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GET /api/t/?collectionID=%22Rare%20Disease%22
{ "count": 247, "next": "?page=2", "previous": null, "list": [ { "name": "SAMtools", "description": "SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods.", "homepage": "http://www.htslib.org/", "biotoolsID": "samtools", "biotoolsCURIE": "biotools:samtools", "version": [ "1.0", "1.1", "1.2", "1.3", "1.3.1", "1.4", "1.4.1", "1.5", "1.6", "1.7", "1.8", "1.9", "1.10", "1.11", "1.12", "1.13", "1.14", "1.15", "1.15.1", "1.16", "1.16.1", "1.17", "1.18", "1.19", "1.19.1", "1.19.2", "1.20", "1.21" ], "otherID": [], "relation": [ { "biotoolsID": "htslib", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0227", "term": "Indexing" }, { "uri": "http://edamontology.org/operation_3096", "term": "Editing" }, { "uri": "http://edamontology.org/operation_1812", "term": "Parsing" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" }, { "uri": "http://edamontology.org/operation_3802", "term": "Sorting" }, { "uri": "http://edamontology.org/operation_3695", "term": "Filtering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_2573", "term": "SAM" }, { "uri": "http://edamontology.org/format_3462", "term": "CRAM" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0924", "term": "Sequence trace" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" }, { "uri": "http://edamontology.org/format_2573", "term": "SAM" }, { "uri": "http://edamontology.org/format_3462", "term": "CRAM" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Suite", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_3325", "term": "Rare diseases" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "C" ], "license": "MIT", "collectionID": [ "Rare Disease", "Animal and Crop Genomics", "SAMtools" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/samtools/samtools", "type": [ "Repository" ], "note": null }, { "url": "http://www.htslib.org/support/#lists", "type": [ "Mailing list" ], "note": null }, { "url": "https://github.com/samtools/samtools/issues", "type": [ "Issue tracker" ], "note": null } ], "download": [ { "url": "http://www.htslib.org/download/", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "http://www.htslib.org/doc/#howtos", "type": [ "Other" ], "note": "HowTos for samtools" }, { "url": "http://www.htslib.org/doc/#manual-pages", "type": [ "User manual" ], "note": null }, { "url": "http://www.htslib.org/download/", "type": [ "Installation instructions" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btp352", "pmid": "19505943", "pmcid": "PMC2723002", "type": [ "Primary" ], "version": null, "note": "The Sequence Alignment/Map format and SAMtools.", "metadata": { "title": "The Sequence Alignment/Map format and SAMtools", "abstract": "Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAM tools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. © 2009 The Author(s).", "date": "2009-08-01T00:00:00Z", "citationCount": 39076, "authors": [ { "name": "Li H." }, { "name": "Handsaker B." }, { "name": "Wysoker A." }, { "name": "Fennell T." }, { "name": "Ruan J." }, { "name": "Homer N." }, { "name": "Marth G." }, { "name": "Abecasis G." }, { "name": "Durbin R." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/gigascience/giab008", "pmid": "33590861", "pmcid": "PMC7931819", "type": [ "Primary" ], "version": null, "note": "Twelve years of SAMtools and BCFtools.", "metadata": { "title": "Twelve years of SAMtools and BCFtools", "abstract": "Background: SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for file format conversion and manipulation, sorting, querying, statistics, variant calling, and effect analysis amongst other methods. Findings: The first version appeared online 12 years ago and has been maintained and further developed ever since, with many new features and improvements added over the years. The SAMtools and BCFtools packages represent a unique collection of tools that have been used in numerous other software projects and countless genomic pipelines. Conclusion: Both SAMtools and BCFtools are freely available on GitHub under the permissive MIT licence, free for both non-commercial and commercial use. Both packages have been installed >1 million times via Bioconda. The source code and documentation are available from https://www.htslib.org.", "date": "2021-02-01T00:00:00Z", "citationCount": 4117, "authors": [ { "name": "Danecek P." }, { "name": "Bonfield J.K." }, { "name": "Liddle J." }, { "name": "Marshall J." }, { "name": "Ohan V." }, { "name": "Pollard M.O." }, { "name": "Whitwham A." }, { "name": "Keane T." }, { "name": "McCarthy S.A." }, { "name": "Davies R.M." } ], "journal": "GigaScience" } }, { "doi": "10.1093/bioinformatics/btr509", "pmid": "21903627", "pmcid": "PMC3198575", "type": [], "version": null, "note": null, "metadata": { "title": "A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data", "abstract": "Motivation: Most existing methods for DNA sequence analysis rely on accurate sequences or genotypes. However, in applications of the next-generation sequencing (NGS), accurate genotypes may not be easily obtained (e.g. multi-sample low-coverage sequencing or somatic mutation discovery). These applications press for the development of new methods for analyzing sequence data with uncertainty. Results: We present a statistical framework for calling SNPs, discovering somatic mutations, inferring population genetical parameters and performing association tests directly based on sequencing data without explicit genotyping or linkage-based imputation. On real data, we demonstrate that our method achieves comparable accuracy to alternative methods for estimating site allele count, for inferring allele frequency spectrum and for association mapping. We also highlight the necessity of using symmetric datasets for finding somatic mutations and confirm that for discovering rare events, mismapping is frequently the leading source of errors. © The Author 2011. Published by Oxford University Press. All rights reserved.", "date": "2011-11-01T00:00:00Z", "citationCount": 4029, "authors": [ { "name": "Li H." } ], "journal": "Bioinformatics" } } ], "credit": [ { "name": "Richard Durbin", "email": "rd@sanger.ac.uk", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": null }, { "name": "Wellcome Sanger Institute", "email": "samtools@sanger.ac.uk", "url": "https://www.sanger.ac.uk/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider", "Primary contact" ], "note": null }, { "name": "Samtools Help mailing list", "email": null, "url": "https://lists.sourceforge.net/lists/listinfo/samtools-help", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Support" ], "note": null } ], "community": { "biolib": { "app_name": "samtools", "author_name": "SAMtools", "author_username": "samtools" } }, "owner": "awhitwham", "additionDate": "2017-01-13T13:16:12Z", "lastUpdate": "2024-09-13T13:57:53.722826Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE", "animalandcropgenomics", "alice", "awhitwham", "sergitobara" ] }, "validated": 1, "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. Furlong", "email": "laura.furlong@disgenet.com", "url": "https://www.linkedin.com/in/laura-ines-furlong-668b9a5/", "orcidid": "https://orcid.org/0000-0002-9383-528X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Contributor", "Documentor", "Support" ], "note": null }, { "name": "Ferran Sanz", "email": "ferran.sanz@upf.edu", "url": null, "orcidid": "http://orcid.org/0000-0002-7534-7661", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "community": null, "owner": "laurafurlong", "additionDate": "2016-04-06T15:00:43Z", "lastUpdate": "2024-08-22T11:39:53.636613Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE", "lfurlong", "janet.pinero" ] }, "validated": 1, "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": null, "pmcid": null, "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": 1635, "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 } ], "community": null, "owner": "dsalgado", "additionDate": "2017-03-04T22:39:22Z", "lastUpdate": "2024-08-21T06:17:25.112892Z", "editPermission": { "type": "group", "authors": [ "lmatalonga", "dsalgado", "khanfarheen" ] }, "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": [ "Primary" ], "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": 15, "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": null, "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 } ], "community": null, "owner": "jvsguerra", "additionDate": "2022-09-20T15:25:01.787084Z", "lastUpdate": "2024-08-02T20:47:49.127493Z", "editPermission": { "type": "group", "authors": [ "jvsguerra" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "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": null, "pmcid": null, "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": 6, "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": null, "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 } ], "community": null, "owner": "jvsguerra", "additionDate": "2024-08-02T20:40:51.771278Z", "lastUpdate": "2024-08-02T20:46:49.944437Z", "editPermission": { "type": "private", "authors": [] }, "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 } ], "community": null, "owner": "jvsguerra", "additionDate": "2022-05-17T20:35:45.357863Z", "lastUpdate": "2024-08-02T20:43:57.210444Z", "editPermission": { "type": "group", "authors": [ "jvsguerra" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "ClinData", "description": "Comprehensive information system for data stewardship in clinical trials, registries and other clinical/scientific databases. It is web-based application accessible via internet browser.", "homepage": "https://clindata.imtm.cz", "biotoolsID": "clindata", "biotoolsCURIE": "biotools:clindata", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" }, { "uri": "http://edamontology.org/operation_3283", "term": "Anonymisation" }, { "uri": "http://edamontology.org/operation_3760", "term": "Service management" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3108", "term": "Experimental measurement" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3861", "term": "Electronic health record" }, "format": [ { "uri": "http://edamontology.org/format_2331", "term": "HTML" }, { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] }, { "data": { "uri": "http://edamontology.org/data_3558", "term": "Clinical trial report" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3577", "term": "Personalised medicine" }, { "uri": "http://edamontology.org/topic_3342", "term": "Translational medicine" }, { "uri": "http://edamontology.org/topic_3379", "term": "Preclinical and clinical studies" } ], "operatingSystem": [ "Linux", "Mac", "Windows" ], "language": [ "SQL", "Java", "JavaScript", "Other" ], "license": "Proprietary", "collectionID": [ "EATRIS-CZ", "EATRIS", "Czech Republic", "Palacky University", "Rare Disease", "COVID-19" ], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Restricted access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://clindata.imtm.cz", "type": [ "Service" ], "note": null }, { "url": "https://confluence.imtm.cz/x/YYBdBg", "type": [ "Other" ], "note": "Documentation" } ], "download": [], "documentation": [ { "url": "https://confluence.imtm.cz/x/YYBdBg", "type": [ "User manual", "General", "Quick start guide", "Terms of use" ], "note": null } ], "publication": [], "credit": [ { "name": "Marian Hajdúch", "email": "marian.hajduch@upol.cz", "url": "https://imtm.cz/users/marian-hajduch", "orcidid": "https://orcid.org/0000-0002-4834-908X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Palacky University", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": "04qxnmv42", "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null }, { "name": "Petr Pavliš", "email": "petr.pavlis@upol.cz", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Maintainer" ], "note": null } ], "community": null, "owner": "ELIXIR-CZ", "additionDate": "2024-06-19T08:17:13.117414Z", "lastUpdate": "2024-06-19T13:45:08.237320Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "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": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null }, { "doi": "10.1093/nar/gkac240", "pmid": null, "pmcid": null, "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": 867, "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": null, "pmcid": null, "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": 3020, "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 } ], "community": null, "owner": "jdispatcher", "additionDate": "2022-11-04T11:11:36.831993Z", "lastUpdate": "2024-05-16T11:03:20.195760Z", "editPermission": { "type": "group", "authors": [ "biomadeira", "nandana" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "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": null, "pmid": "20047655", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "The BridgeDb framework: Standardized access to gene, protein and metabolite identifier mapping services", "abstract": "Background: Many complementary solutions are available for the identifier mapping problem. This creates an opportunity for bioinformatics tool developers. Tools can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This approach requires an interface layer between tools and mapping services.Results: Here we present BridgeDb, a software framework for gene, protein and metabolite identifier mapping. This framework provides a standardized interface layer through which bioinformatics tools can be connected to different identifier mapping services. This approach makes it easier for tool developers to support identifier mapping. Mapping services can be combined or merged to support multi-omics experiments or to integrate custom microarray annotations. BridgeDb provides its own ready-to-go mapping services, both in webservice and local database forms. However, the framework is intended for customization and adaptation to any identifier mapping service. BridgeDb has already been integrated into several bioinformatics applications.Conclusion: By uncoupling bioinformatics tools from mapping services, BridgeDb improves capability and flexibility of those tools. All described software is open source and available at http://www.bridgedb.org. © 2010 van Iersel et al; licensee BioMed Central Ltd.", "date": "2010-01-04T00:00:00Z", "citationCount": 123, "authors": [ { "name": "van Iersel M.P." }, { "name": "Pico A.R." }, { "name": "Kelder T." }, { "name": "Gao J." }, { "name": "Ho I." }, { "name": "Hanspers K." }, { "name": "Conklin B.R." }, { "name": "Evelo C.T." } ], "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 } ], "community": null, "owner": "egonw", "additionDate": "2017-07-20T18:20:28Z", "lastUpdate": "2024-04-22T13:11:17.887951Z", "editPermission": { "type": "group", "authors": [ "ChrisEvelo", "LanfearJ" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "VarAFT", "description": "VarAFT (Variant Analysis and Filtration Tool) is a standalone and multiplatform tool for annotation and prioritization of potential disease causing genes. With this tool users can annotate variant (VCF) files, combine multiple samples from various individuals, prioritize list of variants by multi-filtering parameters. Additionally, users can perform a coverage analysis and quality check from any BAM file.", "homepage": "http://varaft.eu", "biotoolsID": "varaft", "biotoolsCURIE": "biotools:varaft", "version": [ "2.x" ], "otherID": [], "relation": [ { "biotoolsID": "umd-predictor", "type": "uses" }, { "biotoolsID": "human_splicing_finder", "type": "uses" }, { "biotoolsID": "annovar", "type": "uses" }, { "biotoolsID": "bedtools", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3763", "term": "Service invocation" }, { "uri": "http://edamontology.org/operation_3225", "term": "Variant classification" }, { "uri": "http://edamontology.org/operation_3695", "term": "Filtering" }, { "uri": "http://edamontology.org/operation_3436", "term": "Aggregation" }, { "uri": "http://edamontology.org/operation_3218", "term": "Sequencing quality control" }, { "uri": "http://edamontology.org/operation_3661", "term": "SNP annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3498", "term": "Sequence variations" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] }, { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [ { "uri": "http://edamontology.org/format_2572", "term": "BAM" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3053", "term": "Genetics" }, { "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": [ "Java", "Perl" ], "license": "Other", "collectionID": [ "Developed_RD-Connect", "RD-Connect", "Rare Disease", "ELIXIR-FR", "elixir-fr-sdp-2019" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://varaft.eu/download_files/VarAFT_Documentation_V2.pdf", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gky471", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "VarAFT: A variant annotation and filtration system for human next generation sequencing data", "abstract": "© The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.With the rapidly developing high-throughput sequencing technologies known as next generation sequencing or NGS, our approach to gene hunting and diagnosis has drastically changed. In <10 years, these technologies have moved from gene panel to whole genome sequencing and from an exclusively research context to clinical practice. Today, the limit is not the sequencing of one, many or all genes but rather the data analysis. Consequently, the challenge is to rapidly and efficiently identify disease-causing mutations within millions of variants. To do so, we developed the VarAFT software to annotate and pinpoint human disease-causing mutations through access to multiple layers of information. VarAFT was designed both for research and clinical contexts and is accessible to all scientists, regardless of bioinformatics training. Data from multiple samples may be combined to address all Mendelian inheritance modes, cancers or population genetics. Optimized filtration parameters can be stored and re-applied to large datasets. In addition to classical annotations from dbNSFP, VarAFT contains unique features at the disease (OMIM), phenotypic (HPO), gene (Gene Ontology, pathways) and variation levels (predictions from UMD-Predictor and Human Splicing Finder) that can be combined to optimally select candidate pathogenic mutations. VarAFT is freely available at: http://varaft.eu.", "date": "2018-07-02T00:00:00Z", "citationCount": 52, "authors": [ { "name": "Desvignes J.-P." }, { "name": "Bartoli M." }, { "name": "Delague V." }, { "name": "Krahn M." }, { "name": "Miltgen M." }, { "name": "Beroud C." }, { "name": "Salgado D." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Contact form", "email": null, "url": "http://varaft.eu/#contact", "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": "Jean-Pierre Desvignes", "email": "jean-pierre.desvignes@univ-amu.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "community": null, "owner": "dsalgado", "additionDate": "2017-03-05T11:50:24Z", "lastUpdate": "2024-04-02T21:35:23.173094Z", "editPermission": { "type": "group", "authors": [ "ELIXIR-EE", "lmatalonga", "dsalgado", "nbreznik" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }