relation": [ { "biotoolsID": "variant_combinaton_pathogenicity_predictor", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0331", "term": "Variant effect prediction" }, { "uri": "http://edamontology.org/operation_3439", "term": "Pathway or network prediction" }, { "uri": "http://edamontology.org/operation_3083", "term": "Pathway or network visualisation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_1775", "term": "Function analysis" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "CC-BY-4.0", "collectionID": [ "ELIXIR-BE", "RD-connect", "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Belgium" ], "elixirCommunity": [ "Rare Diseases" ], "link": [], "download": [], "documentation": [ { "url": "https://orval.ibsquare.be/documentation", "type": [ "User manual", "FAQ" ], "note": null }, { "url": "https://orval-dev.ibsquare.be/updates", "type": [ "Release notes" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkz437", "pmid": "31147699", "pmcid": "PMC6602484", "type": [], "version": null, "note": null, "metadata": { "title": "ORVAL: a novel platform for the prediction and exploration of disease-causing oligogenic variant combinations", "abstract": "A tremendous amount of DNA sequencing data is being produced around the world with the ambition to capture in more detail the mechanisms underlying human diseases. While numerous bioinformatics tools exist that allow the discovery of causal variants in Mendelian diseases, little to no support is provided to do the same for variant combinations, an essential task for the discovery of the causes of oligogenic diseases. ORVAL (the Oligogenic Resource for Variant AnaLysis), which is presented here, provides an answer to this problem by focusing on generating networks of candidate pathogenic variant combinations in gene pairs, as opposed to isolated variants in unique genes. This online platform integrates innovative machine learning methods for combinatorial variant pathogenicity prediction with visualization techniques, offering several interactive and exploratory tools, such as pathogenic gene and protein interaction networks, a ranking of pathogenic gene pairs, as well as visual mappings of the cellular location and pathway information. ORVAL is the first web-based exploration platform dedicated to identifying networks of candidate pathogenic variant combinations with the sole ambition to help in uncovering oligogenic causes for patients that cannot rely on the classical disease analysis tools. ORVAL is available at https://orval.ibsquare.be.", "date": "2019-07-01T00:00:00Z", "citationCount": 46, "authors": [ { "name": "Renaux A." }, { "name": "Papadimitriou S." }, { "name": "Versbraegen N." }, { "name": "Nachtegael C." }, { "name": "Boutry S." }, { "name": "Nowe A." }, { "name": "Smits G." }, { "name": "Lenaerts T." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Tom Lenaerts", "email": "tlenaert@ulb.ac.be", "url": "https://www.ibsquare.be", "orcidid": "https://orcid.org/0000-0003-3645-1455", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Alexandre Renaux", "email": "alexandre.renaux@ulb.ac.be", "url": "https://www.ibsquare.be", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Interuniversity Institute of Bioinformatics in Brussels", "email": null, "url": "https://www.ibsquare.be", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "tlenaert@ulb.ac.be", "additionDate": "2019-07-03T15:25:53Z", "lastUpdate": "2024-11-24T14:45:30.540434Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE", "emmaver" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "HGMD", "description": "The Human Gene Mutation Database (HGMD) - comprehensive collection of germline mutations in nuclear genes that underlie, or are associated with, human inherited disease. It is a flexible resource that can be adapted to a broad range of applications including searching for an overview of known mutations associated with a particular disease, interpreting clinical test results or looking for the likely causal mutation in a list of variants.", "homepage": "http://www.hgmd.org", "biotoolsID": "hgmd", "biotoolsCURIE": "biotools:hgmd", "version": [], "otherID": [ { "value": "RRID:SCR_001621", "type": "rrid", "version": null } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3224", "term": "Gene set testing" }, { "uri": "http://edamontology.org/operation_3196", "term": "Genotyping" }, { "uri": "http://edamontology.org/operation_3436", "term": "Aggregation" }, { "uri": "http://edamontology.org/operation_3197", "term": "Genetic variation analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_2815", "term": "Human biology" }, { "uri": "http://edamontology.org/topic_0634", "term": "Pathology" }, { "uri": "http://edamontology.org/topic_3366", "term": "Data integration and warehousing" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "RD-connect", "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Restricted access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.hgmd.cf.ac.uk/docs/new_help.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1007/s00439-013-1358-4", "pmid": "24077912", "pmcid": "PMC3898141", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The Human Gene Mutation Database: Building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine", "abstract": "The Human Gene Mutation Database (HGMD®) is a comprehensive collection of germline mutations in nuclear genes that underlie, or are associated with, human inherited disease. By June 2013, the database contained over 141,000 different lesions detected in over 5,700 different genes, with new mutation entries currently accumulating at a rate exceeding 10,000 per annum. HGMD was originally established in 1996 for the scientific study of mutational mechanisms in human genes. However, it has since acquired a much broader utility as a central unified disease-oriented mutation repository utilized by human molecular geneticists, genome scientists, molecular biologists, clinicians and genetic counsellors as well as by those specializing in biopharmaceuticals, bioinformatics and personalized genomics. The public version of HGMD (http://www.hgmd.org) is freely available to registered users from academic institutions/non-profit organizations whilst the subscription version (HGMD Professional) is available to academic, clinical and commercial users under license via BIOBASE GmbH. © 2013 The Author(s).", "date": "2014-01-01T00:00:00Z", "citationCount": 1054, "authors": [ { "name": "Stenson P.D." }, { "name": "Mort M." }, { "name": "Ball E.V." }, { "name": "Shaw K." }, { "name": "Phillips A.D." }, { "name": "Cooper D.N." } ], "journal": "Human Genetics" } }, { "doi": "10.1136/jmg.2007.055210", "pmid": "18245393", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Human Gene Mutation Database: Towards a comprehensive central mutation database", "abstract": "", "date": "2008-02-01T00:00:00Z", "citationCount": 91, "authors": [ { "name": "Stenson P.D." }, { "name": "Ball E." }, { "name": "Howells K." }, { "name": "Phillips A." }, { "name": "Mort M." }, { "name": "Cooper D.N." } ], "journal": "Journal of Medical Genetics" } }, { "doi": "10.1002/humu.10212", "pmid": "12754702", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Human Gene Mutation Database (HGMD®): 2003 Update", "abstract": "The Human Gene Mutation Database (HGMD) constitutes a comprehensive core collection of data on germ-line mutations in nuclear genes underlying or associated with human inherited disease (www.hgmd.org). Data catalogued includes: single base-pair substitutions in coding, regulatory and splicing-relevant regions; micro-deletions and micro-insertions; indels; triplet repeat expansions as well as gross deletions; insertions; duplications; and complex rearrangements. Each mutation is entered into HGMD only once in order to avoid confusion between recurrent and identical-by-descent lesions. By March 2003, the database contained in excess of 39,415 different lesions detected in 1,516 different nuclear genes, with new entries currently accumulating at a rate exceeding 5,000 per annum. Since its inception, HGMD has been expanded to include cDNA reference sequences for more than 87% of listed genes, splice junction sequences, disease-associated and functional polymorphisms, as well as links to data present in publicly available online locus-specific mutation databases. Although HGMD has recently entered into a licensing agreement with Celera Genomics (Rockville, MD), mutation data will continue to be made freely available via the Internet. © 2003 Wiley-Liss, Inc.", "date": "2003-06-16T00:00:00Z", "citationCount": 1522, "authors": [ { "name": "Stenson P.D." }, { "name": "Ball E.V." }, { "name": "Mort M." }, { "name": "Phillips A.D." }, { "name": "Shiel J.A." }, { "name": "Thomas N.S.T." }, { "name": "Abeysinghe S." }, { "name": "Krawczak M." }, { "name": "Cooper D.N." } ], "journal": "Human Mutation" } }, { "doi": "10.1186/gm13", "pmid": "19348700", "pmcid": "PMC2651586", "type": [], "version": null, "note": null, "metadata": { "title": "The human gene mutation database: 2008 update", "abstract": "The Human Gene Mutation Database (HGMD®) is a comprehensive core collection of germlinemutations in nuclear genes that underlie or are associated with human inherited disease. Here we summarize the history of the database and its current resources. By December 2008, thedatabase contained over 85,000 different lesions detected in 3,253 ifferent genes, with new entries currently accumulating at a rate exceeding 9,000 per annum. Although originally established for the scientific study of mutational mechanisms in human genes, HGMD has since acquired a much broader utility for researchers, physicians, clinicians and genetic counselors as well as for companies specializing in biopharmaceuticals, bioinformatics and personalized genomics. HGMD was first made publicly available in April 1996, and a collaboration was initiated in 2006 between HGMD and BIOBASE GmbH. This cooperative agreement covers the exclusive worldwide marketing of the most up-to-date (subscription) version of HGMD, HGMD Professional, to academic, clinical and commercial users. © 2009 BioMed Central Ltd.", "date": "2009-01-22T00:00:00Z", "citationCount": 735, "authors": [ { "name": "Stenson P.D." }, { "name": "Mort M." }, { "name": "Ball E.V." }, { "name": "Howells K." }, { "name": "Phillips P.D." }, { "name": "Cooper D.N." }, { "name": "Thomas N.S.T." } ], "journal": "Genome Medicine" } }, { "doi": "10.1007/s00439-017-1779-6", "pmid": "28349240", "pmcid": "PMC5429360", "type": [], "version": null, "note": null, "metadata": { "title": "The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies", "abstract": "The Human Gene Mutation Database (HGMD®) constitutes a comprehensive collection of published germline mutations in nuclear genes that underlie, or are closely associated with human inherited disease. At the time of writing (March 2017), the database contained in excess of 203,000 different gene lesions identified in over 8000 genes manually curated from over 2600 journals. With new mutation entries currently accumulating at a rate exceeding 17,000 per annum, HGMD represents de facto the central unified gene/disease-oriented repository of heritable mutations causing human genetic disease used worldwide by researchers, clinicians, diagnostic laboratories and genetic counsellors, and is an essential tool for the annotation of next-generation sequencing data. The public version of HGMD (http://www.hgmd.org) is freely available to registered users from academic institutions and non-profit organisations whilst the subscription version (HGMD Professional) is available to academic, clinical and commercial users under license via QIAGEN Inc.", "date": "2017-06-01T00:00:00Z", "citationCount": 1003, "authors": [ { "name": "Stenson P.D." }, { "name": "Mort M." }, { "name": "Ball E.V." }, { "name": "Evans K." }, { "name": "Hayden M." }, { "name": "Heywood S." }, { "name": "Hussain M." }, { "name": "Phillips A.D." }, { "name": "Cooper D.N." } ], "journal": "Human Genetics" } } ], "credit": [ { "name": "Contact Form", "email": null, "url": "http://www.hgmd.cf.ac.uk/docs/comment_form.html", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-EE", "additionDate": "2017-03-04T22:58:49Z", "lastUpdate": "2024-11-24T14:15:54.565147Z", "editPermission": { "type": "group", "authors": [ "sergitobara", "Friederike" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Cytoscape", "description": "Open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.", "homepage": "http://www.cytoscape.org/", "biotoolsID": "cytoscape", "biotoolsCURIE": "biotools:cytoscape", "version": [ "3.7.1" ], "otherID": [], "relation": [ { "biotoolsID": "scnetviz", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3562", "term": "Network simulation" }, { "uri": "http://edamontology.org/operation_3083", "term": "Pathway or network visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Suite" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_0092", "term": "Data visualisation" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": null, "collectionID": [ "Rare Disease", "EBI Training Tools" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "https://cytoscape.org/download.html", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/cytoscape/cytoscape-tutorials/wiki", "type": [ "Training material" ], "note": "Tutorial material" }, { "url": "https://github.com/cytoscape/cytoscape", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1101/gr.1239303", "pmid": "14597658", "pmcid": "PMC403769", "type": [], "version": null, "note": null, "metadata": { "title": "Cytoscape: A software Environment for integrated models of biomolecular interaction networks", "abstract": "Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.", "date": "2003-11-01T00:00:00Z", "citationCount": 33622, "authors": [ { "name": "Shannon P." }, { "name": "Markiel A." }, { "name": "Ozier O." }, { "name": "Baliga N.S." }, { "name": "Wang J.T." }, { "name": "Ramage D." }, { "name": "Amin N." }, { "name": "Schwikowski B." }, { "name": "Ideker T." } ], "journal": "Genome Research" } } ], "credit": [ { "name": null, "email": null, "url": "https://groups.google.com/forum/?fromgroups#!forum/cytoscape-helpdesk", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ebi_training_import", "additionDate": "2017-01-17T15:07:48Z", "lastUpdate": "2024-11-24T14:15:02.391096Z", "editPermission": { "type": "group", "authors": [ "lmatalonga", "johangustafsson", "rioualen" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "WS-SNPs-and-GO", "description": "A web server for predicting disease associated variations from protein sequence and structure.", "homepage": "http://snps.biofold.org/snps-and-go", "biotoolsID": "ws_snps_and_go", "biotoolsCURIE": "biotools:ws_snps_and_go", "version": [ "2.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3225", "term": "Variant classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1127", "term": "PDB ID" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_1467", "term": "Protein chain" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_1176", "term": "GO concept ID" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] }, { "data": { "uri": "http://edamontology.org/data_2209", "term": "Mutation ID" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1622", "term": "Disease report" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": "SNPs&GO 3D", "cmd": null } ], "toolType": [ "Web application", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0123", "term": "Protein properties" }, { "uri": "http://edamontology.org/topic_0634", "term": "Pathology" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Italy" ], "elixirCommunity": [ "Rare Diseases" ], "link": [], "download": [ { "url": "https://hub.docker.com/r/biofold/snps-and-go", "type": "Container file", "note": null, "version": "2.0" } ], "documentation": [ { "url": "http://snps.biofold.org/snps-and-go/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/1471-2105-12-s4-s3", "pmid": "21992054", "pmcid": "PMC3194195", "type": [ "Method" ], "version": null, "note": null, "metadata": { "title": "Improving the prediction of disease-related variants using protein three-dimensional structure", "abstract": "Background: Single Nucleotide Polymorphisms (SNPs) are an important source of human genome variability. Non-synonymous SNPs occurring in coding regions result in single amino acid polymorphisms (SAPs) that may affect protein function and lead to pathology. Several methods attempt to estimate the impact of SAPs using different sources of information. Although sequence-based predictors have shown good performance, the quality of these predictions can be further improved by introducing new features derived from three-dimensional protein structures.Results: In this paper, we present a structure-based machine learning approach for predicting disease-related SAPs. We have trained a Support Vector Machine (SVM) on a set of 3,342 disease-related mutations and 1,644 neutral polymorphisms from 784 protein chains. We use SVM input features derived from the protein's sequence, structure, and function. After dataset balancing, the structure-based method (SVM-3D) reaches an overall accuracy of 85%, a correlation coefficient of 0.70, and an area under the receiving operating characteristic curve (AUC) of 0.92. When compared with a similar sequence-based predictor, SVM-3D results in an increase of the overall accuracy and AUC by 3%, and correlation coefficient by 0.06. The robustness of this improvement has been tested on different datasets and in all the cases SVM-3D performs better than previously developed methods even when compared with PolyPhen2, which explicitly considers in input protein structure information.Conclusion: This work demonstrates that structural information can increase the accuracy of disease-related SAPs identification. Our results also quantify the magnitude of improvement on a large dataset. This improvement is in agreement with previously observed results, where structure information enhanced the prediction of protein stability changes upon mutation. Although the structural information contained in the Protein Data Bank is limiting the application and the performance of our structure-based method, we expect that SVM-3D will result in higher accuracy when more structural date become available. © 2011 Capriotti; licensee BioMed Central Ltd.", "date": "2011-07-05T00:00:00Z", "citationCount": 104, "authors": [ { "name": "Capriotti E." }, { "name": "Altman R.B." } ], "journal": "BMC Bioinformatics" } }, { "doi": "10.1002/humu.21047", "pmid": "19514061", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Functional annotations improve the predictive score of human disease-related mutations in proteins", "abstract": "Single nucleotide polymorphisms (SNPs) are the simplest and most frequent form of human DNA variation, also valuable as genetic markers of disease susceptibility. The most investigated SNPs are missense mutations resulting in residue substitutions in the protein. Here we propose SNPs&GO, an accurate method that, starting from a protein sequence, can predict whether a mutation is disease related or not by exploiting the protein functional annotation. The scoring efficiency of SNPs&GO is as high as 82%, with a Matthews correlation coefficient equal to 0.63 over a wide set of annotated nonsynonymous mutations in proteins, including 16,330 disease-related and 17,432 neutral polymorphisms. SNPs&GO collects in unique framework information derived from protein sequence, evolutionary information, and function as encoded in the Gene Ontology terms, and outperforms other available predictive methods. © 2009 Wiley-Liss, Inc.", "date": "2009-08-01T00:00:00Z", "citationCount": 515, "authors": [ { "name": "Calabrese R." }, { "name": "Capriotti E." }, { "name": "Fariselli P." }, { "name": "Martelli P.L." }, { "name": "Casadio R." } ], "journal": "Human Mutation" } } ], "credit": [ { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": "http://www.biocomp.unibo.it", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Emidio Capriotti", "email": "emidio.capriotti@gmail.com", "url": null, "orcidid": "http://orcid.org/0000-0002-2323-0963", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact" ], "note": null }, { "name": "Rita Casadio", "email": "casadio@biocomp.unibo.it", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2017-03-01T16:16:45Z", "lastUpdate": "2024-11-24T14:11:29.726150Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE", "ELIXIR-ITA-BOLOGNA", "emidio" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PhenPath", "description": "A tool for characterizing biological functions underlying different phenotypes.\n\na web server for associating phenotypes with molecular functional annotations.\n\nPhenPath includes a database and a tool:.\n'", "homepage": "http://phenpath.biocomp.unibo.it", "biotoolsID": "phenpath", "biotoolsCURIE": "biotools:phenpath", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_3501", "term": "Enrichment analysis" }, { "uri": "http://edamontology.org/operation_3672", "term": "Gene functional annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1150", "term": "Disease ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3668", "term": "Disease name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3275", "term": "Phenotype name" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1622", "term": "Disease report" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_0634", "term": "Pathology" }, { "uri": "http://edamontology.org/topic_3305", "term": "Public health and epidemiology" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [], "license": "CC-BY-NC-4.0", "collectionID": [ "Rare Disease", "Bologna Biocomputing Group" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Italy" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://phenpath.biocomp.unibo.it/phenpath/help_page.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1186/s12864-019-5868-x", "pmid": "31307376", "pmcid": "PMC6631446", "type": [], "version": null, "note": null, "metadata": { "title": "PhenPath: A tool for characterizing biological functions underlying different phenotypes", "abstract": "Background: Many diseases are associated with complex patterns of symptoms and phenotypic manifestations. Parsimonious explanations aim at reconciling the multiplicity of phenotypic traits with the perturbation of one or few biological functions. For this, it is necessary to characterize human phenotypes at the molecular and functional levels, by exploiting gene annotations and known relations among genes, diseases and phenotypes. This characterization makes it possible to implement tools for retrieving functions shared among phenotypes, co-occurring in the same patient and facilitating the formulation of hypotheses about the molecular causes of the disease. Results: We introduce PhenPath, a new resource consisting of two parts: PhenPathDB and PhenPathTOOL. The former is a database collecting the human genes associated with the phenotypes described in Human Phenotype Ontology (HPO) and OMIM Clinical Synopses. Phenotypes are then associated with biological functions and pathways by means of NET-GE, a network-based method for functional enrichment of sets of genes. The present version considers only phenotypes related to diseases. PhenPathDB collects information for 18 OMIM Clinical synopses and 7137 HPO phenotypes, related to 4292 diseases and 3446 genes. Enrichment of Gene Ontology annotations endows some 87.7, 86.9 and 73.6% of HPO phenotypes with Biological Process, Molecular Function and Cellular Component terms, respectively. Furthermore, 58.8 and 77.8% of HPO phenotypes are also enriched for KEGG and Reactome pathways, respectively. Based on PhenPathDB, PhenPathTOOL analyzes user-defined sets of phenotypes retrieving diseases, genes and functional terms which they share. This information can provide clues for interpreting the co-occurrence of phenotypes in a patient. Conclusions: The resource allows finding molecular features useful to investigate diseases characterized by multiple phenotypes, and by this, it can help researchers and physicians in identifying molecular mechanisms and biological functions underlying the concomitant manifestation of phenotypes. The resource is freely available at http://phenpath.biocomp.unibo.it.", "date": "2019-07-16T00:00:00Z", "citationCount": 8, "authors": [ { "name": "Babbi G." }, { "name": "Martelli P.L." }, { "name": "Casadio R." } ], "journal": "BMC Genomics" } } ], "credit": [ { "name": "Pier Luigi Martelli", "email": "pierluigi.martelli@unibo.it", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Giulia Babbi", "email": "giulia.babbi@unibo.it", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Primary contact" ], "note": null }, { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2021-01-20T10:58:38Z", "lastUpdate": "2024-11-24T14:10:12.678273Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-ITA-BOLOGNA" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "SNPs and GO", "description": "A server for the prediction of single point protein mutations likely to be involved in the insurgence of diseases in humans.s.", "homepage": "http://snps-and-go.biocomp.unibo.it/snps-and-go/index.html", "biotoolsID": "snps_and_go", "biotoolsCURIE": "biotools:snps_and_go", "version": [ "1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_2414", "term": "Protein function analysis" }, { "uri": "http://edamontology.org/operation_3225", "term": "Variant classification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3021", "term": "UniProt accession" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0896", "term": "Protein report" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": "Prediction", "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" }, { "uri": "http://edamontology.org/topic_3473", "term": "Data mining" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "RD-connect", "Rare Disease", "Bologna Biocomputing Group" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Italy" ], "elixirCommunity": [ "Rare Diseases" ], "link": [], "download": [], "documentation": [ { "url": "http://snps-and-go.biocomp.unibo.it/snps-and-go/help2.htm", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1002/humu.21047", "pmid": "19514061", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Functional annotations improve the predictive score of human disease-related mutations in proteins", "abstract": "Single nucleotide polymorphisms (SNPs) are the simplest and most frequent form of human DNA variation, also valuable as genetic markers of disease susceptibility. The most investigated SNPs are missense mutations resulting in residue substitutions in the protein. Here we propose SNPs&GO, an accurate method that, starting from a protein sequence, can predict whether a mutation is disease related or not by exploiting the protein functional annotation. The scoring efficiency of SNPs&GO is as high as 82%, with a Matthews correlation coefficient equal to 0.63 over a wide set of annotated nonsynonymous mutations in proteins, including 16,330 disease-related and 17,432 neutral polymorphisms. SNPs&GO collects in unique framework information derived from protein sequence, evolutionary information, and function as encoded in the Gene Ontology terms, and outperforms other available predictive methods. © 2009 Wiley-Liss, Inc.", "date": "2009-08-01T00:00:00Z", "citationCount": 515, "authors": [ { "name": "Calabrese R." }, { "name": "Capriotti E." }, { "name": "Fariselli P." }, { "name": "Martelli P.L." }, { "name": "Casadio R." } ], "journal": "Human Mutation" } } ], "credit": [ { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Rita Casadio", "email": "rita.casadio@unibo.it", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Pier Luigi Martelli", "email": "pierluigi.martelli@unibo.it", "url": null, "orcidid": "https://orcid.org/0000-0002-0274-5669", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2015-01-22T11:31:41Z", "lastUpdate": "2024-11-24T14:09:44.753852Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "eDGAR", "description": "A database of Disease-Gene Associations with annotated Relationships among genes.", "homepage": "http://edgar.biocomp.unibo.it", "biotoolsID": "edgar", "biotoolsCURIE": "biotools:edgar", "version": [], "otherID": [ { "value": "doi:10.25504/FAIRsharing.29EHM2", "type": "doi", "version": null } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3561", "term": "Database comparison" }, { "uri": "http://edamontology.org/operation_3197", "term": "Genetic variation analysis" }, { "uri": "http://edamontology.org/operation_2497", "term": "Pathway or network analysis" }, { "uri": "http://edamontology.org/operation_3672", "term": "Gene functional annotation" }, { "uri": "http://edamontology.org/operation_0276", "term": "Protein interaction network analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3668", "term": "Disease name" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1622", "term": "Disease report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": "For each heterogeneous or polygenic disease, eDGAR provides information on the relationship among the proteins encoded by the involved genes.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3561", "term": "Database comparison" }, { "uri": "http://edamontology.org/operation_2497", "term": "Pathway or network analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1153", "term": "OMIM ID" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1622", "term": "Disease report" }, "format": [ { "uri": "http://edamontology.org/format_3752", "term": "CSV" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": "For each heterogeneous or polygenic disease, eDGAR provides information on the relationship among the proteins encoded by the involved genes.", "cmd": null } ], "toolType": [ "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0634", "term": "Pathology" }, { "uri": "http://edamontology.org/topic_3574", "term": "Human genetics" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "JavaScript" ], "license": "CC-BY-4.0", "collectionID": [ "RD-connect", "Rare Disease", "Bologna Biocomputing Group" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Italy" ], "elixirCommunity": [ "Rare Diseases" ], "link": [], "download": [], "documentation": [ { "url": "http://edgar.biocomp.unibo.it/gene_disease_db/tutorial.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1186/s12864-017-3911-3", "pmid": "28812536", "pmcid": "PMC5558190", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "eDGAR: A database of disease-gene associations with annotated relationships among genes", "abstract": "Background: Genetic investigations, boosted by modern sequencing techniques, allow dissecting the genetic component of different phenotypic traits. These efforts result in the compilation of lists of genes related to diseases and show that an increasing number of diseases is associated with multiple genes. Investigating functional relations among genes associated with the same disease contributes to highlighting molecular mechanisms of the pathogenesis. Results: We present eDGAR, a database collecting and organizing the data on gene/disease associations as derived from OMIM, Humsavar and ClinVar. For each disease-associated gene, eDGAR collects information on its annotation. Specifically, for lists of genes, eDGAR provides information on: i) interactions retrieved from PDB, BIOGRID and STRING; ii) co-occurrence in stable and functional structural complexes; iii) shared Gene Ontology annotations; iv) shared KEGG and REACTOME pathways; v) enriched functional annotations computed with NET-GE; vi) regulatory interactions derived from TRRUST; vii) localization on chromosomes and/or co-localisation in neighboring loci. The present release of eDGAR includes 2672 diseases, related to 3658 different genes, for a total number of 5729 gene-disease associations. 71% of the genes are linked to 621 multigenic diseases and eDGAR highlights their common GO terms, KEGG/REACTOME pathways, physical and regulatory interactions. eDGAR includes a network based enrichment method for detecting statistically significant functional terms associated to groups of genes. Conclusions: eDGAR offers a resource to analyze disease-gene associations. In multigenic diseases genes can share physical interactions and/or co-occurrence in the same functional processes. eDGAR is freely available at: edgar. biocomp.unibo.it.", "date": "2017-01-01T00:00:00Z", "citationCount": 48, "authors": [ { "name": "Babbi G." }, { "name": "Martelli P.L." }, { "name": "Profiti G." }, { "name": "Bovo S." }, { "name": "Savojardo C." }, { "name": "Casadio R." } ], "journal": "BMC Genomics" } } ], "credit": [ { "name": "Giulia Babbi", "email": "giulia.babbi3@unibo.it", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "ELIXIR-ITA-BOLOGNA", "email": null, "url": "http://biocomp.unibo.it/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "ELIXIR-ITA-BOLOGNA", "additionDate": "2017-03-13T17:04:55Z", "lastUpdate": "2024-11-24T14:09:23.960492Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE", "lmatalonga" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "BridgeDb API", "description": "BridgeDb is a framework for finding and mapping equivalent database identifiers. It has many facets: it is both a framework, live services, and are identifier mapping files for genes, proteins, and metabolites.", "homepage": "http://www.bridgedb.org/", "biotoolsID": "bridgedb_api", "biotoolsCURIE": "biotools:bridgedb_api", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0842", "term": "Identifier" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0842", "term": "Identifier" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [] } ], "note": "Returns a list of xrefs that map to a given identifier, and data source. Optionally restrict results to a given data source.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1045", "term": "Species name" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0842", "term": "Identifier" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0842", "term": "Identifier" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [] } ], "note": "Returns `true` or `false` based on whether or not an xref exists in the database given an identifier, data source, and organism.", "cmd": null } ], "toolType": [ "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_3345", "term": "Data identity and mapping" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": null, "collectionID": [ "Rare Disease", "BridgeDb" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [ "Interoperability" ], "elixirNode": [ "Netherlands" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "https://www.bridgedb.org/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1186/1471-2105-11-5", "pmid": "20047655", "pmcid": "PMC2824678", "type": [], "version": null, "note": null, "metadata": { "title": "The EDKB: An established knowledge base for endocrine disrupting chemicals", "abstract": "Background: Endocrine disruptors (EDs) and their broad range of potential adverse effects in humans and other animals have been a concern for nearly two decades. Many putative EDs are widely used in commercial products regulated by the Food and Drug Administration (FDA) such as food packaging materials, ingredients of cosmetics, medical and dental devices, and drugs. The Endocrine Disruptor Knowledge Base (EDKB) project was initiated in the mid 1990's by the FDA as a resource for the study of EDs. The EDKB database, a component of the project, contains data across multiple assay types for chemicals across a broad structural diversity. This paper demonstrates the utility of EDKB database, an integral part of the EDKB project, for understanding and prioritizing EDs for testing.Results: The EDKB database currently contains 3,257 records of over 1,800 EDs from different assays including estrogen receptor binding, androgen receptor binding, uterotropic activity, cell proliferation, and reporter gene assays. Information for each compound such as chemical structure, assay type, potency, etc. is organized to enable efficient searching. A user-friendly interface provides rapid navigation, Boolean searches on EDs, and both spreadsheet and graphical displays for viewing results. The search engine implemented in the EDKB database enables searching by one or more of the following fields: chemical structure (including exact search and similarity search), name, molecular formula, CAS registration number, experiment source, molecular weight, etc. The data can be cross-linked to other publicly available and related databases including TOXNET, Cactus, ChemIDplus, ChemACX, Chem Finder, and NCI DTP. . Conclusion: The EDKB database enables scientists and regulatory reviewers to quickly access ED data from multiple assays for specific or similar compounds. The data have been used to categorize chemicals according to potential risks for endocrine activity, thus providing a basis for prioritizing chemicals for more definitive but expensive testing. The EDKB database is publicly available and can be found online at http://edkb.fda.gov/webstart/edkb/index.html.Disclaimer:The views presented in this article do not necessarily reflect those of the US Food and Drug Administration. © 2010 Tong et al; licensee BioMed Central Ltd.", "date": "2010-10-07T00:00:00Z", "citationCount": 80, "authors": [ { "name": "Ding D." }, { "name": "Xu L." }, { "name": "Fang H." }, { "name": "Hong H." }, { "name": "Perkins R." }, { "name": "Harris S." }, { "name": "Bearden E.D." }, { "name": "Shi L." }, { "name": "Tong W." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": null, "email": "bridgedb-discuss@googlegroups.com", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "egonw", "additionDate": "2017-07-20T18:20:28Z", "lastUpdate": "2024-11-24T14:02:46.528009Z", "editPermission": { "type": "group", "authors": [ "ChrisEvelo", "LanfearJ" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Job Dispatcher", "description": "EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies. Example tools include those to compute sequence similarity searches, pairwise/multiple sequence alignment and protein functional analysis.", "homepage": "http://www.ebi.ac.uk/jdispatcher/", "biotoolsID": "jdispatcher", "biotoolsCURIE": "biotools:jdispatcher", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0346", "term": "Sequence similarity search" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_2414", "term": "Protein function analysis" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" }, { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web API", "Web application", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0078", "term": "Proteins" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_1775", "term": "Function analysis" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java", "Perl", "Python" ], "license": null, "collectionID": [ "EBI Tools", "Job Dispatcher Tools", "BioExcel", "Rare Disease", "COVID-19" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.ebi.ac.uk/about/contact/support/job-dispatcher-services", "type": [ "Helpdesk" ], "note": null } ], "download": [], "documentation": [ { "url": "http://www.ebi.ac.uk/about/terms-of-use", "type": [ "Terms of use" ], "note": null }, { "url": "https://www.ebi.ac.uk/jdispatcher/help", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkae241", "pmid": "38597606", "pmcid": "PMC11223882", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The EMBL-EBI Job Dispatcher sequence analysis tools framework in 2024", "abstract": "The EMBL-EBI Job Dispatcher sequence analysis tools framework (https://www.ebi.ac.uk/jdispatcher) enables the scientific community to perform a diverse range of sequence analyses using popular bioinformatics applications. Free access to the tools and required sequence datasets is provided through user-friendly web applications, as well as via RESTful and SOAP-based APIs. These are integrated into popular EMBL-EBI resources such as UniProt, InterPro, ENA and Ensembl Genomes. This paper overviews recent improvements to Job Dispatcher, including its brand new website and documentation, enhanced visualisations, improved job management, and a rising trend of user reliance on the service from low- and middle-income regions.", "date": "2024-07-05T00:00:00Z", "citationCount": 60, "authors": [ { "name": "Madeira F." }, { "name": "Madhusoodanan N." }, { "name": "Lee J." }, { "name": "Eusebi A." }, { "name": "Niewielska A." }, { "name": "Tivey A.R.N." }, { "name": "Lopez R." }, { "name": "Butcher S." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkac240", "pmid": "35412617", "pmcid": "PMC9252731", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Search and sequence analysis tools services from EMBL-EBI in 2022", "abstract": "The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI's data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic.", "date": "2022-07-05T00:00:00Z", "citationCount": 1248, "authors": [ { "name": "Madeira F." }, { "name": "Pearce M." }, { "name": "Tivey A.R.N." }, { "name": "Basutkar P." }, { "name": "Lee J." }, { "name": "Edbali O." }, { "name": "Madhusoodanan N." }, { "name": "Kolesnikov A." }, { "name": "Lopez R." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkz268", "pmid": "30976793", "pmcid": "PMC6602479", "type": [], "version": null, "note": null, "metadata": { "title": "The EMBL-EBI search and sequence analysis tools APIs in 2019", "abstract": "The EMBL-EBI provides free access to popular bioinformatics sequence analysis applications as well as to a full-featured text search engine with powerful cross-referencing and data retrieval capabilities. Access to these services is provided via user-friendly web interfaces and via established RESTful and SOAP Web Services APIs (https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/EMBL-EBI+Web+Services+APIs+-+Data+Retrieval). Both systems have been developed with the same core principles that allow them to integrate an ever-increasing volume of biological data, making them an integral part of many popular data resources provided at the EMBL-EBI. Here, we describe the latest improvements made to the frameworks which enhance the interconnectivity between public EMBL-EBI resources and ultimately enhance biological data discoverability, accessibility, interoperability and reusability.", "date": "2019-07-01T00:00:00Z", "citationCount": 3124, "authors": [ { "name": "Madeira F." }, { "name": "Park Y.M." }, { "name": "Lee J." }, { "name": "Buso N." }, { "name": "Gur T." }, { "name": "Madhusoodanan N." }, { "name": "Basutkar P." }, { "name": "Tivey A.R.N." }, { "name": "Potter S.C." }, { "name": "Finn R.D." }, { "name": "Lopez R." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "EMBL - EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Job Dispatcher", "email": null, "url": "http://www.ebi.ac.uk/jdispatcher/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "jdispatcher", "additionDate": "2022-11-04T11:11:36.831993Z", "lastUpdate": "2024-11-24T14:00:40.196248Z", "editPermission": { "type": "group", "authors": [ "biomadeira", "nandana" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "pyKVFinder", "description": "Python-C Parallel KVFinder (pyKVFinder) is an efficient and integrable Python package for biomolecular cavity detection and characterization in data science. Besides conventional cavity properties such as volume and area, which are stored as Python dictionaries, pyKVFinder computes cavity depth and hydropathy. Similar to cavity points, these spatial and physicochemical properties are stored as Python ndarrays and can be visualized using Python molecular visualization widgets. In general, pyKVFinder is designed for efficient scripting routines built on easy-to-handle data structures, such as Python dictionaries and NumPy N-dimensional arrays (ndarrays), and can be building blocks for data science and drug design applications.", "homepage": "https://github.com/LBC-LNBio/pyKVFinder", "biotoolsID": "pykvfinder", "biotoolsCURIE": "biotools:pykvfinder", "version": [], "otherID": [], "relation": [ { "biotoolsID": "KVFinder", "type": "isNewVersionOf" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3351", "term": "Molecular surface analysis" }, { "uri": "http://edamontology.org/operation_2483", "term": "Structure comparison" }, { "uri": "http://edamontology.org/operation_2575", "term": "Binding site prediction" }, { "uri": "http://edamontology.org/operation_0250", "term": "Protein property calculation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0883", "term": "Structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" }, { "uri": "http://edamontology.org/format_3877", "term": "XYZ" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2878", "term": "Protein structural motif" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Library", "Script", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0081", "term": "Structure analysis" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_3315", "term": "Mathematics" }, { "uri": "http://edamontology.org/topic_1317", "term": "Structural biology" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_3332", "term": "Computational chemistry" }, { "uri": "http://edamontology.org/topic_0166", "term": "Protein structural motifs and surfaces" } ], "operatingSystem": [ "Mac", "Windows", "Linux" ], "language": [ "Python", "C" ], "license": "GPL-3.0", "collectionID": [ "KVFinder suite", "Rare Disease", "COVID-19" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/LBC-LNBio/pyKVFinder", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://lbc-lnbio.github.io/pyKVFinder/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1186/s12859-021-04519-4", "pmid": "34930115", "pmcid": "PMC8685811", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "pyKVFinder: an efficient and integrable Python package for biomolecular cavity detection and characterization in data science", "abstract": "Background: Biomolecular interactions that modulate biological processes occur mainly in cavities throughout the surface of biomolecular structures. In the data science era, structural biology has benefited from the increasing availability of biostructural data due to advances in structural determination and computational methods. In this scenario, data-intensive cavity analysis demands efficient scripting routines built on easily manipulated data structures. To fulfill this need, we developed pyKVFinder, a Python package to detect and characterize cavities in biomolecular structures for data science and automated pipelines. Results: pyKVFinder efficiently detects cavities in biomolecular structures and computes their volume, area, depth and hydropathy, storing these cavity properties in NumPy arrays. Benefited from Python ecosystem interoperability and data structures, pyKVFinder can be integrated with third-party scientific packages and libraries for mathematical calculations, machine learning and 3D visualization in automated workflows. As proof of pyKVFinder’s capabilities, we successfully identified and compared ADRP substrate-binding site of SARS-CoV-2 and a set of homologous proteins with pyKVFinder, showing its integrability with data science packages such as matplotlib, NGL Viewer, SciPy and Jupyter notebook. Conclusions: We introduce an efficient, highly versatile and easily integrable software for detecting and characterizing biomolecular cavities in data science applications and automated protocols. pyKVFinder facilitates biostructural data analysis with scripting routines in the Python ecosystem and can be building blocks for data science and drug design applications.", "date": "2021-12-01T00:00:00Z", "citationCount": 12, "authors": [ { "name": "Guerra J.V.S." }, { "name": "Ribeiro-Filho H.V." }, { "name": "Jara G.E." }, { "name": "Bortot L.O." }, { "name": "Pereira J.G.C." }, { "name": "Lopes-de-Oliveira P.S." } ], "journal": "BMC Bioinformatics" } }, { "doi": "10.1021/acs.jcim.3c00328", "pmid": "37129917", "pmcid": null, "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "Cavity Characterization in Supramolecular Cages", "abstract": "Confining molecular guests within artificial hosts has provided a major driving force in the rational design of supramolecular cages with tailored properties. Over the last 30 years, a set of design strategies have been developed that enabled the controlled synthesis of a myriad of cages. Recently, there has been a growing interest in involving in silico methods in this toolbox. Cavity shape and size are important parameters that can be easily accessed by inexpensive geometric algorithms. Although these algorithms are well developed for the detection of nonartificial cavities (e.g., enzymes), they are not routinely used for the rational design of supramolecular cages. In order to test the capabilities of this tool, we have evaluated the performance and characteristics of seven different cavity characterization software in the context of 22 analogues of well-known supramolecular cages. Among the tested software, KVFinder project and Fpocket proved to be the most software to characterize supramolecular cavities. With the results of this work, we aim to popularize this underused technique within the supramolecular community.", "date": "2023-06-26T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Guerra J.V.S." }, { "name": "Alves L.F.G." }, { "name": "Bourissou D." }, { "name": "Lopes-De-Oliveira P.S." }, { "name": "Szaloki G." } ], "journal": "Journal of Chemical Information and Modeling" } } ], "credit": [ { "name": "João