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{ "count": 1946, "next": "?page=2", "previous": null, "list": [ { "name": "IDIA", "description": "An integrative signal extractor for data-independent acquisition proteomics.", "homepage": "https://github.com/Biocomputing-Research-Group/IDIA", "biotoolsID": "idia", "biotoolsCURIE": "biotools:idia", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3646", "term": "Peptide database search" }, { "uri": "http://edamontology.org/operation_3767", "term": "Protein identification" }, { "uri": "http://edamontology.org/operation_3695", "term": "Filtering" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [ { "uri": "http://edamontology.org/format_3654", "term": "mzXML" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrum" }, "format": [ { "uri": "http://edamontology.org/format_3651", "term": "MGF" }, { "uri": "http://edamontology.org/format_3244", "term": "mzML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_0080", "term": "Sequence analysis" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Java" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1109/BIBM55620.2022.9994873", "pmid": "37034305", "pmcid": "PMC10077956", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "IDIA: An Integrative Signal Extractor for Data-Independent Acquisition Proteomics", "abstract": "In proteomics, data-independent acquisition (DIA)has been shown to provide less biased and more reproducible results than data-dependent acquisition. Recently, many researchers have developed a series of methods to identify peptides and proteins by using spectrum libraries for DIA data. However, spectrum libraries are not always available for novel organisms or microbial communities. To detect peptides and proteins without a spectrum library, we developed IDIA, a library-free method using DIA data to generate pseudo-spectra that can be searched using conventional sequence database searching software. IDIA integrates two isotopic trace detection strategies and employs B-spline and Gaussian filters to help extract high-quality pseudo-spectra from the complex DIA data. The experimental results on human and yeast data demonstrated that our approach remarkably produced more peptide and protein identifications than the two state-of-the-art library-free methods, i.e., DIA-Umpire and Group-DIA. IDIA is freely available under the GNU GPL license at https://github.com/Biocomputing-Research-Group/IDIA.", "date": "2022-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Li J." }, { "name": "Pan C." }, { "name": "Guo X." } ], "journal": "Proceedings - 2022 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2022" } } ], "credit": [ { "name": "Xuan Guo", "email": "xuan.guo@unt.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2023-09-25T20:53:22.903009Z", "lastUpdate": "2023-09-25T20:53:22.905395Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "ProtVar", "description": "ProtVar helps users to contextualise and evaluate human missense variation at a per-residue level. It can be accessed via genomic coordinates, IDs or protein positions in over 92% of human proteins. Functional and structural annotations, predictions and co-located variants can be explored via an interactive UI or accessed programatically via an API.", "homepage": "https://www.ebi.ac.uk/ProtVar/", "biotoolsID": "protvar", "biotoolsCURIE": "biotools:protvar", "version": [], "otherID": [], "relation": [ { "biotoolsID": "open_targets_platform", "type": "usedBy" }, { "biotoolsID": "uniprot", "type": "uses" }, { "biotoolsID": "uniprot", "type": "usedBy" }, { "biotoolsID": "ensembl", "type": "uses" }, { "biotoolsID": "pdbe", "type": "uses" }, { "biotoolsID": "dbsnp", "type": "uses" }, { "biotoolsID": "clinvar", "type": "uses" }, { "biotoolsID": "crossmap", "type": "uses" }, { "biotoolsID": "alphafold_2", "type": "uses" }, { "biotoolsID": "eve", "type": "uses" }, { "biotoolsID": "cadd_phred", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2520", "term": "DNA mapping" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2887", "term": "Nucleic acid sequence record" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2886", "term": "Protein sequence record" }, "format": [ { "uri": "http://edamontology.org/format_2187", "term": "UniProt-like (text)" } ] } ], "note": "ProtVar maps missense variants from genomic coordinates to UniProt protein positions in all isoforms.", "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_3661", "term": "SNP annotation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2887", "term": "Nucleic acid sequence record" }, "format": [ { "uri": "http://edamontology.org/format_3016", "term": "VCF" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3779", "term": "Annotated text" }, "format": [ { "uri": "http://edamontology.org/format_2187", "term": "UniProt-like (text)" } ] } ], "note": "ProtVar annotates missense variant positions with functional and structural information for the amino acid affected, the protein region and the overall protein role from curated and high throughput sources.", "cmd": null } ], "toolType": [ "Web application", "Web API", "Bioinformatics portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3574", "term": "Human genetics" }, { "uri": "http://edamontology.org/topic_1317", "term": "Structural biology" }, { "uri": "http://edamontology.org/topic_2533", "term": "DNA mutation" }, { "uri": "http://edamontology.org/topic_3510", "term": "Protein sites, features and motifs" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Java" ], "license": null, "collectionID": [ "Rare Disease" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://twitter.com/EBIProtVar", "type": [ "Social media" ], "note": null }, { "url": "https://docs.google.com/forms/d/e/1FAIpQLSd7P85zRHVspesU3kgF3qWpzSDSYFsyeGFmnkuyzB00HNDmDw/viewform?usp=sf_link", "type": [ "Mailing list" ], "note": null } ], "download": [], "documentation": [ { "url": "https://www.ebi.ac.uk/ProtVar/help", "type": [ "User manual" ], "note": "This is a link to the help section in ProtVar with annotated screen shots to help you navigate the tool and understand the data." } ], "publication": [], "credit": [ { "name": "James Stephenson", "email": "jstephenson@ebi.ac.uk", "url": "https://www.ebi.ac.uk/people/person/james-stephenson/", "orcidid": "https://orcid.org/0000-0002-6427-5703", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Maintainer", "Documentor" ], "note": null }, { "name": "EMBL-EBI", "email": null, "url": "https://www.ebi.ac.uk/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "Prabhat Totoo", "email": null, "url": "https://www.ebi.ac.uk/people/person/prabhat-totoo/", "orcidid": "https://orcid.org/0000-0001-5923-4467", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Developer", "Maintainer" ], "note": null }, { "name": "Open Targets", "email": null, "url": "https://www.opentargets.org/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Consortium", "typeRole": [], "note": null } ], "community": null, "owner": "JStephenson", "additionDate": "2023-09-21T09:05:33.125111Z", "lastUpdate": "2023-09-25T09:31:39.599149Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "CircularSTAR3D", "description": "Stack-based RNA 3D structural alignment tool for circular matching.", "homepage": "https://github.com/ucfcbb/CircularSTAR3D", "biotoolsID": "circularstar3d", "biotoolsCURIE": "biotools:circularstar3d", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0295", "term": "Structure alignment" }, { "uri": "http://edamontology.org/operation_0502", "term": "RNA secondary structure alignment" }, { "uri": "http://edamontology.org/operation_0495", "term": "Local alignment" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_3216", "term": "Scaffolding" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0659", "term": "Functional, regulatory and non-coding RNA" }, { "uri": "http://edamontology.org/topic_0097", "term": "Nucleic acid structure analysis" }, { "uri": "http://edamontology.org/topic_3512", "term": "Gene transcripts" }, { "uri": "http://edamontology.org/topic_0166", "term": "Protein structural motifs and surfaces" }, { "uri": "http://edamontology.org/topic_0160", "term": "Sequence sites, features and motifs" } ], "operatingSystem": [ "Linux" ], "language": [ "Java" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/NAR/GKAD222", "pmid": "36987885", "pmcid": "PMC10201423", "type": [], "version": null, "note": null, "metadata": { "title": "CircularSTAR3D: A stack-based RNA 3D structural alignment tool for circular matching", "abstract": "The functions of non-coding RNAs usually depend on their 3D structures. Therefore, comparing RNA 3D structures is critical in analyzing their functions. We noticed an interesting phenomenon that two non-coding RNAs may share similar substructures when rotating their sequence order. To the best of our knowledge, no existing RNA 3D structural alignment tools can detect this type of matching. In this article, we defined the RNA 3D structure circular matching problem and developed a software tool named CircularSTAR3D to solve this problem. CircularSTAR3D first uses the conserved stacks (consecutive base pairs with similar 3D structures) in the input RNAs to identify the circular matched internal loops and multiloops. Then it performs a local extension iteratively to obtain the whole circular matched substructures. The computational experiments conducted on a non-redundant RNA structure dataset show that circular matching is ubiquitous. Furthermore, we demonstrated the utility of CircularSTAR3D by detecting the conserved substructures missed by regular alignment tools, including structural motifs and conserved structures between riboswitches and ribozymes from different classes. We anticipate CircularSTAR3D to be a valuable supplement to the existing RNA 3D structural analysis techniques.", "date": "2023-05-22T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Chen X." }, { "name": "Zhang S." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "Shaojie Zhang", "email": "shzhang@cs.ucf.edu", "url": null, "orcidid": "https://orcid.org/0000-0002-4051-5549", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Xiaoli Chen", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2023-09-04T17:21:08.225815Z", "lastUpdate": "2023-09-04T17:21:08.228525Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "KARGVA", "description": "K-mer Antibiotic Resistance Gene Variant Analyzer.", "homepage": "https://github.com/DataIntellSystLab/KARGVA", "biotoolsID": "kargva", "biotoolsCURIE": "biotools:kargva", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3482", "term": "Antimicrobial resistance prediction" }, { "uri": "http://edamontology.org/operation_3472", "term": "k-mer counting" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_3168", "term": "Sequencing" }, { "uri": "http://edamontology.org/topic_0102", "term": "Mapping" }, { "uri": "http://edamontology.org/topic_3697", "term": "Microbial ecology" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Java" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.3389/FMICB.2023.1060891", "pmid": "36960290", "pmcid": "PMC10027697", "type": [], "version": null, "note": null, "metadata": { "title": "The K-mer antibiotic resistance gene variant analyzer (KARGVA)", "abstract": "Characterization of antibiotic resistance genes (ARGs) from high-throughput sequencing data of metagenomics and cultured bacterial samples is a challenging task, with the need to account for both computational (e.g., string algorithms) and biological (e.g., gene transfers, rearrangements) aspects. Curated ARG databases exist together with assorted ARG classification approaches (e.g., database alignment, machine learning). Besides ARGs that naturally occur in bacterial strains or are acquired through mobile elements, there are chromosomal genes that can render a bacterium resistant to antibiotics through point mutations, i.e., ARG variants (ARGVs). While ARG repositories also collect ARGVs, there are only a few tools that are able to identify ARGVs from metagenomics and high throughput sequencing data, with a number of limitations (e.g., pre-assembly, a posteriori verification of mutations, or specification of species). In this work we present the k-mer, i.e., strings of fixed length k, ARGV analyzer – KARGVA – an open-source, multi-platform tool that provides: (i) an ad hoc, large ARGV database derived from multiple sources; (ii) input capability for various types of high-throughput sequencing data; (iii) a three-way, hash-based, k-mer search setup to process data efficiently, linking k-mers to ARGVs, k-mers to point mutations, and ARGVs to k-mers, respectively; (iv) a statistical filter on sequence classification to reduce type I and II errors. On semi-synthetic data, KARGVA provides very high accuracy even in presence of high sequencing errors or mutations (99.2 and 86.6% accuracy within 1 and 5% base change rates, respectively), and genome rearrangements (98.2% accuracy), with robust performance on ad hoc false positive sets. On data from the worldwide MetaSUB consortium, comprising 3,700+ metagenomics experiments, KARGVA identifies more ARGVs than Resistance Gene Identifier (4.8x) and PointFinder (6.8x), yet all predictions are below the expected false positive estimates. The prevalence of ARGVs is correlated to ARGs but ecological characteristics do not explain well ARGV variance. KARGVA is publicly available at https://github.com/DataIntellSystLab/KARGVA under MIT license.", "date": "2023-01-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Marini S." }, { "name": "Boucher C." }, { "name": "Noyes N." }, { "name": "Prosperi M." } ], "journal": "Frontiers in Microbiology" } } ], "credit": [ { "name": "Mattia Prosperi", "email": "m.prosperi@ufl.edu", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Simone Marini", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Christina Boucher", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Noelle Noyes", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2023-08-30T14:26:10.621881Z", "lastUpdate": "2023-08-30T14:26:10.624682Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "APE", "description": "APE (the Automated Pipeline Explorer) as a command-line tool and API for automated composition of scientific workflows. APE is easily configured to a new application domain by providing it with a domain ontology and semantically annotated tools. It can then be used to synthesize purpose-specific workflows based on a specification of the available workflow inputs, desired outputs and possibly additional constraints.", "homepage": "https://github.com/sanctuuary/APE/", "biotoolsID": "ape", "biotoolsCURIE": "biotools:ape", "version": [ "2.1.7" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3633", "term": "Retention time prediction" }, { "uri": "http://edamontology.org/operation_3501", "term": "Enrichment analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool", "Library" ], "topic": [ { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" }, { "uri": "http://edamontology.org/topic_0089", "term": "Ontology and terminology" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Java" ], "license": "Apache-2.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/sanctuuary/ape", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://mvnrepository.com/artifact/io.github.sanctuuary/APE/2.1.7", "type": "Software package", "note": "Download APE java library or the CLI", "version": "2.1.7" } ], "documentation": [ { "url": "https://ape-framework.readthedocs.io/", "type": [ "API documentation" ], "note": null } ], "publication": [ { "doi": "10.1007/978-3-030-50436-6_34", "pmid": null, "pmcid": "PMC7304703", "type": [], "version": null, "note": null, "metadata": null }, { "doi": "10.1021/ACS.JPROTEOME.0C00983", "pmid": "33720735", "pmcid": "PMC8041394", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Vedran Kasalica", "email": "v.kasalica@esciencecenter.nl", "url": null, "orcidid": "https://orcid.org/0000-0002-0097-1056", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Anna-Lena Lamprecht", "email": "anna-lena.lamprecht@uni-potsdam.de", "url": null, "orcidid": "https://orcid.org/0000-0003-1953-5606", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "VKasalica", "additionDate": "2021-01-18T10:10:48Z", "lastUpdate": "2023-08-30T12:49:28.699851Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MoBIE", "description": "Fiji plugin for sharing and exploration of multi-modal cloud-hosted big image data.", "homepage": "https://mobie.github.io/", "biotoolsID": "mobie", "biotoolsCURIE": "biotools:mobie", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Plug-in", "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_3382", "term": "Imaging" }, { "uri": "http://edamontology.org/topic_3308", "term": "Transcriptomics" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python", "Java", "R" ], "license": "BSD-2-Clause", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/mobie", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/mobie/mobie-viewer-fiji", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://mobie.github.io/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1038/S41592-023-01776-4", "pmid": "36765247", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "MoBIE: a Fiji plugin for sharing and exploration of multi-modal cloud-hosted big image data", "abstract": "", "date": "2023-04-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Pape C." }, { "name": "Meechan K." }, { "name": "Moreva E." }, { "name": "Schorb M." }, { "name": "Chiaruttini N." }, { "name": "Zinchenko V." }, { "name": "Martinez Vergara H." }, { "name": "Mizzon G." }, { "name": "Moore J." }, { "name": "Arendt D." }, { "name": "Kreshuk A." }, { "name": "Schwab Y." }, { "name": "Tischer C." } ], "journal": "Nature Methods" } } ], "credit": [ { "name": "Constantin Pape", "email": "constantin.pape@informatik.uni-goettingen.de", "url": null, "orcidid": "http://orcid.org/0000-0001-6562-7187", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Christian Tischer", "email": "christian.tischer@embl.de", "url": null, "orcidid": "http://orcid.org/0000-0003-4105-1990", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2023-08-21T13:50:07.975869Z", "lastUpdate": "2023-08-21T13:50:07.978462Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "PriPath", "description": "PriPath: identifying affected pathways from differential gene expression via grouping, scoring and modeling with an embedded machine learning approach.", "homepage": "https://github.com/malikyousef/PriPath.git", "biotoolsID": "pripath", "biotoolsCURIE": "biotools:pripath", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2436", "term": "Gene-set enrichment analysis" }, { "uri": "http://edamontology.org/operation_0533", "term": "Expression profile pathway mapping" }, { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression profiling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2603", "term": "Expression data" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2343", "term": "Pathway ID (KEGG)" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0951", "term": "Statistical estimate score" }, "format": [ { "uri": "http://edamontology.org/format_3620", "term": "xlsx" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0602", "term": "Molecular interactions, pathways and networks" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_2640", "term": "Oncology" }, { "uri": "http://edamontology.org/topic_0769", "term": "Workflows" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python", "R", "Java" ], "license": "CC-BY-4.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1186/S12859-023-05187-2", "pmid": "36823571", "pmcid": "PMC9947447", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "PriPath: identifying dysregulated pathways from differential gene expression via grouping, scoring, and modeling with an embedded feature selection approach", "abstract": "Background: Cell homeostasis relies on the concerted actions of genes, and dysregulated genes can lead to diseases. In living organisms, genes or their products do not act alone but within networks. Subsets of these networks can be viewed as modules that provide specific functionality to an organism. The Kyoto encyclopedia of genes and genomes (KEGG) systematically analyzes gene functions, proteins, and molecules and combines them into pathways. Measurements of gene expression (e.g., RNA-seq data) can be mapped to KEGG pathways to determine which modules are affected or dysregulated in the disease. However, genes acting in multiple pathways and other inherent issues complicate such analyses. Many current approaches may only employ gene expression data and need to pay more attention to some of the existing knowledge stored in KEGG pathways for detecting dysregulated pathways. New methods that consider more precompiled information are required for a more holistic association between gene expression and diseases. Results: PriPath is a novel approach that transfers the generic process of grouping and scoring, followed by modeling to analyze gene expression with KEGG pathways. In PriPath, KEGG pathways are utilized as the grouping function as part of a machine learning algorithm for selecting the most significant KEGG pathways. A machine learning model is trained to differentiate between diseases and controls using those groups. We have tested PriPath on 13 gene expression datasets of various cancers and other diseases. Our proposed approach successfully assigned biologically and clinically relevant KEGG terms to the samples based on the differentially expressed genes. We have comparatively evaluated the performance of PriPath against other tools, which are similar in their merit. For each dataset, we manually confirmed the top results of PriPath in the literature and found that most predictions can be supported by previous experimental research. Conclusions: PriPath can thus aid in determining dysregulated pathways, which applies to medical diagnostics. In the future, we aim to advance this approach so that it can perform patient stratification based on gene expression and identify druggable targets. Thereby, we cover two aspects of precision medicine.", "date": "2023-12-01T00:00:00Z", "citationCount": 2, "authors": [ { "name": "Yousef M." }, { "name": "Ozdemir F." }, { "name": "Jaber A." }, { "name": "Allmer J." }, { "name": "Bakir-Gungor B." } ], "journal": "BMC Bioinformatics" } } ], "credit": [ { "name": "Malik Yousef", "email": "malik.yousef@gmail.com", "url": null, "orcidid": "https://orcid.org/0000-0001-8780-6303", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2023-08-17T10:20:09.340146Z", "lastUpdate": "2023-08-17T10:20:09.343993Z", "editPermission": { "type": "public", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Sherlock", "description": "Free and Open-Source System for the Computer-Assisted Structure Elucidation of Organic Compounds from NMR Data.", "homepage": "https://github.com/michaelwenk/sherlock", "biotoolsID": "sherlock_nmr", "biotoolsCURIE": "biotools:sherlock_nmr", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_3215", "term": "Peak detection" }, { "uri": "http://edamontology.org/operation_3860", "term": "Spectrum calculation" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_3465", "term": "Correlation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3488", "term": "NMR spectrum" }, "format": [ { "uri": "http://edamontology.org/format_3859", "term": "JCAMP-DX" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Desktop application" ], "topic": [ { "uri": "http://edamontology.org/topic_0593", "term": "NMR" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_3047", "term": "Molecular biology" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Java" ], "license": "MIT", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/michaelwenk/sherlock", "type": [ "Repository" ], "note": null }, { "url": "https://github.com/michaelwenk/sherlock-frontend", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://github.com/michaelwenk/sherlock-frontend/blob/master/public/Sherlock_manual.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.3390/MOLECULES28031448", "pmid": "36771127", "pmcid": "PMC9920390", "type": [], "version": null, "note": null, "metadata": { "title": "Sherlock—A Free and Open-Source System for the Computer-Assisted Structure Elucidation of Organic Compounds from NMR Data", "abstract": "The structure elucidation of small organic molecules (<1500 Dalton) through 1D and 2D nuclear magnetic resonance (NMR) data analysis is a potentially challenging, combinatorial problem. This publication presents Sherlock, a free and open-source Computer-Assisted Structure Elucidation (CASE) software where the user controls the chain of elementary operations through a versatile graphical user interface, including spectral peak picking, addition of automatically or user-defined structure constraints, structure generation, ranking and display of the solutions. A set of forty-five compounds was selected in order to illustrate the new possibilities offered to organic chemists by Sherlock for improving the reliability and traceability of structure elucidation results.", "date": "2023-02-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Wenk M." }, { "name": "Nuzillard J.-M." }, { "name": "Steinbeck C." } ], "journal": "Molecules" } } ], "credit": [ { "name": "Michael Wenk", "email": "michael.wenk@uni-jena.de", "url": null, "orcidid": "https://orcid.org/0000-0002-7868-2473", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Christoph Steinbeck", "email": "christoph.steinbeck@uni-jena.de", "url": null, "orcidid": "https://orcid.org/0000-0001-6966-0814", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "Pub2Tools", "additionDate": "2023-08-08T14:43:10.104936Z", "lastUpdate": "2023-08-08T14:50:20.277099Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "RINspector", "description": "Combines centrality analyses of Residue Interaction Networks (RIN) with DynaMine flexibility predictions.", "homepage": "http://apps.cytoscape.org/apps/rinspector", "biotoolsID": "RINspector", "biotoolsCURIE": "biotools:RINspector", "version": [ "1.3.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0248", "term": "Residue interaction calculation" }, { "uri": "http://edamontology.org/operation_2406", "term": "Protein structure analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Plug-in" ], "topic": [ { "uri": "http://edamontology.org/topic_0130", "term": "Protein folding, stability and design" }, { "uri": "http://edamontology.org/topic_0199", "term": "Genetic variation" }, { "uri": "http://edamontology.org/topic_0736", "term": "Protein folds and structural domains" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": null, "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://sourcesup.renater.fr/scm/?group_id=3888", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [ { "url": "https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/cpbi.66", "type": [ "Training material" ], "note": "Tutorial material" } ], "publication": [ { "doi": "10.1093/bioinformatics/btx586", "pmid": "29028877", "pmcid": "PMC5860209", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "RINspector: A Cytoscape app for centrality analyses and DynaMine flexibility prediction", "abstract": "Motivation Protein function is directly related to amino acid residue composition and the dynamics of these residues. Centrality analyses based on residue interaction networks permit to identify key residues in a protein that are important for its fold or function. Such central residues and their environment constitute suitable targets for mutagenesis experiments. Predicted flexibility and changes in flexibility upon mutation provide valuable additional information for the design of such experiments. Results We combined centrality analyses with DynaMine flexibility predictions in a Cytoscape app called RINspector. The app performs centrality analyses and directly visualizes the results on a graph of predicted residue flexibility. In addition, the effect of mutations on local flexibility can be calculated.", "date": "2018-01-15T00:00:00Z", "citationCount": 19, "authors": [ { "name": "Brysbaert G." }, { "name": "Lorgouilloux K." }, { "name": "Vranken W.F." }, { "name": "Lensink M.F." } ], "journal": "Bioinformatics" } }, { "doi": "10.12688/f1000research.14298.2", "pmid": "29946443", "pmcid": "PMC5998007", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "G. Brysbaert", "email": "guillaume.brysbaert@univ-lille.fr", "url": null, "orcidid": "https://orcid.org/0000-0002-6807-6621", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "gbrysbaert", "additionDate": "2019-06-24T06:59:11Z", "lastUpdate": "2023-06-29T15:17:34.423673Z", "editPermission": { "type": "group", "authors": [ "gbrysbaert" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "BioTransformer", "description": "BioTransformer is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction.", "homepage": "https://biotransformer.ca", "biotoolsID": "biotransformer", "biotoolsCURIE": "biotools:biotransformer", "version": [ "3.1.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3929", "term": "Metabolic pathway prediction" }, { "uri": "http://edamontology.org/operation_0417", "term": "PTM site prediction" }, { "uri": "http://edamontology.org/operation_3803", "term": "Natural product identification" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_1196", "term": "SMILES" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1463", "term": "Small molecule structure" }, "format": [ { "uri": "http://edamontology.org/format_1196", "term": "SMILES" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Desktop application", "Command-line tool", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_3407", "term": "Endocrinology and metabolism" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0152", "term": "Carbohydrates" }, { "uri": "http://edamontology.org/topic_0593", "term": "NMR" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Java" ], "license": "LGPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://bitbucket.org/wishartlab/biotransformer3.0jar/src/master/", "type": [ "Repository" ], "note": null }, { "url": "https://umsa.cerit-sc.cz/root?tool_id=toolshed.g2.bx.psu.edu/repos/recetox/biotransformer/biotransformer/3.0_20230403+galaxy0", "type": [ "Galaxy service" ], "note": "Galaxy tool hosted on UMSA Galaxy" } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1093/NAR/GKAC313", "pmid": "35536252", "pmcid": "PMC9252798", "type": [], "version": null, "note": null, "metadata": { "title": "BioTransformer 3.0 - a web server for accurately predicting metabolic transformation products", "abstract": "BioTransformer 3.0 (https://biotransformer.ca) is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. It combines machine learning approaches with a rule-based system to predict small-molecule metabolism in human tissues, the human gut as well as the external environment (soil and water microbiota). Simply stated, BioTransformer takes a molecular structure as input (SMILES or SDF) and outputs an interactively sortable table of the predicted metabolites or transformation products (SMILES, PNG images) along with the enzymes that are predicted to be responsible for those reactions and richly annotated downloadable files (CSV and JSON). The entire process typically takes less than a minute. Previous versions of BioTransformer focused exclusively on predicting the metabolism of xenobiotics (such as plant natural products, drugs, cosmetics and other synthetic compounds) using a limited number of pre-defined steps and somewhat limited rule-based methods. BioTransformer 3.0 uses much more sophisticated methods and incorporates new databases, new constraints and new prediction modules to not only more accurately predict the metabolic transformation products of exogenous xenobiotics but also the transformation products of endogenous metabolites, such as amino acids, peptides, carbohydrates, organic acids, and lipids. BioTransformer 3.0 can also support customized sequential combinations of these transformations along with multiple iterations to simulate multi-step human biotransformation events. Performance tests indicate that BioTransformer 3.0 is 40-50% more accurate, far less prone to combinatorial 'explosions' and much more comprehensive in terms of metabolite coverage/capabilities than previous versions of BioTransformer.", "date": "2022-07-05T00:00:00Z", "citationCount": 9, "authors": [ { "name": "Wishart D.S." }, { "name": "Tian S." }, { "name": "Allen D." }, { "name": "Oler E." }, { "name": "Peters H." }, { "name": "Lui V.W." }, { "name": "Gautam V." }, { "name": "Djoumbou-Feunang Y." }, { "name": "Greiner R." }, { "name": "Metz T.O." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": "David S Wishart", "email": "david.wishart@ualberta.ca", "url": null, "orcidid": "https://orcid.org/0000-0002-3207-2434", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Thomas O Metz", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "community": null, "owner": "Chan019", "additionDate": "2022-08-11T08:50:37.441150Z", "lastUpdate": "2023-06-22T13:39:47.956118Z", "editPermission": { "type": "public", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" } ] }