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This release repository is being used temporarily during the current testing stage." } ], "download": [], "documentation": [], "publication": [], "credit": [], "owner": "victorsp", "additionDate": "2025-04-24T13:00:12.867477Z", "lastUpdate": "2025-11-04T09:35:56.564173Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "MSNovelist", "description": "De novo structure generation from mass spectra.", "homepage": "https://github.com/meowcat/MSNovelist", "biotoolsID": "msnovelist", "biotoolsCURIE": "biotools:msnovelist", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0476", "term": "Ab initio structure prediction" }, { "uri": "http://edamontology.org/operation_3860", "term": "Spectrum calculation" }, { "uri": "http://edamontology.org/operation_3454", "term": "Phasing" }, { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" }, { "uri": "http://edamontology.org/operation_4009", "term": "Small molecule design" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_3474", "term": "Machine learning" }, { "uri": "http://edamontology.org/topic_0153", "term": "Lipids" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Python", "Java" ], "license": "AGPL-3.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [], "publication": [ { "doi": "10.1038/S41592-022-01486-3", "pmid": "35637304", "pmcid": "PMC9262714", "type": [], "version": null, "note": null, "metadata": { "title": "MSNovelist: de novo structure generation from mass spectra", "abstract": "© 2022, The Author(s).Current methods for structure elucidation of small molecules rely on finding similarity with spectra of known compounds, but do not predict structures de novo for unknown compound classes. We present MSNovelist, which combines fingerprint prediction with an encoder–decoder neural network to generate structures de novo solely from tandem mass spectrometry (MS2) spectra. In an evaluation with 3,863 MS2 spectra from the Global Natural Product Social Molecular Networking site, MSNovelist predicted 25% of structures correctly on first rank, retrieved 45% of structures overall and reproduced 61% of correct database annotations, without having ever seen the structure in the training phase. Similarly, for the CASMI 2016 challenge, MSNovelist correctly predicted 26% and retrieved 57% of structures, recovering 64% of correct database annotations. Finally, we illustrate the application of MSNovelist in a bryophyte MS2 dataset, in which de novo structure prediction substantially outscored the best database candidate for seven spectra. MSNovelist is ideally suited to complement library-based annotation in the case of poorly represented analyte classes and novel compounds.", "date": "2022-07-01T00:00:00Z", "citationCount": 1, "authors": [ { "name": "Stravs M.A." }, { "name": "Duhrkop K." }, { "name": "Bocker S." }, { "name": "Zamboni N." } ], "journal": "Nature Methods" } } ], "credit": [ { "name": "Nicola Zamboni", "email": "zamboni@imsb.biol.ethz.ch", "url": null, "orcidid": "https://orcid.org/0000-0003-1271-1021", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Sebastian Böcker", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-9304-8091", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Kai Dührkop", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-9056-0540", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Michael A. Stravs", "email": null, "url": null, "orcidid": "https://orcid.org/0000-0002-1426-8572", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Jennifer", "additionDate": "2022-09-05T21:19:03.847868Z", "lastUpdate": "2025-11-03T16:47:18.329938Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "PeakForest", "description": "A multi-platform digital infrastructure for interoperable metabolite spectral data and metadata management.", "homepage": "https://peakforest.org", "biotoolsID": "peakforest", "biotoolsCURIE": "biotools:peakforest", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3803", "term": "Natural product identification" }, { "uri": "http://edamontology.org/operation_3801", "term": "Spectral library search" }, { "uri": "http://edamontology.org/operation_3431", "term": "Deposition" }, { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application", "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" }, { "uri": "http://edamontology.org/topic_0593", "term": "NMR" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_0219", "term": "Data submission, annotation and curation" } ], "operatingSystem": [ "Mac", "Linux", "Windows" ], "language": [ "Java", "JavaScript" ], "license": "Other", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/peakforest", "type": [ "Repository" ], "note": null } ], "download": [], "documentation": [], "publication": [ { "doi": "10.1007/S11306-022-01899-3", "pmid": "35699774", "pmcid": "PMC9197906", "type": [], "version": null, "note": null, "metadata": { "title": "PeakForest: a multi-platform digital infrastructure for interoperable metabolite spectral data and metadata management", "abstract": "© 2022, The Author(s).Introduction: Accuracy of feature annotation and metabolite identification in biological samples is a key element in metabolomics research. However, the annotation process is often hampered by the lack of spectral reference data in experimental conditions, as well as logistical difficulties in the spectral data management and exchange of annotations between laboratories. Objectives: To design an open-source infrastructure allowing hosting both nuclear magnetic resonance (NMR) and mass spectra (MS), with an ergonomic Web interface and Web services to support metabolite annotation and laboratory data management. Methods: We developed the PeakForest infrastructure, an open-source Java tool with automatic programming interfaces that can be deployed locally to organize spectral data for metabolome annotation in laboratories. Standardized operating procedures and formats were included to ensure data quality and interoperability, in line with international recommendations and FAIR principles. Results: PeakForest is able to capture and store experimental spectral MS and NMR metadata as well as collect and display signal annotations. This modular system provides a structured database with inbuilt tools to curate information, browse and reuse spectral information in data treatment. PeakForest offers data formalization and centralization at the laboratory level, facilitating shared spectral data across laboratories and integration into public databases. Conclusion: PeakForest is a comprehensive resource which addresses a technical bottleneck, namely large-scale spectral data annotation and metabolite identification for metabolomics laboratories with multiple instruments. PeakForest databases can be used in conjunction with bespoke data analysis pipelines in the Galaxy environment, offering the opportunity to meet the evolving needs of metabolomics research. Developed and tested by the French metabolomics community, PeakForest is freely-available at https://github.com/peakforest.", "date": "2022-06-01T00:00:00Z", "citationCount": 0, "authors": [ { "name": "Paulhe N." }, { "name": "Canlet C." }, { "name": "Damont A." }, { "name": "Peyriga L." }, { "name": "Durand S." }, { "name": "Deborde C." }, { "name": "Alves S." }, { "name": "Bernillon S." }, { "name": "Berton T." }, { "name": "Bir R." }, { "name": "Bouville A." }, { "name": "Cahoreau E." }, { "name": "Centeno D." }, { "name": "Costantino R." }, { "name": "Debrauwer L." }, { "name": "Delabriere A." }, { "name": "Duperier C." }, { "name": "Emery S." }, { "name": "Flandin A." }, { "name": "Hohenester U." }, { "name": "Jacob D." }, { "name": "Joly C." }, { "name": "Jousse C." }, { "name": "Lagree M." }, { "name": "Lamari N." }, { "name": "Lefebvre M." }, { "name": "Lopez-Piffet C." }, { "name": "Lyan B." }, { "name": "Maucourt M." }, { "name": "Migne C." }, { "name": "Olivier M.-F." }, { "name": "Rathahao-Paris E." }, { "name": "Petriacq P." }, { "name": "Pinelli J." }, { "name": "Roch L." }, { "name": "Roger P." }, { "name": "Roques S." }, { "name": "Tabet J.