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{ "count": 407, "next": "?page=2", "previous": null, "list": [ { "name": "lorikeet", "description": "Tools for M. tuberculosis DNA fingerprinting (spoligotyping)", "homepage": "https://github.com/AbeelLab/lorikeet", "biotoolsID": "lorikeet", "biotoolsCURIE": "biotools:lorikeet", "version": [ "20" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/operation_3196", "term": "Genotyping" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Bioinformatics portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0625", "term": "Genotype and phenotype" } ], "operatingSystem": [], "language": [ "Java" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "community": null, "owner": "rlibouban", "additionDate": "2024-03-12T10:56:44.977314Z", "lastUpdate": "2024-03-12T10:56:44.980036Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BBTools", "description": "BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data. BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw, with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supporting Java, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version 7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters.\n\nBBTools is open source and free for unlimited use, and is used regularly by DOE JGI and other institutions around the world.", "homepage": "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/", "biotoolsID": "bbtools", "biotoolsCURIE": "biotools:bbtools", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Suite" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "community": null, "owner": "paulzierep", "additionDate": "2024-03-12T09:39:30.275596Z", "lastUpdate": "2024-03-12T09:39:30.279447Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "legsta", "description": "Performs in silico Legionella pneumophila sequence based typing", "homepage": "https://github.com/tseemann/legsta", "biotoolsID": "legsta", "biotoolsCURIE": "biotools:legsta", "version": [ "0.5.1", "0.3.7", "0.3.2", "0.2" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Bioinformatics portal", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3305", "term": "Public health and epidemiology" } ], "operatingSystem": [], "language": [], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "community": null, "owner": "rlibouban", "additionDate": "2024-03-11T16:40:14.136794Z", "lastUpdate": "2024-03-11T16:40:14.139298Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "kofamscan", "description": "KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool.", "homepage": "https://github.com/takaram/kofam_scan", "biotoolsID": "kofamscan", "biotoolsCURIE": "biotools:kofamscan", "version": [ "1.3.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/operation_3672", "term": "Gene functional annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2976", "term": "Protein sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Bioinformatics portal", "Command-line tool", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" } ], "operatingSystem": [], "language": [], "license": "MIT", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "community": null, "owner": "rlibouban", "additionDate": "2024-03-11T15:00:11.214878Z", "lastUpdate": "2024-03-11T15:00:11.219298Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PlasFlow", "description": "PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs.", "homepage": "https://github.com/smaegol/PlasFlow", "biotoolsID": "plasflow", "biotoolsCURIE": "biotools:plasflow", "version": [ "1.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Bioinformatics portal", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" } ], "operatingSystem": [], "language": [], "license": "GPL-3.0", "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [], "credit": [], "community": null, "owner": "rlibouban", "additionDate": "2024-03-11T13:25:13.344697Z", "lastUpdate": "2024-03-11T13:25:32.934504Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Infernal cmscan (EBI)", "description": "Infernal (\"INFERence of RNA ALignment\") is for searching DNA sequence databases (e.g. Rfam) for RNA structure and sequence similarities.", "homepage": "https://www.ebi.ac.uk/jdispatcher/rna/infernal_cmscan", "biotoolsID": "infernal_cmscan", "biotoolsCURIE": "biotools:infernal_cmscan", "version": [ "1" ], "otherID": [], "relation": [ { "biotoolsID": "infernal", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "EBI Tools", "Job Dispatcher Tools" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.ebi.ac.uk/about/contact/support/job-dispatcher-services", "type": [ "Helpdesk" ], "note": null } ], "download": [ { "url": "http://eddylab.org/infernal/", "type": "Downloads page", "note": null, "version": null } ], "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 }, { "url": "http://eddylab.org/infernal/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/btt509", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Infernal 1.1: 100-fold faster RNA homology searches", "abstract": "Summary: Infernal builds probabilistic profiles of the sequence and secondary structure of an RNA family called covariance models (CMs) from structurally annotated multiple sequence alignments given as input. Infernal uses CMs to search for new family members in sequence databases and to create potentially large multiple sequence alignments. Version 1.1 of Infernal introduces a new filter pipeline for RNA homology search based on accelerated profile hidden Markov model (HMM) methods and HMM-banded CM alignment methods. This enables ∼100-fold acceleration over the previous version and ∼10 000-fold acceleration over exhaustive non-filtered CM searches. © The Author 2013. Published by Oxford University Press. All rights reserved.", "date": "2013-11-15T00:00:00Z", "citationCount": 1686, "authors": [ { "name": "Nawrocki E.P." }, { "name": "Eddy S.R." } ], "journal": "Bioinformatics" } }, { "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": 699, "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" } } ], "credit": [ { "name": "Sean Eddy", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "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": "2015-08-03T09:35:17Z", "lastUpdate": "2024-02-08T11:11:49.257440Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "T-Coffee (EBI)", "description": "Multiple sequence alignment that combines several alignment methods.", "homepage": "https://www.ebi.ac.uk/jdispatcher/msa/tcoffee/", "biotoolsID": "TCoffee_EBI", "biotoolsCURIE": "biotools:TCoffee_EBI", "version": [ "1" ], "otherID": [], "relation": [ { "biotoolsID": "tcoffee", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/operation_0492", "term": "Multiple sequence alignment" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2044", "term": "Sequence" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0863", "term": "Sequence alignment" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [], "license": null, "collectionID": [ "T-Coffee", "EBI Tools", "Job Dispatcher Tools" ], "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": [ { "url": "https://tcoffee.org/Projects/tcoffee/index.html", "type": "Downloads page", "note": null, "version": null } ], "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 }, { "url": "https://tcoffee.org/Projects/tcoffee/index.html", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1006/jmbi.2000.4042", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "T-coffee: A novel method for fast and accurate multiple sequence alignment", "abstract": "We describe a new method (T-Coffee) for multiple sequence alignment that provides a dramatic improvement in accuracy with a modest sacrifice in speed as compared to the most commonly used alternatives. The method is broadly based on the popular progressive approach to multiple alignment but avoids the most serious pitfalls caused by the greedy nature of this algorithm. With T-Coffee we pre-process a data set of all pair-wise alignments between the sequences. This provides us with a library of alignment information that can be used to guide the progressive alignment. Intermediate alignments are then based not only on the sequences to be aligned next but also on how all of the sequences align with each other. This alignment information can be derived from heterogeneous sources such as a mixture of alignment programs and/or structure superposition. Here, we illustrate the power of the approach by using a combination of local and global pair-wise alignments to generate the library. The resulting alignments are significantly more reliable, as determined by comparison with a set of 141 test cases, than any of the popular alternatives that we tried. The improvement, especially clear with the more difficult test cases, is always visible, regardless of the phylogenetic spread of the sequences in the tests. (C) 2000 Academic Press.", "date": "2000-09-08T00:00:00Z", "citationCount": 5641, "authors": [ { "name": "Notredame C." }, { "name": "Higgins D.G." }, { "name": "Heringa J." } ], "journal": "Journal of Molecular Biology" } }, { "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": 651, "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" } } ], "credit": [ { "name": "Cedric Notredame", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "CRG", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Job Dispatcher", "email": null, "url": "https://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": "2015-01-29T15:47:33Z", "lastUpdate": "2024-01-12T16:33:19.565882Z", "editPermission": { "type": "group", "authors": [ "nandana", "biomadeira" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "AltaiR", "description": "AltaiR is a C toolkit for alignment-free and spatial-temporal analysis of multi-FASTA data.\n\nThis method provides alignment-free and spatial-temporal analysis of multi-FASTA data through the implementation of a C toolkit that is highly flexible and with characteristics covering large-scale data, namely extensive collections of genomes/proteomes. This toolkit is ideal for scenarios entangling the presence of multiple sequences from epidemic and pandemic events. AlcoR is implemented in C language using multi-threading to increase the computational speed, is flexible for multiple applications, and does not contain external dependencies. The tool accepts any sequence(s) in (multi-) FASTA format.", "homepage": "https://github.com/cobilab/altair", "biotoolsID": "altair", "biotoolsCURIE": "biotools:altair", "version": [ "1.0.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" }, { "uri": "http://edamontology.org/topic_3303", "term": "Medicine" } ], "operatingSystem": [ "Linux" ], "language": [ "C" ], "license": "GPL-3.0", "collectionID": [ "COVID-19", "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools", "Data" ], "elixirNode": [ "Portugal" ], "elixirCommunity": [], "link": [ { "url": "https://github.com/cobilab/altair", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [], "credit": [ { "name": "Jorge M. Silva", "email": "jorge.miguel.ferreira.silva@ua.pt", "url": null, "orcidid": "http://orcid.org/0000-0002-6331-6091", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Contributor" ], "note": "Researcher at IEETA. J.M.S. has received funding from the EC under grant agreement 101081813, Genomic Data Infrastructure." }, { "name": "Diogo Pratas", "email": "pratas@ua.pt", "url": null, "orcidid": "http://orcid.org/0000-0003-1176-552X", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Funding agency", "typeRole": [ "Contributor" ], "note": "Researcher at IEETA. D.P. is funded by national funds through FCT – Fundação para a Ciência e a Tecnologia, I.P., under the Scientific Employment Stimulus - Institutional Call - reference CEECINST/00026/2018." } ], "community": null, "owner": "jorgeMFS", "additionDate": "2023-12-13T14:54:35.138186Z", "lastUpdate": "2023-12-13T14:54:35.146893Z", "editPermission": { "type": "group", "authors": [ "pratas" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "ViruSurf", "description": "ViruSurf, available at http://gmql.eu/virusurf/, is a large public database of viral sequences and integrated and curated metadata from heterogeneous sources (RefSeq, GenBank, COG-UK, and NMDC); it also exposes computed nucleotide and amino acid variants, called from original sequences. A GISAID-specific ViruSurf database, available at http://gmql.eu/virusurf_gisaid/, offers a subset of these functionalities. \n\nThe database is centered on sequences, described from their biological, technological, and organizational dimensions. In addition, the analytical dimension characterizes the sequence in terms of its annotations and variants. The web interface enables expressing complex search queries in a simple way; arbitrary search queries can freely combine conditions on attributes from the four dimensions, extracting the resulting sequences.", "homepage": "http://gmql.eu/virusurf/", "biotoolsID": "virusurf", "biotoolsCURIE": "biotools:virusurf", "version": [], "otherID": [], "relation": [ { "biotoolsID": "genosurf", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_3227", "term": "Variant calling" }, { "uri": "http://edamontology.org/operation_0292", "term": "Sequence alignment" }, { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_0219", "term": "Data submission, annotation and curation" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0781", "term": "Virology" } ], "operatingSystem": [], "language": [], "license": null, "collectionID": [ "COVID-19" ], "maturity": null, "cost": null, "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "http://gmql.eu/virusurf_gisaid/", "type": [ "Other" ], "note": "GISAID-specific ViruSurf database" } ], "download": [], "documentation": [ { "url": "https://github.com/DEIB-GECO/vue-metadata/wiki", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkaa846", "pmid": "33045721", "pmcid": "PMC7778888", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "ViruSurf: An integrated database to investigate viral sequences", "abstract": "ViruSurf, available at http://gmql.eu/virusurf/, is a large public database of viral sequences and integrated and curated metadata from heterogeneous sources (RefSeq, GenBank, COG-UK and NMDC); it also exposes computed nucleotide and amino acid variants, called from original sequences. A GISAID-specific ViruSurf database, available at http://gmql.eu/virusurf gisaid/, offers a subset of these functionalities. Given the current pandemic outbreak, SARS-CoV-2 data are collected from the four sources; but ViruSurf contains other virus species harmful to humans, including SARS-CoV, MERS-CoV, Ebola and Dengue. The database is centered on sequences, described from their biological, technological and organizational dimensions. In addition, the analytical dimension characterizes the sequence in terms of its annotations and variants. The web interface enables expressing complex search queries in a simple way; arbitrary search queries can freely combine conditions on attributes from the four dimensions, extracting the resulting sequences. Several example queries on the database confirm and possibly improve results from recent research papers; results can be recomputed over time and upon selected populations. Effective search over large and curated sequence data may enable faster responses to future threats that could arise from new viruses.", "date": "2021-01-08T00:00:00Z", "citationCount": 32, "authors": [ { "name": "Canakoglu A." }, { "name": "Pinoli P." }, { "name": "Bernasconi A." }, { "name": "Alfonsi T." }, { "name": "Melidis D.P." }, { "name": "Ceri S." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1186/s12859-022-05022-0", "pmid": null, "pmcid": null, "type": [], "version": null, "note": "Description of the Viral Conceptual Model (VCM) used by ViruSurf", "metadata": { "title": "Semantic interoperability: ontological unpacking of a viral conceptual model", "abstract": "Background: Genomics and virology are unquestionably important, but complex, domains being investigated by a large number of scientists. The need to facilitate and support work within these domains requires sharing of databases, although it is often difficult to do so because of the different ways in which data is represented across the databases. To foster semantic interoperability, models are needed that provide a deep understanding and interpretation of the concepts in a domain, so that the data can be consistently interpreted among researchers. Results: In this research, we propose the use of conceptual models to support semantic interoperability among databases and assess their ontological clarity to support their effective use. This modeling effort is illustrated by its application to the Viral Conceptual Model (VCM) that captures and represents the sequencing of viruses, inspired by the need to understand the genomic aspects of the virus responsible for COVID-19. For achieving semantic clarity on the VCM, we leverage the “ontological unpacking” method, a process of ontological analysis that reveals the ontological foundation of the information that is represented in a conceptual model. This is accomplished by applying the stereotypes of the OntoUML ontology-driven conceptual modeling language.As a result, we propose a new OntoVCM, an ontologically grounded model, based on the initial VCM, but with guaranteed interoperability among the data sources that employ it. Conclusions: We propose and illustrate how the unpacking of the Viral Conceptual Model resolves several issues related to semantic interoperability, the importance of which is recognized by the “I” in FAIR principles. The research addresses conceptual uncertainty within the domain of SARS-CoV-2 data and knowledge.The method employed provides the basis for further analyses of complex models currently used in life science applications, but lacking ontological grounding, subsequently hindering the interoperability needed for scientists to progress their research.", "date": "2022-11-01T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Bernasconi A." }, { "name": "Guizzardi G." }, { "name": "Pastor O." }, { "name": "Storey V.C." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Stefano Ceri", "email": "stefano.ceri@polimi.it", "url": "https://ceri.faculty.polimi.it/", "orcidid": "https://orcid.org/0000-0003-0671-2415", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": "Professor of Database Systems at Politecnico di Milano" }, { "name": "Arif Canakoglu", "email": "arif.canakoglu@polimi.it", "url": "https://www.deib.polimi.it/eng/people/details/626632", "orcidid": "https://orcid.org/0000-0003-4528-6586", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": "Research assistant at Politecnico di Milano" }, { "name": "Pietro Pinoli", "email": "pietro.pinoli@polimi.it", "url": "https://www.deib.polimi.it/ita/personale/dettagli/585322", "orcidid": "https://orcid.org/0000-0001-9786-2851", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Contributor" ], "note": "Researcher at Politecnico di Milano" }, { "name": "Anna Bernasconi", "email": "anna.bernasconi@polimi.it", "url": "https://annabernasconi.faculty.polimi.it/", "orcidid": "https://orcid.org/0000-0001-8016-5750", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Contributor" ], "note": "Research assistant at Politecnico di Milano" }, { "name": "ELIXIR-ITA", "email": null, "url": "https://elixir-italy.org/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [], "note": null }, { "name": "ELIXIR-ITA-POLIMI", "email": null, "url": "https://www.deib.polimi.it/eng/elixir-iib", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [], "note": null } ], "community": null, "owner": "abernasconi", "additionDate": "2021-01-18T10:20:32Z", "lastUpdate": "2023-12-03T20:55:22.756702Z", "editPermission": { "type": "group", "authors": [ "abernasconi", "arif.canakoglu@polimi.it", "ELIXIR-ITA-POLIMI" ] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "GENESPACE", "description": "GENESPACE: an R package for synteny- and orthology-constrained comparative genomics", "homepage": "https://github.com/jtlovell/GENESPACE", "biotoolsID": "genespace", "biotoolsCURIE": "biotools:genespace", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3182", "term": "Genome alignment" }, { "uri": "http://edamontology.org/operation_2403", "term": "Sequence analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0797", "term": "Comparative genomics" } ], "operatingSystem": [], "language": [ "R" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/jtlovell/GENESPACE", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.7554/eLife.78526", "pmid": null, "pmcid": null, "type": [], "version": null, "note": null, "metadata": null } ], "credit": [], "community": null, "owner": "alexcorm", "additionDate": "2023-11-06T09:29:56.888140Z", "lastUpdate": "2023-11-06T09:31:59.658628Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }