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{ "count": 958, "next": "?page=2", "previous": null, "list": [ { "name": "SKM", "description": "Stress Knowledge Map: A compilation of knowledge on mechanisms underlying responses of plants to stress, the so called stress signalling network.", "homepage": "https://skm.nib.si/", "biotoolsID": "skm", "biotoolsCURIE": "biotools:skm", "version": [], "otherID": [], "relation": [ { "biotoolsID": "gomapman", "type": "uses" }, { "biotoolsID": "newt-ve", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2299", "term": "Gene name" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2080", "term": "Database search results" }, "format": [ { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_3619", "term": "sif" } ] } ], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [], "output": [ { "data": { "uri": "http://edamontology.org/data_0950", "term": "Mathematical model" }, "format": [ { "uri": "http://edamontology.org/format_2585", "term": "SBML" }, { "uri": "http://edamontology.org/format_3692", "term": "SBGN-ML" }, { "uri": "http://edamontology.org/format_3619", "term": "sif" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_2259", "term": "Systems biology" }, { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [ "Slovenia" ], "elixirCommunity": [ "Plant Sciences" ], "link": [ { "url": "https://skm.nib.si/contact", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [ { "url": "https://skm.nib.si/documentation", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1016/j.xplc.2024.100920", "pmid": "38616489", "pmcid": null, "type": [ "Primary" ], "version": null, "note": "Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses", "metadata": { "title": "Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses", "abstract": "Stress Knowledge Map (SKM; https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs that describe the current knowledge of biochemical, signaling, and regulatory molecular interactions in plants: a highly curated model of plant stress signaling (PSS; 543 reactions) and a large comprehensive knowledge network (488 390 interactions). Both were constructed by domain experts through systematic curation of diverse literature and database resources. SKM provides a single entry point for investigations of plant stress response and related growth trade-offs, as well as interactive explorations of current knowledge. PSS is also formulated as a qualitative and quantitative model for systems biology and thus represents a starting point for a plant digital twin. Here, we describe the features of SKM and show, through two case studies, how it can be used for complex analyses, including systematic hypothesis generation and design of validation experiments, or to gain new insights into experimental observations in plant biology.", "date": "2024-06-10T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Bleker C." }, { "name": "Ramsak" }, { "name": "Bittner A." }, { "name": "Podpecan V." }, { "name": "Zagorscak M." }, { "name": "Wurzinger B." }, { "name": "Baebler" }, { "name": "Petek M." }, { "name": "Kriznik M." }, { "name": "van Dieren A." }, { "name": "Gruber J." }, { "name": "Afjehi-Sadat L." }, { "name": "Weckwerth W." }, { "name": "Zupanic A." }, { "name": "Teige M." }, { "name": "Vothknecht U.C." }, { "name": "Gruden K." } ], "journal": "Plant Communications" } } ], "credit": [ { "name": "National Institute of Biology, Department of Biotechnology and Systems Biology", "email": null, "url": "http://www.nib.si/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Carissa Bleker", "email": "carissarobyn.bleker@nib.si", "url": null, "orcidid": "https://orcid.org/0000-0003-1617-7145", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "Kristina Gruden", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Živa Ramšak", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Vid Podpečan", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Developer" ], "note": null } ], "community": null, "owner": "carissa", "additionDate": "2022-05-16T13:26:15.720803Z", "lastUpdate": "2024-07-18T13:44:24.623632Z", "editPermission": { "type": "group", "authors": [ "zagor" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "scTE", "description": "scTE builds genome indices for the fast alignment of reads to genes and Transposable elements (TEs).", "homepage": "https://github.com/JiekaiLab/scTE", "biotoolsID": "scte", "biotoolsCURIE": "biotools:scte", "version": [ "1.0.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3800", "term": "RNA-Seq quantification" }, { "uri": "http://edamontology.org/operation_0361", "term": "Sequence annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1383", "term": "Nucleic acid sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] }, { "data": { "uri": "http://edamontology.org/data_1276", "term": "Nucleic acid features" }, "format": [ { "uri": "http://edamontology.org/format_2306", "term": "GTF" } ] }, { "data": { "uri": "http://edamontology.org/data_3002", "term": "Annotation track" }, "format": [ { "uri": "http://edamontology.org/format_3003", "term": "BED" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3112", "term": "Gene expression matrix" }, "format": [ { "uri": "http://edamontology.org/format_3590", "term": "HDF5" }, { "uri": "http://edamontology.org/format_3752", "term": "CSV" } ] } ], "note": null, "cmd": "scTE_build -te TEs.bed -gene Genes.gtf -o custome\nscTE -i inp.bam -o out -x mm10.exclusive.idx --hdf5 True" } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0659", "term": "Functional, regulatory and non-coding RNA" }, { "uri": "http://edamontology.org/topic_0798", "term": "Mobile genetic elements" }, { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/JiekaiLab/scTE", "type": [ "Repository" ], "note": null }, { "url": "https://zenodo.org/records/4420937", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/JiekaiLab/scTE/releases/tag/scTE.v1.0.0", "type": "Downloads page", "note": null, "version": "v1.0.0" }, { "url": "https://anaconda.org/bioconda/scte", "type": "Software package", "note": null, "version": null } ], "documentation": [], "publication": [ { "doi": "10.1038/s41467-021-21808-x", "pmid": "33674594", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Identifying transposable element expression dynamics and heterogeneity during development at the single-cell level with a processing pipeline scTE", "abstract": "Transposable elements (TEs) make up a majority of a typical eukaryote’s genome, and contribute to cell heterogeneity in unclear ways. Single-cell sequencing technologies are powerful tools to explore cells, however analysis is typically gene-centric and TE expression has not been addressed. Here, we develop a single-cell TE processing pipeline, scTE, and report the expression of TEs in single cells in a range of biological contexts. Specific TE types are expressed in subpopulations of embryonic stem cells and are dynamically regulated during pluripotency reprogramming, differentiation, and embryogenesis. Unexpectedly, TEs are expressed in somatic cells, including human disease-specific TEs that are undetectable in bulk analyses. Finally, we apply scTE to single-cell ATAC-seq data, and demonstrate that scTE can discriminate cell type using chromatin accessibly of TEs alone. Overall, our results classify the dynamic patterns of TEs in single cells and their contributions to cell heterogeneity.", "date": "2021-12-01T00:00:00Z", "citationCount": 64, "authors": [ { "name": "He J." }, { "name": "Babarinde I.A." }, { "name": "Sun L." }, { "name": "Xu S." }, { "name": "Chen R." }, { "name": "Shi J." }, { "name": "Wei Y." }, { "name": "Li Y." }, { "name": "Ma G." }, { "name": "Zhuang Q." }, { "name": "Hutchins A.P." }, { "name": "Chen J." } ], "journal": "Nature Communications" } } ], "credit": [ { "name": "Jiangping He", "email": null, "url": null, "orcidid": "http://orcid.org/0000-0002-1425-3530", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "Jiekai Chen", "email": "chen_jiekai@gibh.ac.cn", "url": null, "orcidid": "http://orcid.org/0000-0001-5168-7074", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "billsfriend", "additionDate": "2024-07-18T11:34:53.652671Z", "lastUpdate": "2024-07-18T11:36:30.859044Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "DISGENET", "description": "DISGENET is a comprehensive knowledge database integrating and standardizing information on disease-associated genes and variants. It covers the full spectrum of human diseases as well as normal and abnormal traits, including adverse events of drugs. Due to the adherence to FAIR data principles, DISGENET is an interoperable resource supporting a variety of applications in genomic medicine and drug R&D.\n\nDISGENET simplifies the process of accessing genetic evidence for diseases and therefore can streamline the incorporation of this type of evidence in research, drug R&D and precision medicine applications.\n\nDISGENET is available for free for academic users. License fees are applicable for the commercial use of DISGENET. Learn more here https://www.disgenet.com/plans\n\nDISGENET is the new evolution of the community-recognized DisGeNET platform, cited by over 6000 publications and one of the ELIXIR Recommended Interoperability Resources.", "homepage": "http://www.disgenet.com/", "biotoolsID": "disgenet", "biotoolsCURIE": "biotools:disgenet", "version": [ "Database version 24.2", "disgenet2r R package Version: 1.1.9", "DISGENET Cytoscape App Version 8.0.0" ], "otherID": [], "relation": [ { "biotoolsID": "uniprot", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_3226", "term": "Variant prioritisation" }, { "uri": "http://edamontology.org/operation_3083", "term": "Pathway or network visualisation" }, { "uri": "http://edamontology.org/operation_3436", "term": "Aggregation" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_3925", "term": "Network visualisation" }, { "uri": "http://edamontology.org/operation_0306", "term": "Text mining" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3021", "term": "UniProt accession" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1106", "term": "dbSNP ID" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2858", "term": "Ontology concept" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1025", "term": "Gene identifier" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2080", "term": "Database search results" }, "format": [ { "uri": "http://edamontology.org/format_3475", "term": "TSV" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_2331", "term": "HTML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Plug-in", "Web API", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_3344", "term": "Biomedical science" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_0218", "term": "Natural language processing" }, { "uri": "http://edamontology.org/topic_0089", "term": "Ontology and terminology" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3366", "term": "Data integration and warehousing" }, { "uri": "http://edamontology.org/topic_3345", "term": "Data identity and mapping" }, { "uri": "http://edamontology.org/topic_3342", "term": "Translational medicine" }, { "uri": "http://edamontology.org/topic_0634", "term": "Pathology" }, { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" }, { "uri": "http://edamontology.org/topic_3063", "term": "Medical informatics" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": "Proprietary", "collectionID": [ "Drug Research and Development", "Rare Disease", "COVID-19", "Complex Disease", "Mendelian Disease", "ELIXIR-ES", "RIS3CAT VEIS", "TransQST", "IMPaCT-Data" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [ "Interoperability" ], "elixirNode": [ "Spain" ], "elixirCommunity": [], "link": [ { "url": "http://www.disgenet.com/", "type": [ "Repository" ], "note": null }, { "url": "https://apps.cytoscape.org/apps/disgenetapp", "type": [ "Software catalogue" ], "note": null }, { "url": "https://www.linkedin.com/showcase/disgenet/", "type": [ "Social media" ], "note": null }, { "url": "https://gitlab.com/medbio/disgenet2r", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://gitlab.com/medbio/disgenet2r", "type": "Software package", "note": "disgenet2r R package", "version": null }, { "url": "https://apps.cytoscape.org/apps/disgenetapp", "type": "Software package", "note": "DISGENET Cytoscape App", "version": null }, { "url": "https://www.disgenet.com/Tools#console", "type": "API specification", "note": "DISGENET REST API", "version": null } ], "documentation": [ { "url": "https://www.disgenet.com/About", "type": [ "General" ], "note": null }, { "url": "https://www.disgenet.com/Tools#console", "type": [ "API documentation" ], "note": null }, { "url": "https://www.disgenet.com/FAQ", "type": [ "FAQ" ], "note": null } ], "publication": [ { "doi": "10.1093/database/bav028", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "DisGeNET: A discovery platform for the dynamical exploration of human diseases and their genes", "abstract": "DisGeNET is a comprehensive discovery platform designed to address a variety of questions concerning the genetic underpinning of human diseases. DisGeNET contains over 380 000 associations between >16 000 genes and 13 000 diseases, which makes it one of the largest repositories currently available of its kind. DisGeNET integrates expert-curated databases with text-mined data, covers information on Mendelian and complex diseases, and includes data from animal disease models. It features a score based on the supporting evidence to prioritize gene-disease associations. It is an open access resource available through a web interface, a Cytoscape plugin and as a Semantic Web resource. The web interface supports user-friendly data exploration and navigation. DisGeNET data can also be analysed via the DisGeNET Cytoscape plugin, and enriched with the annotations of other plugins of this popular network analysis software suite. Finally, the information contained in DisGeNET can be expanded and complemented using Semantic Web technologies and linked to a variety of resources already present in the Linked Data cloud. Hence, DisGeNET offers one of the most comprehensive collections of human gene-disease associations and a valuable set of tools for investigating the molecular mechanisms underlying diseases of genetic origin, designed to fulfill the needs of different user profiles, including bioinformaticians, biologists and health-care practitioners.", "date": "2015-01-01T00:00:00Z", "citationCount": 761, "authors": [ { "name": "Pinero J." }, { "name": "Queralt-Rosinach N." }, { "name": "Bravo A." }, { "name": "Deu-Pons J." }, { "name": "Bauer-Mehren A." }, { "name": "Baron M." }, { "name": "Sanz F." }, { "name": "Furlong L.I." } ], "journal": "Database" } }, { "doi": "10.1093/nar/gkw943", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "DisGeNET: A comprehensive platform integrating information on human disease-associated genes and variants", "abstract": "The information about the genetic basis of human diseases lies at the heart of precision medicine and drug discovery. However, to realize its full potential to support these goals, several problems, such as fragmentation, heterogeneity, availability and different conceptualization of the data must be overcome. To provide the community with a resource free of these hurdles, we have developed DisGeNET (http://www.disgenet.org), one of the largest available collections of genes and variants involved in human diseases. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models and the scientific literature. DisGeNET data are homogeneously annotated with controlled vocabularies and community-driven ontologies. Additionally, several original metrics are provided to assist the prioritization of genotype-phenotype relationships. The information is accessible through a web interface, a Cytoscape App, an RDF SPARQL endpoint, scripts in several programming languages and an R package. DisGeNET is a versatile platform that can be used for different research purposes including the investigation of the molecular underpinnings of specific human diseases and their comorbidities, the analysis of the properties of disease genes, the generation of hypothesis on drug therapeutic action and drug adverse effects, the validation of computationally predicted disease genes and the evaluation of text-mining methods performance.", "date": "2017-01-01T00:00:00Z", "citationCount": 1604, "authors": [ { "name": "Pinero J." }, { "name": "Bravo A." }, { "name": "Queralt-Rosinach N." }, { "name": "Gutierrez-Sacristan A." }, { "name": "Deu-Pons J." }, { "name": "Centeno E." }, { "name": "Garcia-Garcia J." }, { "name": "Sanz F." }, { "name": "Furlong L.I." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/bioinformatics/btq538", "pmid": null, "pmcid": null, "type": [ "Method" ], "version": null, "note": null, "metadata": { "title": "DisGeNET: A Cytoscape plugin to visualize, integrate, search and analyze gene-disease networks", "abstract": "Summary: DisGeNET is a plugin for Cytoscape to query and analyze human gene-disease networks. DisGeNET allows user-friendly access to a new gene-disease database that we have developed by integrating data from several public sources. DisGeNET permits queries restricted to (i) the original data source, (ii) the association type, (iii) the disease class or (iv) specific gene(s)/disease(s). It represents gene-disease associations in terms of bipartite graphs and provides gene centric and disease centric views of the data. It assists the user in the interpretation and exploration of the genetic basis of human diseases by a variety of built-in functions. Moreover, DisGeNET permits multicolouring of nodes (genes/diseases) according to standard disease classification for expedient visualization. © The Author 2010. Published by Oxford University Press. All rights reserved.", "date": "2010-11-01T00:00:00Z", "citationCount": 177, "authors": [ { "name": "Bauer-Mehren A." }, { "name": "Rautschka M." }, { "name": "Sanz F." }, { "name": "Furlong L.I." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/bioinformatics/btw214", "pmid": null, "pmcid": null, "type": [ "Method" ], "version": null, "note": null, "metadata": { "title": "DisGeNET-RDF: Harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases", "abstract": "Motivation: DisGeNET-RDF makes available knowledge on the genetic basis of human diseases in the Semantic Web. Gene-disease associations (GDAs) and their provenance metadata are published as human-readable and machine-processable web resources. The information on GDAs included in DisGeNET-RDF is interlinked to other biomedical databases to support the development of bioinformatics approaches for translational research through evidence-based exploitation of a rich and fully interconnected linked open data. Availability and implementation: http://rdf.disgenet.org/ Contact:", "date": "2016-07-15T00:00:00Z", "citationCount": 45, "authors": [ { "name": "Queralt-Rosinach N." }, { "name": "Pinero J." }, { "name": "Bravo A." }, { "name": "Sanz F." }, { "name": "Furlong L.I." } ], "journal": "Bioinformatics" } }, { "doi": "10.1371/journal.pone.0020284", "pmid": null, "pmcid": null, "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "Gene-disease network analysis reveals functional modules in mendelian, complex and environmental diseases", "abstract": "Background: Scientists have been trying to understand the molecular mechanisms of diseases to design preventive and therapeutic strategies for a long time. For some diseases, it has become evident that it is not enough to obtain a catalogue of the disease-related genes but to uncover how disruptions of molecular networks in the cell give rise to disease phenotypes. Moreover, with the unprecedented wealth of information available, even obtaining such catalogue is extremely difficult. Principal Findings: We developed a comprehensive gene-disease association database by integrating associations from several sources that cover different biomedical aspects of diseases. In particular, we focus on the current knowledge of human genetic diseases including mendelian, complex and environmental diseases. To assess the concept of modularity of human diseases, we performed a systematic study of the emergent properties of human gene-disease networks by means of network topology and functional annotation analysis. The results indicate a highly shared genetic origin of human diseases and show that for most diseases, including mendelian, complex and environmental diseases, functional modules exist. Moreover, a core set of biological pathways is found to be associated with most human diseases. We obtained similar results when studying clusters of diseases, suggesting that related diseases might arise due to dysfunction of common biological processes in the cell. Conclusions: For the first time, we include mendelian, complex and environmental diseases in an integrated gene-disease association database and show that the concept of modularity applies for all of them. We furthermore provide a functional analysis of disease-related modules providing important new biological insights, which might not be discovered when considering each of the gene-disease association repositories independently. Hence, we present a suitable framework for the study of how genetic and environmental factors, such as drugs, contribute to diseases. Availability: The gene-disease networks used in this study and part of the analysis are available at http://ibi.imim.es/DisGeNET/DisGeNETweb.html#Download. © 2011 Bauer-Mehren et al.", "date": "2011-06-20T00:00:00Z", "citationCount": 140, "authors": [ { "name": "Bauer-Mehren A." }, { "name": "Bundschus M." }, { "name": "Rautschka M." }, { "name": "Mayer M.A." }, { "name": "Sanz F." }, { "name": "Furlong L.I." } ], "journal": "PLoS ONE" } }, { "doi": "10.1093/nar/gkw943", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "DisGeNET: A comprehensive platform integrating information on human disease-associated genes and variants", "abstract": "The information about the genetic basis of human diseases lies at the heart of precision medicine and drug discovery. However, to realize its full potential to support these goals, several problems, such as fragmentation, heterogeneity, availability and different conceptualization of the data must be overcome. To provide the community with a resource free of these hurdles, we have developed DisGeNET (http://www.disgenet.org), one of the largest available collections of genes and variants involved in human diseases. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models and the scientific literature. DisGeNET data are homogeneously annotated with controlled vocabularies and community-driven ontologies. Additionally, several original metrics are provided to assist the prioritization of genotype-phenotype relationships. The information is accessible through a web interface, a Cytoscape App, an RDF SPARQL endpoint, scripts in several programming languages and an R package. DisGeNET is a versatile platform that can be used for different research purposes including the investigation of the molecular underpinnings of specific human diseases and their comorbidities, the analysis of the properties of disease genes, the generation of hypothesis on drug therapeutic action and drug adverse effects, the validation of computationally predicted disease genes and the evaluation of text-mining methods performance.", "date": "2017-01-01T00:00:00Z", "citationCount": 1604, "authors": [ { "name": "Pinero J." }, { "name": "Bravo A." }, { "name": "Queralt-Rosinach N." }, { "name": "Gutierrez-Sacristan A." }, { "name": "Deu-Pons J." }, { "name": "Centeno E." }, { "name": "Garcia-Garcia J." }, { "name": "Sanz F." }, { "name": "Furlong L.I." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1093/nar/gkz1021", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "The DisGeNET knowledge platform for disease genomics: 2019 update", "abstract": "One of the most pressing challenges in genomic medicine is to understand the role played by genetic variation in health and disease. Thanks to the exploration of genomic variants at large scale, hundreds of thousands of disease-Associated loci have been uncovered. However, the identification of variants of clinical relevance is a significant challenge that requires comprehensive interrogation of previous knowledge and linkage to new experimental results. To assist in this complex task, we created DisGeNET (http://www.disgenet.org/), a knowledge management platform integrating and standardizing data about disease associated genes and variants from multiple sources, including the scientific literature. DisGeNET covers the full spectrum of human diseases as well as normal and abnormal traits. The current release covers more than 24 000 diseases and traits, 17 000 genes and 117 000 genomic variants. The latest developments of DisGeNET include new sources of data, novel data attributes and prioritization metrics, a redesigned web interface and recently launched APIs. Thanks to the data standardization, the combination of expert curated information with data automatically mined from the scientific literature, and a suite of tools for accessing its publicly available data, DisGeNET is an interoperable resource supporting a variety of applications in genomic medicine and drug R&D.", "date": "2020-01-01T00:00:00Z", "citationCount": 1444, "authors": [ { "name": "Pinero J." }, { "name": "Ramirez-Anguita J.M." }, { "name": "Sauch-Pitarch J." }, { "name": "Ronzano F." }, { "name": "Centeno E." }, { "name": "Sanz F." }, { "name": "Furlong L.I." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Janet Piñero", "email": "janet.pinero@disgenet.com", "url": "https://www.linkedin.com/in/janet-pinero/", "orcidid": "http://orcid.org/0000-0003-1244-7654", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor", "Developer", "Maintainer", "Support" ], "note": null }, { "name": "Laura I. 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null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null } ], "community": null, "owner": "shaze", "additionDate": "2024-06-20T19:11:19.688666Z", "lastUpdate": "2024-06-20T19:11:50.666691Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Goslin", "description": "Goslin is the Grammar of succinct lipid nomenclature project. It defines multiple grammers compatible with ANTLRv4 for different sources of shorthand lipid nomenclature. 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Goslin was designed to address the following pressing issues in the lipidomics field: (1) to simplify the implementation of lipid name handling for developers of mass spectrometry-based lipidomics tools, (2) to offer a tool that unifies and normalizes the main existing lipid name dialects enabling a lipidomics analysis in a high-throughput fashion, and (3) to provide a consistent mapping from lipid shorthand names to lipid building blocks and structural properties. We provide implementations of Goslin in four major programming languages, namely, C++, Java, Python 3, and R to kick-start adoption and integration. Further, we set up a web service for users to work with Goslin directly. All implementations are available free of charge under a permissive open source license.", "date": "2020-08-18T00:00:00Z", "citationCount": 14, "authors": [ { "name": "Kopczynski D." }, { "name": "Hoffmann N." }, { "name": "Peng B." }, { "name": "Ahrends R." } ], "journal": "Analytical Chemistry" } } ], "credit": [ { "name": "Nils Hoffmann", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-6540-6875", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer", "Developer" ], "note": null }, { "name": "Dominik Kopczynski", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-5885-4568", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer", "Developer" ], "note": null }, { "name": "Bing Peng", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0001-5006-7041", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Robert Ahrends", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0003-0232-3375", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null } ], "community": null, "owner": "nils.hoffmann", "additionDate": "2020-06-23T10:03:06Z", "lastUpdate": "2024-06-19T10:01:39.705679Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "NetMHCIIpan", "description": "Predict binding of peptides to MHC class II molecules. The predictions are available for all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ, as well as mouse molecules.", "homepage": "http://www.cbs.dtu.dk/services/NetMHCIIpan/", "biotoolsID": "netmhciipan", "biotoolsCURIE": "biotools:netmhciipan", "version": [ "3.0", "4.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0416", "term": "Epitope mapping" }, { "uri": "http://edamontology.org/operation_2575", "term": "Protein binding site prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "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" } ] } ], "note": "Predicts binding of peptides to MHC class II molecules.", "cmd": null } ], "toolType": [ "Command-line tool", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3534", "term": "Protein binding sites" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [], "license": "Other", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge (with restrictions)", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://www.cbs.dtu.dk/services", "type": [ "Software catalogue" ], "note": null }, { "url": "https://www-nature-com.proxy1-bib.sdu.dk/articles/s42003-023-04749-7", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [ { "url": "http://www.cbs.dtu.dk/services/NetMHCIIpan/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1007/s00251-013-0720-y", "pmid": "23900783", "pmcid": "PMC3809066", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "NetMHCIIpan-3.0, a common pan-specific MHC class II prediction method including all three human MHC class II isotypes, HLA-DR, HLA-DP and HLA-DQ", "abstract": "Major histocompatibility complex class II (MHCII) molecules play an important role in cell-mediated immunity. They present specific peptides derived from endosomal proteins for recognition by T helper cells. The identification of peptides that bind to MHCII molecules is therefore of great importance for understanding the nature of immune responses and identifying T cell epitopes for the design of new vaccines and immunotherapies. Given the large number of MHC variants, and the costly experimental procedures needed to evaluate individual peptide-MHC interactions, computational predictions have become particularly attractive as first-line methods in epitope discovery. However, only a few so-called pan-specific prediction methods capable of predicting binding to any MHC molecule with known protein sequence are currently available, and all of them are limited to HLA-DR. Here, we present the first pan-specific method capable of predicting peptide binding to any HLA class II molecule with a defined protein sequence. The method employs a strategy common for HLA-DR, HLA-DP and HLA-DQ molecules to define the peptide-binding MHC environment in terms of a pseudo sequence. This strategy allows the inclusion of new molecules even from other species. The method was evaluated in several benchmarks and demonstrates a significant improvement over molecule-specific methods as well as the ability to predict peptide binding of previously uncharacterised MHCII molecules. To the best of our knowledge, the NetMHCIIpan-3.0 method is the first pan-specific predictor covering all HLA class II molecules with known sequences including HLA-DR, HLA-DP, and HLA-DQ. The NetMHCpan-3.0 method is available at http://www.cbs.dtu.dk/services/NetMHCIIpan-3.0. © 2013 Springer-Verlag Berlin Heidelberg.", "date": "2013-10-01T00:00:00Z", "citationCount": 216, "authors": [ { "name": "Karosiene E." }, { "name": "Rasmussen M." }, { "name": "Blicher T." }, { "name": "Lund O." }, { "name": "Buus S." }, { "name": "Nielsen M." } ], "journal": "Immunogenetics" } } ], "credit": [ { "name": "Edita Karosiene", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "CBS", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Morten Nielsen", "email": "mniel@cbs.dtu.dk", "url": null, "orcidid": "http://orcid.org/0000-0001-7885-4311", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "CBS", "additionDate": "2015-01-21T13:29:28Z", "lastUpdate": "2024-06-18T14:36:35.863186Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MolStar", "description": "Mol* is a web application for visualization of biomacromolecular structures including experimental data (for example electron densities) and annotations. 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In addition, emerging integrative or hybrid methods (I/HM) are producing structural models of huge macromolecular machines and assemblies, sometimes containing 100s of millions of non-hydrogen atoms. The performance requirements for visualization and analysis tools delivering these data are increasing rapidly. Significant progress in developing online, web-native three-dimensional (3D) visualization tools was previously accomplished with the introduction of the LiteMol suite and NGL Viewers. Thereafter, Mol∗ development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of LiteMol (developed by PDBe) and NGL (developed by RCSB PDB). The web-native Mol∗ Viewer enables 3D visualization and streaming of macromolecular coordinate and experimental data, together with capabilities for displaying structure quality, functional, or biological context annotations. High-performance graphics and data management allows users to simultaneously visualise up to hundreds of (superimposed) protein structures, stream molecular dynamics simulation trajectories, render cell-level models, or display huge I/HM structures. It is the primary 3D structure viewer used by PDBe and RCSB PDB. It can be easily integrated into third-party services. Mol∗ Viewer is open source and freely available at https://molstar.org/.", "date": "2021-07-02T00:00:00Z", "citationCount": 468, "authors": [ { "name": "Sehnal D." }, { "name": "Bittrich S." }, { "name": "Deshpande M." }, { "name": "Svobodova R." }, { "name": "Berka K." }, { "name": "Bazgier V." }, { "name": "Velankar S." }, { "name": "Burley S.K." }, { "name": "Koca J." }, { "name": "Rose A.S." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "David Sehnal", "email": "david.sehnal@mail.muni.cz", "url": null, "orcidid": "https://orcid.org/0000-0002-0682-3089", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer" ], "note": null } ], "community": null, "owner": "ELIXIR-CZ", "additionDate": "2020-10-14T12:12:55Z", "lastUpdate": "2024-06-17T09:23:20.185979Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Omada", "description": "We have developed a suite of tools to automate RNAseq clustering processes and make robust unsupervised clustering of transcriptomic data more accessible through automated machine learning based functions. The efficiency of each tool was tested with four datasets characterised by different expression signal strengths. Our toolkit’s decisions reflected the real number of stable partitions in datasets where the subgroups are discernible. 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