-C." }, { "name": "Tremblay-Franco M." }, { "name": "Traikia M." }, { "name": "Warnet A." }, { "name": "Zhendre V." }, { "name": "Rolin D." }, { "name": "Jourdan F." }, { "name": "Thevenot E." }, { "name": "Moing A." }, { "name": "Jamin E." }, { "name": "Fenaille F." }, { "name": "Junot C." }, { "name": "Pujos-Guillot E." }, { "name": "Giacomoni F." } ], "journal": "Metabolomics" } } ], "credit": [ { "name": "Franck Giacomoni", "email": "Franck.Giacomoni@inrae.fr", "url": null, "orcidid": "https://orcid.org/0000-0001-6063-4214", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null }, { "name": "Estelle Pujos-Guillot", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "Christophe Junot", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null }, { "name": "François Fenaille", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [], "note": null } ], "owner": "Jennifer", "additionDate": "2022-09-04T23:10:37.868759Z", "lastUpdate": "2025-11-03T16:47:12.424836Z", "editPermission": { "type": "group", "authors": [ "recetox-specdatri" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "MetaboAnalyst", "description": "Statistical, functional and integrative analysis of metabolomics data , interpretation, and integration with other omics data.", "homepage": "http://www.metaboanalyst.ca", "biotoolsID": "metaboanalyst", "biotoolsCURIE": "biotools:metaboanalyst", "version": [ "4.0", "5.0" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3501", "term": "Enrichment analysis" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2409", "term": "Data handling" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2238", "term": "Statistical calculation" } ], "input": [], "output": [], "note": null, "cmd": null }, { "operation": [ { "uri": "http://edamontology.org/operation_2497", "term": "Pathway or network analysis" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3172", "term": "Metabolomics" }, { "uri": "http://edamontology.org/topic_3174", "term": "Metagenomics" }, { "uri": "http://edamontology.org/topic_0154", "term": "Small molecules" } ], "operatingSystem": [], "language": [ "R", "Java" ], "license": "GPL-3.0", "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [ { "url": "http://www.metaboanalyst.ca/faces/docs/Resources.xhtml", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "http://www.metaboanalyst.ca/faces/docs/Faqs.xhtml", "type": [ "General" ], "note": null }, { "url": "http://www.metaboanalyst.ca/faces/docs/Tutorial.xhtml", "type": [ "Training material" ], "note": null }, { "url": "http://www.metaboanalyst.ca/faces/docs/Contact.xhtml", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gky310", "pmid": "29762782", "pmcid": "PMC6030889", "type": [], "version": null, "note": null, "metadata": { "title": "MetaboAnalyst 4.0: Towards more transparent and integrative metabolomics analysis", "abstract": "We present a new update to MetaboAnalyst (version 4.0) for comprehensive metabolomic data analysis, interpretation, and integration with other omics data. Since the last major update in 2015, MetaboAnalyst has continued to evolve based on user feedback and technological advancements in the field. For this year's update, four newkey features have been added to MetaboAnalyst 4.0, including: (1) real-time R command tracking and display coupled with the release of a companion MetaboAnalystR package; (2) a MS Peaks to Pathways module for prediction of pathway activity from untargeted mass spectral data using themummichog algorithm; (3) a Biomarker Metaanalysis module for robust biomarker identification through the combination of multiple metabolomic datasets and (4) a Network Explorer module for integrative analysis of metabolomics, metagenomics, and/or transcriptomics data. The user interface of MetaboAnalyst 4.0 has been reengineered to provide a more modern look and feel, as well as to give more space and flexibility to introduce new functions. The underlying knowledgebases (compound libraries, metabolite sets, and metabolic pathways) have also been updated based on the latest data from the Human Metabolome Database (HMDB). A Docker image of MetaboAnalyst is also available to facilitate download and local installation of Metabo-Analyst.", "date": "2018-07-02T00:00:00Z", "citationCount": 2833, "authors": [ { "name": "Chong J." }, { "name": "Soufan O." }, { "name": "Li C." }, { "name": "Caraus I." }, { "name": "Li S." }, { "name": "Bourque G." }, { "name": "Wishart D.S." }, { "name": "Xia J." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.1038/s41596-022-00710-w", "pmid": "35715522", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Using MetaboAnalyst 5.0 for LC–HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data", "abstract": "Liquid chromatography coupled with high-resolution mass spectrometry (LC–HRMS) has become a workhorse in global metabolomics studies with growing applications across biomedical and environmental sciences. However, outstanding bioinformatics challenges in terms of data processing, statistical analysis and functional interpretation remain critical barriers to the wider adoption of this technology. To help the user community overcome these barriers, we have made major updates to the well-established MetaboAnalyst platform (www.metaboanalyst.ca) This protocol extends the previous 2011 Nature Protocol by providing stepwise instructions on how to use MetaboAnalyst 5.0 to: optimize parameters for LC–HRMS spectra processing; obtain functional insights from peak list data; integrate metabolomics data with transcriptomics data or combine multiple metabolomics datasets; conduct exploratory statistical analysis with complex metadata. 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In particular, XNAT enables qualitycontrol procedures and provides secure access to and storage of data. XNAT follows a threetiered architecture that includes a data archive, user interface, and middleware engine. Data can be entered into the archive as XML or through data entry forms. Newly added data are stored in a virtual quarantine until an authorized user has validated it. XNAT subsequently maintains a history profile to track all changes made to the managed data. User access to the archive is provided by a secure web application. The web application provides a number of quality control and productivity features, including data entry forms, data-type-specific searches, searches that combine across data types, detailed reports, and listings of experimental data, upload/download tools, access to standard laboratory workflows, and administration and security tools. XNAT also includes an online image viewer that supports a number of common neuroimaging formats, including DICOM and Analyze. The viewer can be extended to support additional formats and to generate custom displays. By managing data with XNAT, laboratories are prepared to better maintain the long-term integrity of their data, to explore emergent relations across data types, and to share their data with the broader neuroimaging community. © Copyright 2007 by Humana Press Inc. All rights of any nature whatsoever are reserved.", "date": "2007-03-01T00:00:00Z", "citationCount": 378, "authors": [ { "name": "Marcus D.S." }, { "name": "Olsen T.R." }, { "name": "Ramaratnam M." }, { "name": "Buckner R.L." } ], "journal": "Neuroinformatics" } }, { "doi": "10.1162/jocn.2009.21407", "pmid": "19929323", "pmcid": "PMC2895005", "type": [ "Usage" ], "version": null, "note": null, "metadata": { "title": "Open access series of imaging studies: Longitudinal MRI data in nondemented and demented older adults", "abstract": "The Open Access Series of Imaging Studies is a series of neuroimaging data sets that are publicly available for study and analysis. The present MRI data set consists of a longitudinal collection of 150 subjects aged 60 to 96 years all acquired on the same scanner using identical sequences. Each subject was scanned on two or more visits, separated by at least 1 year for a total of 373 imaging sessions. Subjects were characterized using the Clinical Dementia Rating (CDR) as either nondemented or with very mild tomild Alzheimer's disease. Seventy-two of the subjects were characterized as nondemented throughout the study. Sixty-four of the included subjects were characterized as demented at the time of their initial visits and remained so for subsequent scans, including 51 individuals with CDR 0.5 similar level of impairment to individuals elsewhere considered to have \"mild cognitive impairment.\" Another 14 subjects were characterized as nondemented at the time of their initial visit (CDR 0) and were subsequently characterized as demented at a later visit (CDR > 0). The subjects were all right-handed and include bothmen (n=62) and women (n = 88). For each scanning session, three or four individual T1-weighted MRI scans were obtained. Multiple withinsession acquisitions provide extremely high contrast to noise, making the data amenable to a wide range of analytic approaches including automated computational analysis. Automated calculation of whole-brain volume is presented to demonstrate use of the data for measuring differences associated with normal aging and Alzheimer's disease. © 2010 Massachusetts Institute of Technology.", "date": "2010-12-01T00:00:00Z", "citationCount": 461, "authors": [ { "name": "Marcus D.S." }, { "name": "Fotenos A.F." }, { "name": "Csernansky J.G." }, { "name": "Morris J.C." }, { "name": "Buckner R.L." } ], "journal": "Journal of Cognitive Neuroscience" } } ], "credit": [ { "name": "Daniel Marcus", "email": "dmarcus@wustl.edu", "url": "https://profiles.wustl.edu/en/persons/daniel-marcus", "orcidid": "https://orcid.org/0000-0001-5662-5358", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "hachterberg", "additionDate": "2025-07-24T08:48:17.637773Z", "lastUpdate": "2025-09-30T08:14:29.721796Z", "editPermission": { "type": "group", "authors": [ "vedrankasalica", "VKasalica" ] }, 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Its current implementations supported by URGI are: WheatIS, Plant, RARe.", "homepage": "https://urgi.versailles.inrae.fr/data-discovery/", "biotoolsID": "DataDiscovery", "biotoolsCURIE": "biotools:DataDiscovery", "version": [], "otherID": [], "relation": [ { "biotoolsID": "wheatis", "type": "usedBy" }, { "biotoolsID": "RARe", "type": "usedBy" }, { "biotoolsID": "Plant_DataDiscovery", "type": "usedBy" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2421", "term": "Database search" }, { "uri": "http://edamontology.org/operation_3625", "term": "Relation extraction" }, { "uri": "http://edamontology.org/operation_0227", "term": "Indexing" }, { "uri": "http://edamontology.org/operation_3908", "term": "Information retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0968", "term": "Keyword" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2353", "term": "Ontology data" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2080", "term": "Database search results" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2093", "term": "Data reference" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_0842", "term": "Identifier" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web API", "Web application", "Web service", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0780", "term": "Plant biology" }, { "uri": "http://edamontology.org/topic_0610", "term": "Ecology" }, { "uri": "http://edamontology.org/topic_3071", "term": "Biological databases" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_3810", "term": "Agricultural science" } ], "operatingSystem": [ "Linux" ], "language": [ "JavaScript", "Java", "Bash" ], "license": "BSD-3-Clause", "collectionID": [ "elixir-fr-sdp-2019", "URGI" ], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Data", "Tools", "Interoperability" ], "elixirNode": [ "France" ], "elixirCommunity": [], "link": [ { "url": "https://forgemia.inra.fr/urgi-is/data-discovery", "type": [ "Repository" ], "note": "GitLab code repository for DataDiscovery" }, { "url": "https://github.com/gnpis/DataDiscovery/", "type": [ "Mirror" ], "note": "Code repository mirror link for DataDiscovery" } ], "download": [], "documentation": [ { "url": "https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/LEGAL-MENTIONS.md", "type": [ "Terms of use" ], "note": "General terms of use" }, { "url": "https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/README.md#contribute", "type": [ "Contributions policy" ], "note": "How to contribute" }, { "url": "https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/HELP.md", "type": [ "User manual" ], "note": "How to use" }, { "url": "https://forgemia.inra.fr/urgi-is/data-discovery/blob/master/README.md#setup", "type": [ "Installation instructions" ], "note": "How to install" } ], "publication": [ { "doi": "10.3835/plantgenome2015.06.0038", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": "1-\tSpannagl, M., Alaux, M., Lange, M., Bolser, D. M., Bader, K. C., Letellier, T., Kimmel, E., Flores, R.-G., Pommier, C., Kerhornou, A., Walts, B., Nussbaumer, T., Grabmuller, C., Chen, J., Colmsee, C., Beier, S., Mascher, M., Schmutzer, T., Arend, D., Thanki, A., Ramirez-Gonzalez, R., Ayling, M., Ayling, S., Caccamo, M., Mayer, K. F. X., Scholz, U., Steinbach, D., Quesneville, H., Kersey, P. (2016). TransPLANT resources for triticeae genomic data. Plant Genome, 9 (1), 13 p.", "metadata": { "title": "TransPLANT resources for triticeae genomic data", "abstract": "The genome sequences of many important Triticeae species, including bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), remained uncharacterized for a long time because their high repeat content, large sizes, and polyploidy. As a result of improvements in sequencing technologies and novel analyses strategies, several of these have recently been deciphered. These efforts have generated new insights into Triticeae biology and genome organization and have important implications for downstream usage by breeders, experimental biologists, and comparative genomicists. transPLANT (http://www.transplantdb.eu) is an EU-funded project aimed at constructing hardware, software, and data infrastructure for genome-scale research in the life sciences. Since the Triticeae data are intrinsically complex, heterogenous, and distributed, the transPLANT consortium has undertaken efforts to develop common data formats and tools that enable the exchange and integration of data from distributed resources. Here we present an overview of the individual Triticeae genome resources hosted by transPLANT partners, introduce the objectives of transPLANT, and outline common developments and interfaces supporting integrated data access.", "date": "2016-03-01T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Spannagl M." }, { "name": "Alaux M." }, { "name": "Lange M." }, { "name": "Bolser D.M." }, { "name": "Bader K.C." }, { "name": "Letellier T." }, { "name": "Kimmel E." }, { "name": "Flores R." }, { "name": "Pommier C." }, { "name": "Kerhornou A." }, { "name": "Walts B." }, { "name": "Nussbaumer T." }, { "name": "Grabmuller C." }, { "name": "Chen J." }, { "name": "Colmsee C." }, { "name": "Beier S." }, { "name": "Mascher M." }, { "name": "Schmutzer T." }, { "name": "Arend D." }, { "name": "Thanki A." }, { "name": "Ramirez-Gonzalez R." }, { "name": "Ayling M." }, { "name": "Ayling S." }, { "name": "Caccamo M." }, { "name": "Mayer K.F.X." }, { "name": "Scholz U." }, { "name": "Steinbach D." }, { "name": "Quesneville H." }, { "name": "Kersey P.J." } ], "journal": "Plant Genome" } }, { "doi": "10.1038/hortres.2016.56", "pmid": null, "pmcid": null, "type": [], "version": null, "note": "2-\tAdam-Blondon, A.-F., Alaux, M., Pommier, C., Cantu, D., Cheng, Z.-M., Cramer, G. R., Davies, C., Delrot, S., Deluc, L., di Gaspero, G., Grimplet, J., Fennell, A., Londo, J. P., Kersey, P., Mattivi, F., Naithani, S., Neveu, P., Nikolski, M., Pezzotti, M., Reisch, B. I., Topfer, R., Vivier, M., Ware, D., Quesneville, H. (2016). Towards an open grapevine information system. Horticulture Research, 3, 8 p. , DOI : 10.1038/hortres.2016.56", "metadata": { "title": "Towards an open grapevine information system", "abstract": "Viticulture, like other fields of agriculture, is currently facing important challenges that will be addressed only through sustained, dedicated and coordinated research. Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature, in many domains of study, including grapevine research, there is a need to improve the findability, accessibility, interoperability and reusability (FAIR-ness) of these data. Considering the heterogeneous nature of the data produced, the transnational nature of the scientific community and the experience gained elsewhere, we have formed an open working group, in the framework of the International Grapevine Genome Program (www.vitaceae.org) to construct a coordinated federation of information systems holding grapevine data distributed around the world, providing an integrated set of interfaces supporting advanced data modeling, rich semantic integration and the next generation of data mining tools. To achieve this goal, it will be critical to develop, implement and adopt appropriate standards for data annotation and formatting. The development of this system, the GrapeIS, linking genotypes to phenotypes, and scientific research to agronomical and oeneological data, should provide new insights into grape biology, and allow the development of new varieties to meet the challenges of biotic and abiotic stress, environmental change, and consumer demand.", "date": "2016-11-23T00:00:00Z", "citationCount": 37, "authors": [ { "name": "Adam-Blondon A.-F." }, { "name": "Alaux M." }, { "name": "Pommier C." }, { "name": "Cantu D." }, { "name": "Cheng Z.-M." }, { "name": "Cramer G." }, { "name": "Davies C." }, { "name": "Delrot S." }, { "name": "Deluc L." }, { "name": "Di Gaspero G." }, { "name": "Grimplet J." }, { "name": "Fennell A." }, { "name": "Londo J." }, { "name": "Kersey P." }, { "name": "Mattivi F." }, { "name": "Naithani S." }, { "name": "Neveu P." }, { "name": "Nikolski M." }, { "name": "Pezzotti M." }, { "name": "Reisch B." }, { "name": "Topfer R." }, { "name": "Vivier M." }, { "name": "Ware D." }, { "name": "Quesneville H." } ], "journal": "Horticulture Research" } }, { "doi": "10.1186/s13059-018-1491-4", "pmid": null, "pmcid": null, "type": [], "version": null, "note": "3-\tAlaux M, Rogers J, Letellier T, Flores R, Alfama F, Pommier C, Mohellibi N, Durand S, Kimmel E, Michotey C, Guerche C, Loaec M, Lainé M, Steinbach D, Choulet F, Rimbert H, Leroy P, Guilhot N, Salse J, Feuillet C, International Wheat Genome Sequencing Consortium, Paux E, Eversole K, Adam-Blondon A-F, Quesneville H (2018) Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data. Genome Biology, 19:111.", "metadata": { "title": "Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data", "abstract": "The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in-depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. The portal provides enhanced search and browser features that will facilitate the deployment of the latest genomics resources in wheat improvement.", "date": "2018-08-17T00:00:00Z", "citationCount": 181, "authors": [ { "name": "Alaux M." }, { "name": "Rogers J." }, { "name": "Letellier T." }, { "name": "Flores R." }, { "name": "Alfama F." }, { "name": "Pommier C." }, { "name": "Mohellibi N." }, { "name": "Durand S." }, { "name": "Kimmel E." }, { "name": "Michotey C." }, { "name": "Guerche C." }, { "name": "Loaec M." }, { "name": "Laine M." }, { "name": "Steinbach D." }, { "name": "Choulet F." }, { "name": "Rimbert H." }, { "name": "Leroy P." }, { "name": "Guilhot N." }, { "name": "Salse J." }, { "name": "Feuillet C." }, { "name": "Paux E." }, { "name": "Eversole K." }, { "name": "Adam-Blondon A.-F." }, { "name": "Quesneville H." } ], "journal": "Genome Biology" } } ], "credit": [ { "name": "urgi-support", "email": "urgi-support@inrae.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": null, "typeRole": [ "Primary contact", "Support" ], "note": null } ], "owner": "nfrancillon", "additionDate": "2020-01-21T16:40:38Z", "lastUpdate": "2025-07-29T13:42:39.375595Z", "editPermission": { "type": "group", "authors": [ "urgi-contact", "cpommier", "cmichotey", "erlefloch", "raphael.flores" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "OakMine", "description": "Quercus robur annotation database", "homepage": "https://urgi.versailles.inra.fr/OakMine_PM1N", "biotoolsID": "OakMine", "biotoolsCURIE": "biotools:OakMine", "version": [ "2.3" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_2436", "term": "Gene-set enrichment analysis" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1255", "term": "Sequence features" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2353", "term": "Ontology data" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3753", "term": "Over-representation data" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3786", "term": "Query script" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1255", "term": "Sequence features" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Web service", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3071", "term": "Data management" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "R", "Ruby", "Java", "Python", "JavaScript", "Perl" ], "license": "LGPL-2.1", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://registry.intermine.org", "type": [ "Software catalogue" ], "note": null }, { "url": "http://intermine.org", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [ { "url": "http://intermine.readthedocs.org/en/latest/web-services/", "type": [ "API documentation" ], "note": null }, { "url": "https://flymine.readthedocs.io/en/latest/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bts577", "pmid": "23023984", "pmcid": "PMC3516146", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "InterMine: A flexible data warehouse system for the integration and analysis of heterogeneous biological data", "abstract": "InterMine is an open-source data warehouse system that facilitates the building of databases with complex data integration requirements and a need for a fast customizable query facility. Using InterMine, large biological databases can be created from a range of heterogeneous data sources, and the extensible data model allows for easy integration of new data types. The analysis tools include a flexible query builder, genomic region search and a library of 'widgets' performing various statistical analyses. The results can be exported in many commonly used formats. InterMine is a fully extensible framework where developers can add new tools and functionality. Additionally, there is a comprehensive set of web services, for which client libraries are provided in five commonly used programming languages. © The Author 2012. Published by Oxford University Press. All rights reserved.", "date": "2012-12-01T00:00:00Z", "citationCount": 202, "authors": [ { "name": "Smith R.N." }, { "name": "Aleksic J." }, { "name": "Butano D." }, { "name": "Carr A." }, { "name": "Contrino S." }, { "name": "Hu F." }, { "name": "Lyne M." }, { "name": "Lyne R." }, { "name": "Kalderimis A." }, { "name": "Rutherford K." }, { "name": "Stepan R." }, { "name": "Sullivan J." }, { "name": "Wakeling M." }, { "name": "Watkins X." }, { "name": "Micklem G." } ], "journal": "Bioinformatics" } } ], "credit": [], "owner": "InterMine", "additionDate": "2019-11-27T10:47:08Z", "lastUpdate": "2025-07-29T13:42:35.424110Z", "editPermission": { "type": "group", "authors": [ "cmichotey" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "WheatMine", "description": "Wheat IWGSC RefSeq v1.0", "homepage": "https://urgi.versailles.inra.fr/WheatMine", "biotoolsID": "WheatMine", "biotoolsCURIE": "biotools:WheatMine", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_0337", "term": "Visualisation" }, { "uri": "http://edamontology.org/operation_2436", "term": "Gene-set enrichment analysis" }, { "uri": "http://edamontology.org/operation_0224", "term": "Query and retrieval" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_1255", "term": "Sequence features" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_2353", "term": "Ontology data" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_3753", "term": "Over-representation data" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3786", "term": "Query script" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_1255", "term": "Sequence features" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Web service", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_3071", "term": "Data management" }, { "uri": "http://edamontology.org/topic_0622", "term": "Genomics" }, { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" } ], "operatingSystem": [ "Linux", "Mac" ], "language": [ "R", "Ruby", "Java", "Python", "JavaScript", "Perl" ], "license": "LGPL-2.1", "collectionID": [], "maturity": "Mature", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://registry.intermine.org", "type": [ "Software catalogue" ], "note": null }, { "url": "http://intermine.org", "type": [ "Other" ], "note": null } ], "download": [], "documentation": [ { "url": "http://intermine.readthedocs.org/en/latest/web-services/", "type": [ "API documentation" ], "note": null }, { "url": "https://flymine.readthedocs.io/en/latest/", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bts577", "pmid": "23023984", "pmcid": "PMC3516146", "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "InterMine: A flexible data warehouse system for the integration and analysis of heterogeneous biological data", "abstract": "InterMine is an open-source data warehouse system that facilitates the building of databases with complex data integration requirements and a need for a fast customizable query facility. Using InterMine, large biological databases can be created from a range of heterogeneous data sources, and the extensible data model allows for easy integration of new data types. The analysis tools include a flexible query builder, genomic region search and a library of 'widgets' performing various statistical analyses. The results can be exported in many commonly used formats. InterMine is a fully extensible framework where developers can add new tools and functionality. Additionally, there is a comprehensive set of web services, for which client libraries are provided in five commonly used programming languages. © The Author 2012. Published by Oxford University Press. All rights reserved.", "date": "2012-12-01T00:00:00Z", "citationCount": 202, "authors": [ { "name": "Smith R.N." }, { "name": "Aleksic J." }, { "name": "Butano D." }, { "name": "Carr A." }, { "name": "Contrino S." }, { "name": "Hu F." }, { "name": "Lyne M." }, { "name": "Lyne R." }, { "name": "Kalderimis A." }, { "name": "Rutherford K." }, { "name": "Stepan R." }, { "name": "Sullivan J." }, { "name": "Wakeling M." }, { "name": "Watkins X." }, { "name": "Micklem G." } ], "journal": "Bioinformatics" } } ], "credit": [], "owner": "InterMine", "additionDate": "2019-11-27T10:47:40Z", "lastUpdate": "2025-07-29T13:42:33.209390Z", "editPermission": { "type": "group", "authors": [ "cmichotey" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Online SBML Validator", "description": "Check the syntax and internal consistency of files in SBML (The Systems Biology Markup Language) format.", "homepage": "https://sbml.bioquant.uni-heidelberg.de/validator_servlet/", "biotoolsID": "online_sbml_validator", "biotoolsCURIE": "biotools:online_sbml_validator", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" }, { "uri": "http://edamontology.org/operation_0336", "term": "Format validation" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0950", "term": "Mathematical model" }, "format": [ { "uri": "http://edamontology.org/format_3686", "term": "COMBINE OMEX" }, { "uri": "http://edamontology.org/format_2585", "term": "SBML" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web API", "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_2259", "term": "Systems biology" }, { "uri": "http://edamontology.org/topic_3071", "term": "Data management" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java", "Python" ], "license": "LGPL-2.0", "collectionID": [], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://sbml.org/facilities/", "type": [ "Service" ], "note": null } ], "download": [], "documentation": [ { "url": "https://web.archive.org/web/20210507040418/http://sbml.org/Facilities/Documentation/Validator_Web_API", "type": [ "API documentation" ], "note": null } ], "publication": [], "credit": [ { "name": "Frank Bergmann", "email": null, "url": "https://www.biocatalogue.org", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Documentor" ], "note": null }, { "name": "Frank Bergmann", "email": "frank.bergmann@bioquant.uni-heidelberg.de", "url": null, "orcidid": "https://orcid.org/0000-0001-5553-4702", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "frankbergmann", "additionDate": "2015-08-03T09:36:21Z", "lastUpdate": "2025-07-07T11:10:03.422874Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Virtual Imaging Platform", "description": "VIP is a web portal for medical imaging applications. It allows users to access scientific applications as a service (directly through the web browser with no installation required), as well as distributed computing resources in a transparent manner. It exploits the resources available in the biomed virtual organization of the EGI e-infrastructure to offer an open service to researchers worldwide.", "homepage": "https://vip.creatis.insa-lyon.fr", "biotoolsID": "virtual_imaging_platform", "biotoolsCURIE": "biotools:virtual_imaging_platform", "version": [ "3.0.1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3443", "term": "Image analysis" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2968", "term": "Image" }, "format": [ { "uri": "http://edamontology.org/format_2333", "term": "Binary format" } ] } ], "output": [], "note": null, "cmd": null } ], "toolType": [ "Bioinformatics portal" ], "topic": [], "operatingSystem": [], "language": [ "Java" ], "license": "CECILL-B", "collectionID": [ "EUCAIM" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://vip.creatis.insa-lyon.fr/", "type": [ "Service" ], "note": null } ], "download": [ { "url": "https://github.com/virtual-imaging-platform/", "type": "Source code", "note": null, "version": "3.0.1" } ], "documentation": [ { "url": "https://github.com/virtual-imaging-platform/VIP-portal/wiki", "type": [ "Other" ], "note": null } ], "publication": [ { "doi": "10.1109/tmi.2012.2220154", "pmid": "23014715", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "A virtual imaging platform for multi-modality medical image simulation", "abstract": "This paper presents the Virtual Imaging Platform (VIP), a platform accessible at http://vip.creatis.insa-lyon.fr to facilitate the sharing of object models and medical image simulators, and to provide access to distributed computing and storage resources. A complete overview is presented, describing the ontologies designed to share models in a common repository, the workflow template used to integrate simulators, and the tools and strategies used to exploit computing and storage resources. Simulation results obtained in four image modalities and with different models show that VIP is versatile and robust enough to support large simulations. The platform currently has 200 registered users who consumed 33 years of CPU time in 2011. © 1982-2012 IEEE.", "date": "2013-01-10T00:00:00Z", "citationCount": 88, "authors": [ { "name": "Glatard T." }, { "name": "Lartizien C." }, { "name": "Gibaud B." }, { "name": "Da Silva R.F." }, { "name": "Forestier G." }, { "name": "Cervenansky F." }, { "name": "Alessandrini M." }, { "name": "Benoit-Cattin H." }, { "name": "Bernard O." }, { "name": "Camarasu-Pop S." }, { "name": "Cerezo N." }, { "name": "Clarysse P." }, { "name": "Gaignard A." }, { "name": "Hugonnard P." }, { "name": "Liebgott H." }, { "name": "Marache S." }, { "name": "Marion A." }, { "name": "Montagnat J." }, { "name": "Tabary J." }, { "name": "Friboulet D." } ], "journal": "IEEE Transactions on Medical Imaging" } } ], "credit": [], "owner": "sorina.pop", "additionDate": "2023-06-14T13:47:49.064543Z", "lastUpdate": "2025-06-06T11:51:24.125664Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "RSpace", "description": "RSpace is an open-source platform that orchestrates research workflows into FAIR data management ecosystems.\nRSpace is a continuously evolving community-inspired open-source research data management platform for research organizations and cloud/commons providers compliant with regulatory standards by design. Researchers and Research Data Managers create FAIR data workflows through a modern and user-centric research data management frontend with electronic laboratory notebook, intuitive research sample management, and file management solutions integrated seamlessly with research data management tools and infrastructure researchers and their organizations already use.", "homepage": "https://www.researchspace.com", "biotoolsID": "rspace", "biotoolsCURIE": "biotools:rspace", "version": [ "2.1" ], "otherID": [], "relation": [], "function": [], "toolType": [ "Web application", "Web API", "Command-line tool", "Web service" ], "topic": [ { "uri": "http://edamontology.org/topic_4019", "term": "Biosciences" }, { "uri": "http://edamontology.org/topic_3314", "term": "Chemistry" }, { "uri": "http://edamontology.org/topic_4012", "term": "FAIR data" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0607", "term": "Laboratory information management" }, { "uri": "http://edamontology.org/topic_3318", "term": "Physics" }, { "uri": "http://edamontology.org/topic_4012", "term": "FAIR data" }, { "uri": "http://edamontology.org/topic_3678", "term": "Experimental design and studies" } ], "operatingSystem": [], "language": [ "Java", "JavaScript" ], "license": "AGPL-3.0", "collectionID": [], "maturity": "Mature", "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://www.researchspace.com", "type": [ "Service" ], "note": "ResearchSpace provides services and support around RSpace" }, { "url": "https://github.com/rspace-os", "type": [ "Repository" ], "note": "GitHub organisation page with all relevant repositories for RSpace" }, { "url": "https://bsky.app/profile/researchspace.com", "type": [ "Social media" ], "note": null } ], "download": [], "documentation": [ { "url": "https://documentation.researchspace.com/", "type": [ "General" ], "note": null } ], "publication": [], "credit": [], "owner": "tilomat", "additionDate": "2025-05-23T06:39:06.695509Z", "lastUpdate": "2025-05-23T06:39:06.698074Z", "editPermission": { "type": "private", "authors": [] }, "validated": 0, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "SpliceMachine", "description": "Splice site prediction.", "homepage": "http://bioinformatics.psb.ugent.be/software/details/SpliceMachine", "biotoolsID": "splicemachine", "biotoolsCURIE": "biotools:splicemachine", "version": [ "1" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0433", "term": "Splice site prediction" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_2977", "term": "Nucleic acid sequence" }, "format": [ { "uri": "http://edamontology.org/format_1929", "term": "FASTA" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_2070", "term": "Sequence motif (nucleic acid)" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_3511", "term": "Nucleic acid sites, features and motifs" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": null, "collectionID": [ "BIG N2N", "VIB", "Plant Systems Biology", "UGent" ], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://bioinformatics.psb.ugent.be/webtools/splicemachine/help/", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/bioinformatics/bti166", "pmid": "15564294", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "ugent.be", "email": null, "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": null, "email": "yves.vandepeer@psb.vib-ugent.be", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "owner": "Katrijn.Vannerum@ugent.be", "additionDate": "2016-05-17T10:18:56Z", "lastUpdate": "2025-05-13T13:36:17.236762Z", "editPermission": { "type": "group", "authors": [ "Bharathi" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "PIA - Protein Inference Algorithms", "description": "The main focus lays on the integrated inference algorithms, concluding the proteins from a set of identified spectra. But it also allows you to integrate results of various search engines, inspect your peptide spectrum matches, calculate FDR values across different results and visualize the correspondence between PSMs, peptides and proteins.", "homepage": "https://github.com/medbioinf/pia", "biotoolsID": "pia", "biotoolsCURIE": "biotools:pia", "version": [ "1.5" ], "otherID": [], "relation": [ { "biotoolsID": "knime", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3767", "term": "Protein identification" }, { "uri": "http://edamontology.org/operation_3649", "term": "Target-Decoy" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_0943", "term": "Mass spectrometry spectra" }, "format": [ { "uri": "http://edamontology.org/format_3713", "term": "Mascot .dat file" }, { "uri": "http://edamontology.org/format_3247", "term": "mzIdentML" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" }, { "uri": "http://edamontology.org/format_3684", "term": "PRIDE XML" }, { "uri": "http://edamontology.org/format_3711", "term": "X!Tandem XML" }, { "uri": "http://edamontology.org/format_3702", "term": "MSF" }, { "uri": "http://edamontology.org/format_3681", "term": "mzTab" } ] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_0945", "term": "Peptide identification" }, "format": [ { "uri": "http://edamontology.org/format_2206", "term": "Sequence feature table format (text)" }, { "uri": "http://edamontology.org/format_3765", "term": "KNIME datatable format" }, { "uri": "http://edamontology.org/format_3764", "term": "idXML" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" }, { "uri": "http://edamontology.org/format_3681", "term": "mzTab" }, { "uri": "http://edamontology.org/format_3247", "term": "mzIdentML" } ] }, { "data": { "uri": "http://edamontology.org/data_0989", "term": "Protein identifier" }, "format": [ { "uri": "http://edamontology.org/format_2206", "term": "Sequence feature table format (text)" }, { "uri": "http://edamontology.org/format_3765", "term": "KNIME datatable format" }, { "uri": "http://edamontology.org/format_3764", "term": "idXML" }, { "uri": "http://edamontology.org/format_3475", "term": "TSV" }, { "uri": "http://edamontology.org/format_3681", "term": "mzTab" }, { "uri": "http://edamontology.org/format_3247", "term": "mzIdentML" } ] } ], "note": "PIA allows you to inspect the results of common proteomics spectrum identification search engines, combine them seamlessly and conduct statistical analyses. The main focus of PIA lays on the integrated inference algorithms, i.e. concluding the proteins from a set of identified spectra. But it also allows you to inspect your peptide spectrum matches, calculate FDR values across different search engine results and visualize the correspondence between PSMs, peptides and proteins. Search engine results in several formats peptide spectrum matches (PSMs) and peptides Inferred Proteins", "cmd": null } ], "toolType": [ "Command-line tool", "Library", "Desktop application", "Workflow" ], "topic": [ { "uri": "http://edamontology.org/topic_0121", "term": "Proteomics" }, { "uri": "http://edamontology.org/topic_3520", "term": "Proteomics experiment" }, { "uri": "http://edamontology.org/topic_3120", "term": "Protein variants" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": "BSD-3-Clause", "collectionID": [ "KNIME", "de.NBI", "Proteomics", "BioInfra.Prot", "CUBiMed.RUB" ], "maturity": "Mature", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [ "Proteomics" ], "link": [ { "url": "https://github.com/medbioinf/pia", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/mpc-bioinformatics/pia", "type": "Source code", "note": null, "version": null }, { "url": "http://bioconda.github.io/recipes/pia/README.html", "type": "Software package", "note": null, "version": null }, { "url": "https://github.com/mpc-bioinformatics/pia/releases", "type": "Binaries", "note": null, "version": null }, { "url": "https://hub.docker.com/r/julianusz/pia", "type": "Container file", "note": null, "version": null } ], "documentation": [ { "url": "https://github.com/medbioinf/pia/wiki", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1021/acs.jproteome.5b00121", "pmid": "25938255", "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface", "abstract": "Protein inference connects the peptide spectrum matches (PSMs) obtained from database search engines back to proteins, which are typically at the heart of most proteomics studies. Different search engines yield different PSMs and thus different protein lists. Analysis of results from one or multiple search engines is often hampered by different data exchange formats and lack of convenient and intuitive user interfaces. We present PIA, a flexible software suite for combining PSMs from different search engine runs and turning these into consistent results. PIA can be integrated into proteomics data analysis workflows in several ways. A user-friendly graphical user interface can be run either locally or (e.g., for larger core facilities) from a central server. For automated data processing, stand-alone tools are available. PIA implements several established protein inference algorithms and can combine results from different search engines seamlessly. On several benchmark data sets, we show that PIA can identify a larger number of proteins at the same protein FDR when compared to that using inference based on a single search engine. PIA supports the majority of established search engines and data in the mzIdentML standard format. It is implemented in Java and freely available at https://github.com/mpc-bioinformatics/pia.", "date": "2015-07-02T00:00:00Z", "citationCount": 57, "authors": [ { "name": "Uszkoreit J." }, { "name": "Maerkens A." }, { "name": "Perez-Riverol Y." }, { "name": "Meyer H.E." }, { "name": "Marcus K." }, { "name": "Stephan C." }, { "name": "Kohlbacher O." }, { "name": "Eisenacher M." } ], "journal": "Journal of Proteome Research" } }, { "doi": "10.1021/acs.jproteome.8b00723", "pmid": "30474983", "pmcid": null, "type": [], "version": null, "note": null, "metadata": { "title": "Protein Inference Using PIA Workflows and PSI Standard File Formats", "abstract": "Proteomics using LC-MS/MS has become one of the main methods to analyze the proteins in biological samples in high-throughput. But the existing mass-spectrometry instruments are still limited with respect to resolution and measurable mass ranges, which is one of the main reasons why shotgun proteomics is the major approach. Here proteins are digested, which leads to the identification and quantification of peptides instead. While often neglected, the important step of protein inference needs to be conducted to infer from the identified peptides to the actual proteins in the original sample. In this work, we highlight some of the previously published and newly added features of the tool PIA - Protein Inference Algorithms, which helps the user with the protein inference of measured samples. We also highlight the importance of the usage of PSI standard file formats, as PIA is the only current software supporting all available standards used for spectrum identification and protein inference. Additionally, we briefly describe the benefits of working with workflow environments for proteomics analyses and show the new features of the PIA nodes for the KNIME Analytics Platform. Finally, we benchmark PIA against a recently published data set for isoform detection. PIA is open source and available for download on GitHub (https://github.com/mpc-bioinformatics/pia) or directly via the community extensions inside the KNIME analytics platform.", "date": "2019-02-01T00:00:00Z", "citationCount": 30, "authors": [ { "name": "Uszkoreit J." }, { "name": "Perez-Riverol Y." }, { "name": "Eggers B." }, { "name": "Marcus K." }, { "name": "Eisenacher M." } ], "journal": "Journal of Proteome Research" } } ], "credit": [ { "name": "Julian Uszkoreit", "email": "julian.uszkoreit@rub.de", "url": null, "orcidid": "http://orcid.org/0000-0001-7522-4007", "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact", "Developer", "Maintainer" ], "note": null }, { "name": "CUBiMed.RUB", "email": "cubimed@rub.de", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null } ], "owner": "julianu", "additionDate": "2016-07-12T10:54:05Z", "lastUpdate": "2025-05-02T13:15:26.717477Z", "editPermission": { "type": "private", "authors": [] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "Gemma", "description": "Gemma provides data, experimental design annotations, and differential expression analysis results for thousands of microarray and RNA-seq experiments. We re-analyze raw data from public sources (primarily NCBI GEO), annotate experimental conditions, conduct quality control and compute differential expression using standardized procedures. We have especially good coverage of experiments relevant to the nervous system.", "homepage": "https://gemma.msl.ubc.ca/", "biotoolsID": "gemma", "biotoolsCURIE": "biotools:gemma", "version": [ "1.31.13" ], "otherID": [], "relation": [ { "biotoolsID": "rsem", "type": "uses" }, { "biotoolsID": "multiqc", "type": "uses" }, { "biotoolsID": "cutadapt", "type": "uses" }, { "biotoolsID": "star", "type": "uses" }, { "biotoolsID": "ncbi_geo", "type": "uses" }, { "biotoolsID": "sradb", "type": "uses" }, { "biotoolsID": "ncbi_gene", "type": "uses" } ], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3223", "term": "Differential gene expression profiling" } ], "input": [ { "data": { "uri": "http://edamontology.org/data_3112", "term": "Gene expression matrix" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3110", "term": "Raw microarray data" }, "format": [] } ], "output": [ { "data": { "uri": "http://edamontology.org/data_1636", "term": "Heat map" }, "format": [] }, { "data": { "uri": "http://edamontology.org/data_3914", "term": "Quality control report" }, "format": [] } ], "note": null, "cmd": null } ], "toolType": [ "Web application", "Web API" ], "topic": [ { "uri": "http://edamontology.org/topic_3170", "term": "RNA-Seq" }, { "uri": "http://edamontology.org/topic_0203", "term": "Gene expression" }, { "uri": "http://edamontology.org/topic_3053", "term": "Genetics" }, { "uri": "http://edamontology.org/topic_3518", "term": "Microarray experiment" }, { "uri": "http://edamontology.org/topic_0219", "term": "Data curation and archival" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java", "JavaScript" ], "license": "CC-BY-NC-4.0", "collectionID": [], "maturity": "Mature", "cost": "Free of charge (with restrictions)", "accessibility": "Open access (with restrictions)", "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/PavlidisLab/Gemma", "type": [ "Repository", "Issue tracker" ], "note": null } ], "download": [ { "url": "https://github.com/PavlidisLab/Gemma/releases", "type": "Downloads page", "note": null, "version": null } ], "documentation": [ { "url": "https://pavlidislab.github.io/Gemma/", "type": [ "General" ], "note": null }, { "url": "https://gemma.msl.ubc.ca/resources/restapidocs/", "type": [ "API documentation" ], "note": "Documentation for the Gemma REST API." } ], "publication": [ { "doi": "10.1093/bioinformatics/btp259", "pmid": "19376825", "pmcid": "PMC2687992", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Application and evaluation of automated semantic annotation of gene expression experiments", "abstract": "Motivation: Many microarray datasets are available online with formalized standards describing the probe sequences and expression values. Unfortunately, the description, conditions and parameters of the experiments are less commonly formalized and often occur as natural language text. This hinders searching, high-throughput analysis, organization and integration of the datasets. Results: We use the lexical resources and software tools from the Unified Medical Language System (UMLS) to extract concepts from text. We then link the UMLS concepts to classes in open biomedical ontologies. The result is accessible and clear semantic annotations of gene expression experiments. We applied the method to 595 expression experiments from Gemma, a resource for re-use and meta-analysis of gene expression profiling data. We evaluated and corrected all stages of the annotation process. The majority of missed annotations were due to a lack of cross-references. The most error-prone stage was the extraction of concepts from phrases. Final review of the annotations in context of the experiments revealed 89% precision. A naive system, lacking the phrase to concept corrections is 68% precise. We have integrated this annotation pipeline into Gemma. © 2009 The Author(s).", "date": "2009-06-09T00:00:00Z", "citationCount": 9, "authors": [ { "name": "French L." }, { "name": "Lane S." }, { "name": "Law T." }, { "name": "Xu L." }, { "name": "Pavlidis P." } ], "journal": "Bioinformatics" } }, { "doi": "10.1093/database/baab006", "pmid": "33599246", "pmcid": "PMC7904053", "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Curation of over 10 000 transcriptomic studies to enable data reuse", "abstract": "Vast amounts of transcriptomic data reside in public repositories, but effective reuse remains challenging. Issues include unstructured dataset metadata, inconsistent data processing and quality control, and inconsistent probe-gene mappings across microarray technologies. Thus, extensive curation and data reprocessing are necessary prior to any reuse. The Gemma bioinformatics system was created to help address these issues. Gemma consists of a database of curated transcriptomic datasets, analytical software, a web interface and web services. Here we present an update on Gemma's holdings, data processing and analysis pipelines, our curation guidelines, and software features. As of June 2020, Gemma contains 10 811 manually curated datasets (primarily human, mouse and rat), over 395 000 samples and hundreds of curated transcriptomic platforms (both microarray and RNA sequencing). Dataset topics were represented with 10 215 distinct terms from 12 ontologies, for a total of 54 316 topic annotations (mean topics/dataset = 5.2). While Gemma has broad coverage of conditions and tissues, it captures a large majority of available brain-related datasets, accounting for 34% of its holdings. Users can access the curated data and differential expression analyses through the Gemma website, RESTful service and an R package. 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BTO contains different anatomical structures, tissues, cell types and cell lines, classified under generic categories corresponding to the rules and formats of the Gene Ontology Consortium and organized as a directed acyclic graph (DAG). A versatile web interface with several search and navigation functionalities allows convenient online access to the BTO and to the enzymes isolated from the tissues.", "homepage": "http://www.BTO.brenda-enzymes.org", "biotoolsID": "bto", "biotoolsCURIE": "biotools:bto", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_3352", "term": "Ontology comparison" }, { "uri": "http://edamontology.org/operation_0314", "term": "Gene expression profiling" }, { "uri": "http://edamontology.org/operation_3559", "term": "Ontology visualisation" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0089", "term": "Ontology and terminology" }, { "uri": "http://edamontology.org/topic_0821", "term": "Enzymes" }, { "uri": "http://edamontology.org/topic_0621", "term": "Model organisms" }, { "uri": "http://edamontology.org/topic_3337", "term": "Biobank" }, { "uri": "http://edamontology.org/topic_0140", "term": "Protein targeting and localisation" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": "CC-BY-4.0", "collectionID": [ "DSMZ Digital Diversity", "de.NBI-biodata" ], "maturity": null, "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [], "elixirNode": [ "Germany" ], "elixirCommunity": [], "link": [ { "url": "https://www.dsmz.de/", "type": [ "Other" ], "note": null }, { "url": "https://hub.dsmz.de/#/", "type": [ "Service" ], "note": null }, { "url": "https://www.brenda-enzymes.org/", "type": [ "Repository" ], "note": "BRENDA enzyme database" } ], "download": [], "documentation": [ { "url": "http://www.bto.brenda-enzymes.org/tutorial.php", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gkq968", "pmid": "21030441", "pmcid": "PMC3013802", "type": [], "version": null, "note": null, "metadata": { "title": "The BRENDA Tissue Ontology (BTO): The first all-integrating ontology of all organisms for enzyme sources", "abstract": "BTO, the BRENDA Tissue Ontology (http://www.BTO.brenda-enzymes.org) represents a comprehensive structured encyclopedia of tissue terms. The project started in 2003 to create a connection between the enzyme data collection of the BRENDA enzyme database and a structured network of source tissues and cell types. Currently, BTO contains more than 4600 different anatomical structures, tissues, cell types and cell lines, classified under generic categories corresponding to the rules and formats of the Gene Ontology Consortium and organized as a directed acyclic graph (DAG). Most of the terms are endowed with comments on their derivation or definitions. The content of the ontology is constantly curated with ̃1000 new terms each year. Four different types of relationships between the terms are implemented. A versatile web interface with several search and navigation functionalities allows convenient online access to the BTO and to the enzymes isolated from the tissues. Important areas of applications of the BTO terms are the detection of enzymes in tissues and the provision of a solid basis for text-mining approaches in this field. It is widely used by lab scientists, curators of genomic and biochemical databases and bioinformaticians. The BTO is freely available at http://www.obofoundry.org. © The Author(s) 2010.", "date": "2011-01-01T00:00:00Z", "citationCount": 141, "authors": [ { "name": "Gremse M." }, { "name": "Chang A." }, { "name": "Schomburg I." }, { "name": "Grote A." }, { "name": "Scheer M." }, { "name": "Ebeling C." }, { "name": "Schomburg D." } ], "journal": "Nucleic Acids Research" } } ], "credit": [ { "name": null, "email": "contact@brenda-enzymes.org", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Project", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures", "email": null, "url": "https://www.dsmz.de/", "orcidid": null, "gridid": null, "rorid": "02tyer376", "fundrefid": null, "typeEntity": "Institute", "typeRole": [], "note": null } ], "owner": "AJaede", "additionDate": "2017-04-22T18:19:39Z", "lastUpdate": "2025-01-28T08:45:24.895767Z", "editPermission": { "type": "group", "authors": [ "AJaede", "juh22" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": "tool" }, { "name": "Assembly PCR Oligo Maker", "description": "Assembly PCR Oligo Maker is a tool for designing oligodeoxynucleotides for the PCR based construction of long DNA molecules.", "homepage": "http://www.yorku.ca/pjohnson/AssemblyPCRoligomaker.html", "biotoolsID": "assembly_pcr_oligo_maker", "biotoolsCURIE": "biotools:assembly_pcr_oligo_maker", "version": [], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0307", "term": "Virtual PCR" }, { "uri": "http://edamontology.org/operation_0310", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/operation_0308", "term": "PCR primer design" } ], "input": [], "output": [], "note": null, "cmd": null } ], "toolType": [ "Web application" ], "topic": [ { "uri": "http://edamontology.org/topic_0196", "term": "Sequence assembly" }, { "uri": "http://edamontology.org/topic_3519", "term": "PCR experiment" }, { "uri": "http://edamontology.org/topic_0654", "term": "DNA" }, { "uri": "http://edamontology.org/topic_0632", "term": "Probes and primers" } ], "operatingSystem": [ "Linux", "Windows", "Mac" ], "language": [ "Java" ], "license": null, "collectionID": [], "maturity": null, "cost": null, "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [], "download": [], "documentation": [ { "url": "http://www.yorku.ca/pjohnson/oligo/manual.pdf", "type": [ "User manual" ], "note": null } ], "publication": [ { "doi": "10.1093/nar/gki380", "pmid": "15980526", "pmcid": "PMC1160141", "type": [], "version": null, "note": null, "metadata": null } ], "credit": [ { "name": "Philip E. 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Beside its enormous scientific value as a safeguard of plant biodiversity, the plant genetic resources maintained are also of high importance for breeders to provide new impulses. The complex processes of managing such a collection are supported by the Genebank Information System (GBIS). GBIS is an important source of information for researchers and plant breeders, e.g. for identifying appropriate germplasm for breeding purposes. In addition, the access to genebank material as a sovereign task is also of high interest to the general public. 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