V. S. Guerra", "email": "joao.guerra@lnbio.cnpem.br", "url": "https://github.com/jvsguerra", "orcidid": "https://orcid.org/0000-0002-6800-4425", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null }, { "name": "Helder V. Ribeiro-Filho", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Gabriel E. Jara", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Leandro O. Bortot", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "José G. C. Pereira", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Paulo S. Lopes-de-Oliveira", "email": "paulo.oliveira@lnbio.cnpem.br", "url": null, "orcidid": "https://orcid.org/0000-0002-1287-8019", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Provider" ], "note": null } ], "owner": "jvsguerra", "additionDate": "2022-05-17T20:35:45.357863Z", "lastUpdate": "2024-11-24T13:49:46.803306Z", "editPermission": { "type": "group", "authors": [ "jvsguerra" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "KVFinder-web", "description": "KVFinder-web is an open-source web-based application of an updated version of parKVFinder software (v1.2.0) for cavity detection and characterization of any type of biomolecular structure, including but not limited to proteins and nucleic acids. \n\nKVFinder-web employs a geometric grid-and-sphere-based method with a dual-probe system for efficient cavity detection. The web-based application provides comprehensive characterizations, including shape, volume, area, depth, constitutional, and hydropathy informations. Fo", "homepage": "https://kvfinder-web.cnpem.br/", "biotoolsID": "kvfinder-web", "biotoolsCURIE": "biotools:kvfinder-web", "version": [], "otherID": [], "relation": [ { "biotoolsID": "parKVFinder", "type": "uses" }, { "biotoolsID": "KVFinder", "type": "isNewVersionOf" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2575", "term": "Binding site prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0883", "term": "Structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2878", "term": "Protein structural motif" }, "format": [ { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web service", "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_1317", "term": "Structural biology" }, { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_0166", "term": "Protein structural motifs and surfaces" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "R", "C", "Other" ], "license": "Apache-2.0", "collectionID": [ "COVID-19", "Rare Disease", "KVFinder suite" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/LBC-LNBio/KVFinder-web", "type": [ "Other" ], "note": null }, { "url": "https://github.com/LBC-LNBio/KVFinder-web-service", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/LBC-LNBio/KVFinder-web-portal", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/LBC-LNBio/PyMOL-KVFinder-web-Tools", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://lbc-lnbio.github.io/KVFinder-web/", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkad324", "pmid": "37140050", "pmcid": "PMC10320092", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "KVFinder-web: A web-based application for detecting and characterizing biomolecular cavities", "abstract": "Molecular interactions that modulate catalytic processes occur mainly in cavities throughout the molecular surface. Such interactions occur with specific small molecules due to geometric and physicochemical complementarity with the receptor. In this scenario, we present KVFinder-web, an open-source web-based application of parKVFinder software for cavity detection and characterization of biomolecular structures. The KVFinder-web has two independent components: A RESTful web service and a web graphical portal. Our web service, KVFinder-web service, handles client requests, manages accepted jobs, and performs cavity detection and characterization on accepted jobs. Our graphical web portal, KVFinder-web portal, provides a simple and straightforward page for cavity analysis, which customizes detection parameters, submits jobs to the web service component, and displays cavities and characterizations. We provide a publicly available KVFinder-web at https://kvfinder-web.cnpem.br, running in a cloud environment as docker containers. Further, this deployment type allows KVFinder-web components to be configured locally and customized according to user demand. Hence, users may run jobs on a locally configured service or our public KVFinder-web.", "date": "2023-07-05T00:00:00Z", "citationCount": 7, "authors": [ { "name": "Guerra J.V.S." }, { "name": "Ribeiro-Filho H.V." }, { "name": "Pereira J.G.C." }, { "name": "Lopes-De-Oliveira P.S." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1021/acs.jcim.3c00328", "pmid": "37129917", "pmcid": null, "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "Cavity Characterization in Supramolecular Cages", "abstract": "Confining molecular guests within artificial hosts has provided a major driving force in the rational design of supramolecular cages with tailored properties. Over the last 30 years, a set of design strategies have been developed that enabled the controlled synthesis of a myriad of cages. Recently, there has been a growing interest in involving in silico methods in this toolbox. Cavity shape and size are important parameters that can be easily accessed by inexpensive geometric algorithms. Although these algorithms are well developed for the detection of nonartificial cavities (e.g., enzymes), they are not routinely used for the rational design of supramolecular cages. In order to test the capabilities of this tool, we have evaluated the performance and characteristics of seven different cavity characterization software in the context of 22 analogues of well-known supramolecular cages. Among the tested software, KVFinder project and Fpocket proved to be the most software to characterize supramolecular cavities. With the results of this work, we aim to popularize this underused technique within the supramolecular community.", "date": "2023-06-26T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Guerra J.V.S." }, { "name": "Alves L.F.G." }, { "name": "Bourissou D." }, { "name": "Lopes-De-Oliveira P.S." }, { "name": "Szaloki G." } ], "journal": "Journal of Chemical Information and Modeling" } } ], "credit": [ { "name": "João V. S. Guerra", "email": "joao.guerra@lnbio.cnpem.br", "url": "https://github.com/jvsguerra", "orcidid": "https://orcid.org/0000-0002-6800-4425", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer", "Primary contact" ], "note": null }, { "name": "Helder V. Ribeiro-Filho", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "José G. C. Pereira", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Paulo S. Lopes-de-Oliveira", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact" ], "note": null } ], "owner": "jvsguerra", "additionDate": "2024-08-02T20:40:51.771278Z", "lastUpdate": "2024-11-24T13:49:43.565927Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "parKVFinder", "description": "Parallel KVFinder (parKVFinder) is an open-source software designed for the detection and spatial characterization (shape, volume, area and surrounding residues) of any type of biomolecular cavity. parKVFinder is available alongside an easy-to-use PyMOL plugin (PyMOL2 parKVFinder Tools) with an intuitive graphical user interface that allows users to explore customizable parameters for cavity detection and characterization.", "homepage": "https://github.com/LBC-LNBio/parKVFinder", "biotoolsID": "parkvfinder", "biotoolsCURIE": "biotools:parkvfinder", "version": [], "otherID": [], "relation": [ { "biotoolsID": "KVFinder", "type": "isNewVersionOf" }, { "biotoolsID": "KVFinder-web", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2575", "term": "Binding site prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0883", "term": "Structure" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2878", "term": "Protein structural motif" }, "format": [ { "uri": "http://edamontology.org/format_1476", "term": "PDB" }, { "uri": "http://edamontology.org/format_2330", "term": "Textual format" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Plug-in", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_1317", "term": "Structural biology" }, { "uri": "http://edamontology.org/topic_3332", "term": "Computational chemistry" }, { "uri": "http://edamontology.org/topic_0081", "term": "Structure analysis" }, { "uri": "http://edamontology.org/topic_0166", "term": "Protein structural motifs and surfaces" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "C", "PyMOL" ], "license": "GPL-3.0", "collectionID": [ "KVFinder suite", "COVID-19", "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/LBC-LNBio/parKVFinder", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/LBC-LNBio/parKVFinder-win", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/LBC-LNBio/parKVFinder/wiki", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1016/j.softx.2020.100606", "pmid": null, "pmcid": null, "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "ParKVFinder: A thread-level parallel approach in biomolecular cavity detection", "abstract": "Biological processes are regulated mainly by the binding of small molecules into cavities distributed throughout the biomolecular structure. Computational tools to detect these cavities have an essential role in rational drug design. With the exponential availability of high-order 3D atomic structures and large sets of atomic models, the tools must balance accuracy and speed. In this sense, we developed parKVFinder, a parallelized software for geometry-based cavity detection. Here, we described its functionalities and presented its easy-to-use PyMOL plugin and command-line interface. Finally, we demonstrated parKVFinder by identifying an important HIV-1 protease cavity and compared it with other geometry-based programs.", "date": "2020-07-01T00:00:00Z", "citationCount": 16, "authors": [ { "name": "Guerra J.V.D.S." }, { "name": "Ribeiro Filho H.V." }, { "name": "Bortot L.O." }, { "name": "Honorato R.V." }, { "name": "Pereira J.G.D.C." }, { "name": "Lopes-de-Oliveira P.S." } ], "journal": "SoftwareX" } }, { "doi": "10.1021/acs.jcim.3c00328", "pmid": "37129917", "pmcid": null, "type": [ "Benchmarking study" ], "version": null, "note": null, "metadata": { "title": "Cavity Characterization in Supramolecular Cages", "abstract": "Confining molecular guests within artificial hosts has provided a major driving force in the rational design of supramolecular cages with tailored properties. Over the last 30 years, a set of design strategies have been developed that enabled the controlled synthesis of a myriad of cages. Recently, there has been a growing interest in involving in silico methods in this toolbox. Cavity shape and size are important parameters that can be easily accessed by inexpensive geometric algorithms. Although these algorithms are well developed for the detection of nonartificial cavities (e.g., enzymes), they are not routinely used for the rational design of supramolecular cages. In order to test the capabilities of this tool, we have evaluated the performance and characteristics of seven different cavity characterization software in the context of 22 analogues of well-known supramolecular cages. Among the tested software, KVFinder project and Fpocket proved to be the most software to characterize supramolecular cavities. With the results of this work, we aim to popularize this underused technique within the supramolecular community.", "date": "2023-06-26T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Guerra J.V.S." }, { "name": "Alves L.F.G." }, { "name": "Bourissou D." }, { "name": "Lopes-De-Oliveira P.S." }, { "name": "Szaloki G." } ], "journal": "Journal of Chemical Information and Modeling" } } ], "credit": [ { "name": "João Victor da Silva Guerra", "email": "joao.guerra@lnbio.cnpem.br", "url": "https://github.com/jvsguerra", "orcidid": "https://orcid.org/0000-0002-6800-4425", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null }, { "name": "Helder Veras Ribeiro-Filho", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Leandro Oliveira Bortot", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Rodrigo Vargas Honorato", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "José Geraldo de Carvalho Pereira", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Paulo Sergio Lopes-de-Oliveira", "email": "paulo.oliveira@lnbio.cnpem.br", "url": null, "orcidid": "https://orcid.org/0000-0002-1287-8019", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "jvsguerra", "additionDate": "2022-09-20T15:25:01.787084Z", "lastUpdate": "2024-11-24T13:49:40.862143Z", "editPermission": { "type": "group", "authors": [ "jvsguerra" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Human Splicing Finder", "description": "The Human Splicing Finder (HSF) system combines 12 different algorithms to identify and predict mutations’ effect on splicing motifs including the acceptor and donor splice sites, the branch point and auxiliary sequences known to either enhance or repress splicing: Exonic Splicing Enhancers (ESE) and Exonic Splicing Silencers (ESS).", "homepage": "http://www.umd.be/HSF3/", "biotoolsID": "human_splicing_finder", "biotoolsCURIE": "biotools:human_splicing_finder", "version": [], "otherID": [ { "value": "RRID:SCR_005181", "type": "rrid", "version": null } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0264", "term": "Splice transcript prediction" }, { "uri": "http://edamontology.org/operation_0433", "term": "Splice site prediction" }, { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_3197", "term": "Genetic variation analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3512", "term": "Gene transcripts" }, { "uri": "http://edamontology.org/topic_3320", "term": "RNA splicing" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3571", "term": "Data governance" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" }, { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" } ], "operatingSystem": [ "Windows", "Mac" ], "language": [ "JavaScript" ], "license": null, "collectionID": [ "Developed_RD-Connect", "RD-Connect", "Rare Disease", "ELIXIR-FR" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.umd.be/HSF3/technicaltips.html", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkp215", "pmid": "19339519", "pmcid": "PMC2685110", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Human Splicing Finder: An online bioinformatics tool to predict splicing signals", "abstract": "Thousands of mutations are identified yearly. Although many directly affect protein expression, an increasing proportion of mutations is now believed to influence mRNA splicing. They mostly affect existing splice sites, but synonymous, non-synonymous or nonsense mutations can also create or disrupt splice sites or auxiliary cis-splicing sequences. To facilitate the analysis of the different mutations, we designed Human Splicing Finder (HSF), a tool to predict the effects of mutations on splicing signals or to identify splicing motifs in any human sequence. It contains all available matrices for auxiliary sequence prediction as well as new ones for binding sites of the 9G8 and Tra2-β Serine-Arginine proteins and the hnRNP A1 ribonucleoprotein. We also developed new Position Weight Matrices to assess the strength of 5′ and 3′ splice sites and branch points. We evaluated HSF efficiency using a set of 83 intronic and 35 exonic mutations known to result in splicing defects. We showed that the mutation effect was correctly predicted in almost all cases. HSF could thus represent a valuable resource for research, diagnostic and therapeutic (e.g. therapeutic exon skipping) purposes as well as for global studies, such as the GEN2PHEN European Project or the Human Variome Project. © 2009 The Author(s).", "date": "2009-06-08T00:00:00Z", "citationCount": 2087, "authors": [ { "name": "Desmet F.-O." }, { "name": "Hamroun D." }, { "name": "Lalande M." }, { "name": "Collod-Beroud G." }, { "name": "Claustres M." }, { "name": "Beroud C." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Contact Form", "email": null, "url": "http://www.umd.be/HSF3/contactus.html", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "David Salgado", "email": "david.salgado@univ-amu.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Christophe Béroud", "email": "christophe.beroud@inserm.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "dsalgado", "additionDate": "2017-03-04T22:39:22Z", "lastUpdate": "2024-11-24T13:49:29.814329Z", "editPermission": { "type": "group", "authors": [ "lmatalonga", "dsalgado", "khanfarheen" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }