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description Publicationkeyboard_double_arrow_right Article , Other literature type 2020 Luxembourg, Italy, France, United Kingdom, Italy, France, Germany, Spain EnglishPublisher:Public Library of Science (PLoS) Funded by:EC | ELIXIR-EXCELERATEEC| ELIXIR-EXCELERATEGurwitz, Kim T; Singh Gaur, Prakash; Bellis, Louisa J; Larcombe, Lee; Alloza, Eva; Balint, Balint Laszlo; Botzki, Alexander; Dimec, Jure; Dominguez Del Angel, Victoria; Fernandes, Pedro L; Korpelainen, Eija; Krause, Roland; Kuzak, Mateusz; Le Pera, Loredana; Leskošek, Brane; Lindvall, Jessica M; Marek, Diana; Martinez, Paula A; Muyldermans, Tuur; Nygård, Ståle; Palagi, Patricia M; Peterson, Hedi; Psomopoulos, Fotis; Spiwok, Vojtech; Van Gelder, Celia WG; Via, Allegra; Vidak, Marko; Wibberg, Daniel; Morgan, Sarah L; Rustici, Gabriella;ELIXIR is a pan-European intergovernmental organisation for life science that aims to coordinate bioinformatics resources in a single infrastructure across Europe; bioinformatics training is central to its strategy, which aims to develop a training community that spans all ELIXIR member states. In an evidence-based approach for strengthening bioinformatics training programmes across Europe, the ELIXIR Training Platform, led by the ELIXIR EXCELERATE Quality and Impact Assessment Subtask in collaboration with the ELIXIR Training Coordinators Group, has implemented an assessment strategy to measure quality and impact of its entire training portfolio. Here, we present ELIXIR’s framework for assessing training quality and impact, which includes the following: specifying assessment aims, determining what data to collect in order to address these aims, and our strategy for centralised data collection to allow for ELIXIR-wide analyses. In addition, we present an overview of the ELIXIR training data collected over the past 4 years. We highlight the importance of a coordinated and consistent data collection approach and the relevance of defining specific metrics and answer scales for consortium-wide analyses as well as for comparison of data across iterations of the same course. ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559 (https://ec.europa.eu/programmes/horizon2020/en/area/researchinfrastructures). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7377377Data sources: PubMed CentralServeur académique lausannoisArticle . 2020License: CC BYData sources: Serveur académique lausannoisPLoS Computational Biology; Publications at Bielefeld University; Recolector de Ciencia Abierta, RECOLECTA; CNR ExploRAOther literature type . Article . 2020 . Peer-reviewedLicense: CC BYRecolector de Ciencia Abierta, RECOLECTAOther literature type . Article . 2020License: CC BYData sources: Recolector de Ciencia Abierta, RECOLECTAUPCommons. Portal del coneixement obert de la UPCOther literature type . Article . 2020License: CC BYData sources: UPCommons. Portal del coneixement obert de la UPCOpen Repository and Bibliography - LuxembourgArticle . 2020Data sources: Open Repository and Bibliography - Luxembourgadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1371/journal.pcbi.1007976&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 6 citations 6 popularity Top 10% influence Average impulse Top 10% Powered by BIP!visibility 125visibility views 125 download downloads 204 Powered bymore_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7377377Data sources: PubMed CentralServeur académique lausannoisArticle . 2020License: CC BYData sources: Serveur académique lausannoisPLoS Computational Biology; Publications at Bielefeld University; Recolector de Ciencia Abierta, RECOLECTA; CNR ExploRAOther literature type . Article . 2020 . Peer-reviewedLicense: CC BYRecolector de Ciencia Abierta, RECOLECTAOther literature type . Article . 2020License: CC BYData sources: Recolector de Ciencia Abierta, RECOLECTAUPCommons. Portal del coneixement obert de la UPCOther literature type . Article . 2020License: CC BYData sources: UPCommons. Portal del coneixement obert de la UPCOpen Repository and Bibliography - LuxembourgArticle . 2020Data sources: Open Repository and Bibliography - Luxembourgadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1371/journal.pcbi.1007976&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2020 France EnglishPublisher:Public Library of Science (PLoS) Funded by:EC | ELIXIR-EXCELERATE, ANR | IFB (ex Renabi-IFB)EC| ELIXIR-EXCELERATE ,ANR| IFB (ex Renabi-IFB)Chennen, Kirsley; Weber, Thomas; Lornage, Xavière; Kress, Arnaud; Böhm, Johann; Thompson, Julie; Laporte, Jocelyn; Poch, Olivier;pmc: PMC7394404
pmid: 32735577
International audience; The diffusion of next-generation sequencing technologies has revolutionized research and diagnosis in the field of rare Mendelian disorders, notably via whole-exome sequencing (WES). However, one of the main issues hampering achievement of a diagnosis via WES analyses is the extended list of variants of unknown significance (VUS), mostly composed of missense variants. Hence, improved solutions are needed to address the challenges of identifying potentially deleterious variants and ranking them in a prioritized short list. We present MISTIC (MISsense deleTeriousness predICtor), a new prediction tool based on an original combination of two complementary machine learning algorithms using a soft voting system that integrates 113 missense features, ranging from multi-ethnic minor allele frequencies and evolutionary conservation, to physiochemical and biochemical properties of amino acids. Our approach also uses training sets with a wide spectrum of variant profiles, including both high-confidence positive (deleterious) and negative (benign) variants. Compared to recent state-of-the-art prediction tools in various benchmark tests and independent evaluation scenarios, MISTIC exhibits the best and most consistent performance, notably with the highest AUC value (> 0.95). Importantly, MISTIC maintains its high performance in the specific case of discriminating deleterious variants from benign variants that are rare or population-specific. In a clinical context, MISTIC drastically reduces the list of VUS (<30%) and significantly improves the ranking of "causative" deleterious variants. Pre-computed MISTIC scores for all possible human missense variants are available at http://lbgi.fr/mistic.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7394404Data sources: PubMed CentralHAL-Inserm; Hal-DiderotArticle . 2020add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=PMC7394404&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 13 citations 13 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7394404Data sources: PubMed CentralHAL-Inserm; Hal-DiderotArticle . 2020add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=PMC7394404&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2020Embargo end date: 01 Jan 2020 FrancePublisher:arXiv Funded by:ANR | PHENOME, ANR | FooSIN, ANR | FRIMOUSS +3 projectsANR| PHENOME ,ANR| FooSIN ,ANR| FRIMOUSS ,EC| EOSC-Life ,ANR| METABOHUB ,EC| EPPN2020Authors: Jacob, Daniel; David, Romain; Aubin, Sophie; Gibon, Yves;Jacob, Daniel; David, Romain; Aubin, Sophie; Gibon, Yves;International audience; Making data compliant with the FAIR Data principles (Findable, Accessible, Interoperable, Reusable) is still a challenge for many researchers, who are not sure which criteria should be met first and how. Illustrated from experimental data tables associated with a Design of Experiments, we propose an approach that can serve as a model for a research data management that allows researchers to disseminate their data by satisfying the main FAIR criteria without insurmountable efforts. More importantly, this approach aims to facilitate the FAIRification process by providing researchers with tools to improve their data management practices.
GigaScience arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7736789Data sources: PubMed CentralHAL Descartes; Mémoires en Sciences de l'Information et de la Communication; Hal-DiderotArticle . 2020License: CC BYFull-Text: https://hal.inrae.fr/hal-02883355v4/documenthttps://doi.org/10.48550/arxiv...Article . 2020License: arXiv Non-Exclusive DistributionData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.48550/arxiv.2012.09435&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 4 citations 4 popularity Top 10% influence Average impulse Average Powered by BIP!visibility 13visibility views 13 Powered bymore_vert GigaScience arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7736789Data sources: PubMed CentralHAL Descartes; Mémoires en Sciences de l'Information et de la Communication; Hal-DiderotArticle . 2020License: CC BYFull-Text: https://hal.inrae.fr/hal-02883355v4/documenthttps://doi.org/10.48550/arxiv...Article . 2020License: arXiv Non-Exclusive DistributionData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.48550/arxiv.2012.09435&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2019 Denmark, Italy, Norway, Denmark, Netherlands, Denmark, Spain, France, Netherlands, Sweden, Netherlands EnglishPublisher:Springer Science and Business Media LLC Funded by:EC | OLISSIPO, EC | ELIXIR-EXCELERATE, WTEC| OLISSIPO ,EC| ELIXIR-EXCELERATE ,WTJon Ison; Hans Ienasescu; Piotr Jaroslaw Chmura; Emil Karol Rydza; Hervé Ménager; Matúš Kalaš; Veit Schwämmle; Björn Grüning; Niall Beard; Rodrigo Lopez; Séverine Duvaud; Heinz Stockinger; Bengt Persson; Radka Svobodová Vařeková; Tomáš Raček; Jiří Vondrášek; Hedi Peterson; Ahto Salumets; Inge Jonassen; Rob Hooft; Tommi Nyrönen; Alfonso Valencia; Salvador Capella; Josep Lluís Gelpí; Federico Zambelli; Babis Savakis; Brane Leskošek; Kristoffer Rapacki; Christophe Blanchet; Rafael C. Jimenez; Arlindo L. Oliveira; Gert Vriend; Olivier Collin; Jacques van Helden; Peter Løngreen; Søren Brunak;Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue ( https://bio.tools ) of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information. Contains fulltext : 208582.pdf (Publisher’s version ) (Open Access)
NARCIS arrow_drop_down Genome BiologyArticle . 2019Full-Text: http://europepmc.org/articles/PMC6691543Data sources: PubMed CentralRadboud Repository; Genome Biology; Archivio Istituzionale della Ricerca dell'Università degli Studi di MilanoOther literature type . Article . 2019 . Peer-reviewedLicense: CC BYDiposit Digital de la Universitat de Barcelona; Recolector de Ciencia Abierta, RECOLECTAArticle . 2019License: CC BYOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyCopenhagen University Research Information SystemArticle . 2019Data sources: Copenhagen University Research Information SystemUniversity of Southern Denmark Research OutputArticle . 2019Data sources: University of Southern Denmark Research OutputBergen Open Research Archive - UiBArticle . 2019 . Peer-reviewedLicense: CC BYData sources: Bergen Open Research Archive - UiBadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1186/s13059-019-1772-6&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 34 citations 34 popularity Top 1% influence Top 10% impulse Top 10% Powered by BIP!visibility 56visibility views 56 download downloads 103 Powered bymore_vert NARCIS arrow_drop_down Genome BiologyArticle . 2019Full-Text: http://europepmc.org/articles/PMC6691543Data sources: PubMed CentralRadboud Repository; Genome Biology; Archivio Istituzionale della Ricerca dell'Università degli Studi di MilanoOther literature type . Article . 2019 . Peer-reviewedLicense: CC BYDiposit Digital de la Universitat de Barcelona; Recolector de Ciencia Abierta, RECOLECTAArticle . 2019License: CC BYOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyCopenhagen University Research Information SystemArticle . 2019Data sources: Copenhagen University Research Information SystemUniversity of Southern Denmark Research OutputArticle . 2019Data sources: University of Southern Denmark Research OutputBergen Open Research Archive - UiBArticle . 2019 . Peer-reviewedLicense: CC BYData sources: Bergen Open Research Archive - UiBadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1186/s13059-019-1772-6&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint , Other literature type 2019 France, Netherlands, Belgium, United States, Luxembourg, France, United States, Spain, DenmarkPublisher:Springer Science and Business Media LLC Funded by:NIH | Unraveling the mammalian ..., EC | SysMedPDNIH| Unraveling the mammalian secretory pathway through systems biology and algorithm development ,EC| SysMedPDLaurent Heirendt; Sylvain Arreckx; Thomas Pfau; Sebastián N. Mendoza; Anne Richelle; Almut Heinken; Hulda S. Haraldsdóttir; Jacek Wachowiak; Sarah M. Keating; Vanja Vlasov; Stefania Magnusdottir; Chiam Yu Ng; German Preciat; Alise Žagare; Siu Hung Joshua Chan; Maike K. Aurich; Catherine M. Clancy; Jennifer Modamio; John T. Sauls; Alberto Noronha; Aarash Bordbar; Benjamin Cousins; Diana C. El Assal; Luis Vitores Valcárcel; Iñigo Apaolaza; Susan Ghaderi; Masoud Ahookhosh; Marouen Ben Guebila; Andrejs Kostromins; Nicolas Sompairac; Hoai M. Le; Ding Ma; Yuekai Sun; Lin Wang; James T. Yurkovich; Miguel A.P. Oliveira; Phan Tu Vuong; Lemmer P. El Assal; Inna Kuperstein; Andrei Zinovyev; H. Scott Hinton; William A. Bryant; Francisco J. Aragón Artacho; Francisco J. Planes; Egils Stalidzans; Alejandro Maass; Santosh Vempala; Michael Hucka; Michael A. Saunders; Costas D. Maranas; Nathan E. Lewis; Thomas Sauter; Bernhard O. Palsson; Ines Thiele; Ronan M. T. Fleming;pmid: 30787451
pmc: PMC6635304
Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental molecular systems biology data and quantitative prediction of physicochemically and biochemically feasible phenotypic states. The COBRA Toolbox is a comprehensive desktop software suite of interoperable COBRA methods. It has found widespread application in biology, biomedicine, and biotechnology because its functions can be flexibly combined to implement tailored COBRA protocols for any biochemical network. This protocol is an update to the COBRA Toolbox v.1.0 and v.2.0. Version 3.0 includes new methods for quality-controlled reconstruction, modeling, topological analysis, strain and experimental design, and network visualization, as well as network integration of chemoinformatic, metabolomic, transcriptomic, proteomic, and thermochemical data. New multi-lingual code integration also enables an expansion in COBRA application scope via high-precision, high-performance, and nonlinear numerical optimization solvers for multi-scale, multi-cellular, and reaction kinetic modeling, respectively. This protocol provides an overview of all these new features and can be adapted to generate and analyze constraint-based models in a wide variety of scenarios. The COBRA Toolbox v.3.0 provides an unparalleled depth of COBRA methods. This study was funded by the National Centre of Excellence in Research (NCER) on Parkinson’s disease, the U.S. Department of Energy, Offices of Advanced Scientific Computing Research and the Biological and Environmental Research as part of the Scientific Discovery Through Advanced Computing program, grant no. DE-SC0010429. This project also received funding from the European Union’s HORIZON 2020 Research and Innovation Programme under grant agreement no. 668738 and the Luxembourg National Research Fund (FNR) ATTRACT program (FNR/A12/01) and OPEN (FNR/O16/11402054) grants. N.E.L. was supported by NIGMS (R35 GM119850) and the Novo Nordisk Foundation (NNF10CC1016517). M.A.P.O. was supported by the Luxembourg National Research Fund (FNR) grant AFR/6669348. A.R. was supported by the Lilly Innovation Fellows Award. F.J.P. was supported by the Minister of Economy and Competitiveness of Spain (BIO2016-77998-R) and the ELKARTEK Programme of the Basque Government (KK-2016/00026). I.A. was supported by a Basque Government predoctoral grant (PRE_2016_2_0044). B.Ø.P. was supported by the Novo Nordisk Foundation through the Center for Biosustainability at the Technical University of Denmark (NNF10CC1016517).
Recolector de Cienci... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTAArticle . 2019Full-Text: https://doi.org/10.1038/s41596-018-0098-2Data sources: Recolector de Ciencia Abierta, RECOLECTAOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyeScholarship - University of CaliforniaArticle . 2018Data sources: eScholarship - University of CaliforniaRepositorio Institucional de la Universidad de AlicanteArticle . 2019Data sources: Repositorio Institucional de la Universidad de AlicanteeScholarship - University of CaliforniaArticle . 2019Data sources: eScholarship - University of CaliforniaOpen Repository and Bibliography - LuxembourgArticle . 2019Data sources: Open Repository and Bibliography - Luxembourghttps://doi.org/10.48550/arxiv...Article . 2017License: arXiv Non-Exclusive DistributionData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1038/s41596-018-0098-2&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen bronze 773 citations 773 popularity Top 0.01% influence Top 1% impulse Top 0.01% Powered by BIP!more_vert Recolector de Cienci... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTAArticle . 2019Full-Text: https://doi.org/10.1038/s41596-018-0098-2Data sources: Recolector de Ciencia Abierta, RECOLECTAOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyeScholarship - University of CaliforniaArticle . 2018Data sources: eScholarship - University of CaliforniaRepositorio Institucional de la Universidad de AlicanteArticle . 2019Data sources: Repositorio Institucional de la Universidad de AlicanteeScholarship - University of CaliforniaArticle . 2019Data sources: eScholarship - University of CaliforniaOpen Repository and Bibliography - LuxembourgArticle . 2019Data sources: Open Repository and Bibliography - Luxembourghttps://doi.org/10.48550/arxiv...Article . 2017License: arXiv Non-Exclusive DistributionData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1038/s41596-018-0098-2&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2018 FrancePublisher:Cold Spring Harbor Laboratory Funded by:EC | VIROGENESIS, ANR | INCEPTIONEC| VIROGENESIS ,ANR| INCEPTIONAuthors: Sohta A. Ishikawa; Anna Zhukova; Wataru Iwasaki; Olivier Gascuel;Sohta A. Ishikawa; Anna Zhukova; Wataru Iwasaki; Olivier Gascuel;AbstractThe reconstruction of ancestral scenarios is widely used to study the evolution of characters along phylogenetic trees. One commonly uses the marginal posterior probabilities of the character states, or the joint reconstruction of the most likely scenario. However, marginal reconstructions provide users with state probabilities, which are difficult to interpret and visualize, whereas joint reconstructions select a unique state for every tree node and thus do not reflect the uncertainty of inferences.We propose a simple and fast approach, which is in between these two extremes. We use decision-theory concepts (namely, the Brier score) to associate each node in the tree to a set of likely states. A unique state is predicted in tree regions with low uncertainty, whereas several states are predicted in uncertain regions, typically around the tree root. To visualize the results, we cluster the neighboring nodes associated with the same states and use graph visualization tools. The method is implemented in the PastML program and web server.The results on simulated data demonstrate the accuracy and robustness of the approach. PastML was applied to the phylogeography of Dengue serotype 2 (DENV2), and the evolution of drug resistances in a large HIV data set. These analyses took a few minutes and provided convincing results. PastML retrieved the main transmission routes of human DENV2 and showed the uncertainty of the human-sylvatic DENV2 geographic origin. With HIV, the results show that resistance mutations mostly emerge independently under treatment pressure, but resistance clusters are found, corresponding to transmissions among untreated patients.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6735705Data sources: PubMed CentralbioRxivPreprint . 2018Molecular Biology and EvolutionArticle . 2019 . Peer-reviewedLicense: CC BY NCData sources: CrossrefHAL Descartes; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2019License: CC BY NCadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/379529&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen hybrid 144 citations 144 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6735705Data sources: PubMed CentralbioRxivPreprint . 2018Molecular Biology and EvolutionArticle . 2019 . Peer-reviewedLicense: CC BY NCData sources: CrossrefHAL Descartes; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2019License: CC BY NCadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/379529&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2018 France EnglishPublisher:Oxford University Press (OUP) Funded by:EC | PhenoMeNal, WT | Institutional Strategic S...EC| PhenoMeNal ,WT| Institutional Strategic Support Fund Phase2 FY2014/16Cottret, Ludovic; Frainay, Clément; Chazalviel, Maxime; Cabanettes, Floréal; Gloaguen, Yoann; Camenen, Etienne; Merlet, Benjamin; Heux, Stéphanie; Portais, Jean-Charles; Poupin, Nathalie; Vinson, Florence; Jourdan, Fabien;pmc: PMC6030842
pmid: 29718355
Abstract Metabolism of an organism is composed of hundreds to thousands of interconnected biochemical reactions responding to environmental or genetic constraints. This metabolic network provides a rich knowledge to contextualize omics data and to elaborate hypotheses on metabolic modulations. Nevertheless, performing this kind of integrative analysis is challenging for end users with not sufficiently advanced computer skills since it requires the use of various tools and web servers. MetExplore offers an all-in-one online solution composed of interactive tools for metabolic network curation, network exploration and omics data analysis. In particular, it is possible to curate and annotate metabolic networks in a collaborative environment. The network exploration is also facilitated in MetExplore by a system of interactive tables connected to a powerful network visualization module. Finally, the contextualization of metabolic elements in the network and the calculation of over-representation statistics make it possible to interpret any kind of omics data. MetExplore is a sustainable project maintained since 2010 freely available at https://metexplore.toulouse.inra.fr/metexplore2/.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2018Full-Text: http://europepmc.org/articles/PMC6030842Data sources: PubMed CentralInstitutional Repository for Molecular Medicine (MDC)Article . 2018 . Peer-reviewedData sources: Institutional Repository for Molecular Medicine (MDC)HAL Descartes; Mémoires en Sciences de l'Information et de la Communication; HAL-INSA ToulouseArticle . 2018License: CC BY NCFull-Text: https://hal.science/hal-01886470/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen 49 citations 49 popularity Top 10% influence Top 10% impulse Top 1% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2018Full-Text: http://europepmc.org/articles/PMC6030842Data sources: PubMed CentralInstitutional Repository for Molecular Medicine (MDC)Article . 2018 . Peer-reviewedData sources: Institutional Repository for Molecular Medicine (MDC)HAL Descartes; Mémoires en Sciences de l'Information et de la Communication; HAL-INSA ToulouseArticle . 2018License: CC BY NCFull-Text: https://hal.science/hal-01886470/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2017 France, France, Italy, United KingdomPublisher:American Chemical Society (ACS) Funded by:EC | PhenoMeNal, ANR | METABOHUB, UKRI | MICA: UK MEDical BIOinfor... +5 projectsEC| PhenoMeNal ,ANR| METABOHUB ,UKRI| MICA: UK MEDical BIOinformatics partnership - aggregation, integration, visualisation and analysis of large, complex data (UK MED-BIO). ,UKRI| Open source pipelines for integrated metabolomics analysis by NMR and mass spectrometry ,UKRI| Open source pipelines for integrated metabolomics analysis by NMR and mass spectrometry ,UKRI| Sharing of metabolomics data and their analyses as Galaxy workflows through a UK-China collaboration ,NSERC ,CIHRSchober, D; Jacob, D; Wilson, M; Cruz, JA; Marcu, A; Grant, JR; Moing, A; Deborde, C; De Figueiredo, LF; Haug, K; Rocca-Serra, P; Easton, J; Ebbels, TMD; Hao, J; Ludwig, C; Günther, UL; Rosato, A; Klein, MS; Lewis, IA; Luchinat, C; Jones, AR; Grauslys, A; Larralde, M; Yokochi, M; Kobayashi, N; Porzel, A; Griffin, JL; Viant, MR; Wishart, DS; Steinbeck, C; Salek, RM; Neumann, S;UMR BFP - Equipe Métabolisme; International audience; NMR is a widely used analytical technique with a growing number of repositories available. As a result, demands for a vendor-agnostic, open data format for long-term archiving of NMR data have emerged with the aim to ease and encourage sharing, comparison and reuse of NMR data. Here we present nmrML, an open XML-based exchange and storage format for NMR spectral data. The nmrML format is intended to be fully compatible with existing NMR data for chemical, biochemical and metabolomics experiments. nmrML can capture raw NMR data, spectral data acquisition parameters and, where available, spectral metadata such as chemical structures associated with spectral assignments. The nmrML format is compatible with pure-compound NMR data for reference spectral libraries as well as NMR data from complex bio-mixtures i.e. metabolomics experiments. To facilitate format conversions, we provide nmrML converters for Bruker and Agilent/Varian vendor formats. In addition, easy-to-use web-based spectral viewing, processing and spectral assignment tools that read and write nmrML have been developed. Software libraries and web services for data validation are available for tool developers and end-users. The nmrML format has already been adopted for capturing and disseminating NMR data for small molecules by several open source data processing tools and metabolomics reference spectral libraries, e.g. serving as storage format for the MetaboLights data repository. The nmrML open access data standard has been endorsed by the Metabolomics Standards Initiative (MSI) and we here encourage user participation and feedback to increase usability and make it a successful standard.
Analytical Chemistry arrow_drop_down Spiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital RepositoryOxford University Research Archive; Flore (Florence Research Repository); Analytical ChemistryOther literature type . Article . 2019 . 2017 . 2018 . Peer-reviewedadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess Routeshybrid 47 citations 47 popularity Top 1% influence Top 10% impulse Top 10% Powered by BIP!visibility 14visibility views 14 download downloads 80 Powered bymore_vert Analytical Chemistry arrow_drop_down Spiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital RepositoryOxford University Research Archive; Flore (Florence Research Repository); Analytical ChemistryOther literature type . Article . 2019 . 2017 . 2018 . Peer-reviewedadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Other literature type , Conference object , Article 2017 France Funded by:EC | OpenMinTeDEC| OpenMinTeDAuthors: Chaix, Estelle; Deléger, Louise; Bossy, Robert; Nédellec, Claire;Chaix, Estelle; Deléger, Louise; Bossy, Robert; Nédellec, Claire;pmid: 30910089
pmc: PMC6460834
Introduction Information on food microbial biodiversity is scattered across millions of scientific papers (2 million references in the PubMed bibliographic database in 2017). It is impossible to manually achieve an exhaustive analysis of these documents. Text-mining and knowledge engineering methods can assist the researcher in finding relevant information. Material & MethodsWe propose to study bacterial biodiversity using text-mining tools from the Alvis platform. First, we analyzed terms that designate Microbial and Habitat entities in text. Microorganism names were predicted using the NCBI taxonomy. Habitat entities were detected using the syntactic structure of the terms and the OntoBiotope ontology. This ontology has been specifically enriched for the recognition of food terms in text. In a second time, we predicted links between microorganisms and their habitats (labeled “Lives_in” relationships) using pattern and machine-learning based methods. The results of text-mining predictions are indexed and presented in a semantic search engine. Result The AlvisIR search engine for microbe literature gives online access to 1.2 million PubMed abstracts in 2015, among which 13% are specific to food. This tool makes it possible to use text-mining results to search for information on bacterial biodiversity. It covers all types of microbial habitats to help understand the origin of microbial presence in food. Significance This work presents the first semantic search engine dedicated to better understand microbial food biodiversity from text.
Europe PubMed Centra... arrow_drop_down HAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotConference object . 2017Mémoires en Sciences de l'Information et de la CommunicationConference object . 2017Full-Text: https://hal.science/hal-01602552/documentHAL Descartes; Mémoires en Sciences de l'Information et de la Communication; Hal-DiderotArticle . 2019License: CC BYFull-Text: https://hal.inrae.fr/hal-02628265/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen 10 citations 10 popularity Top 10% influence Average impulse Average Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down HAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotConference object . 2017Mémoires en Sciences de l'Information et de la CommunicationConference object . 2017Full-Text: https://hal.science/hal-01602552/documentHAL Descartes; Mémoires en Sciences de l'Information et de la Communication; Hal-DiderotArticle . 2019License: CC BYFull-Text: https://hal.inrae.fr/hal-02628265/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Other literature type 2017 Netherlands, Netherlands, Italy, United Kingdom, United Kingdom, Netherlands, Netherlands, France, United Kingdom, Spain EnglishPublisher:HAL CCSD Funded by:EC | PhenoMeNalEC| PhenoMeNalvan Rijswijk, M; van Rijswijk, M; Beirnaert, C; Beirnaert, C; Caron, C; Cascante, M; Dominguez, V; Dunn, WB; Ebbels, TMD; Giacomoni, F; Gonzalez-Beltran, A; Hankemeier, T; Haug, K; Haug, K; Izquierdo-Garcia, JL; Jimenez, RC; Jimenez, RC; Jourdan, F; Kale, N; Klapa, MI; Kohlbacher, O; Koort, K; Kultima, K; Le Corguillé, G; Moreno, P; Moschonas, NK; Moschonas, NK; Neumann, S; O'Donovan, C; Reczko, M; Rocca-Serra, P; Rosato, A; Rosato, A; Rosato, A; Salek, RM; Salek, RM; Sansone, S-A; Satagopam, V; Schober, D; Shimmo, R; Spicer, RA; Spicer, RA; Spjuth, O; Spjuth, O; Spjuth, O; Thévenot, EA; Thévenot, EA; Viant, MR; Weber, RJM; Willighagen, EL; Willighagen, EL; Zanetti, G; Steinbeck, C; Steinbeck, C;Metabolomics, the youngest of the major omics technologies, is supported by an active community of researchers and infrastructure developers across Europe. To coordinate and focus efforts around infrastructure building for metabolomics within Europe, a workshop on the "Future of metabolomics in ELIXIR" was organised at Frankfurt Airport in Germany. This one-day strategic workshop involved representatives of ELIXIR Nodes, members of the PhenoMeNal consortium developing an e-infrastructure that supports workflow-based metabolomics analysis pipelines, and experts from the international metabolomics community. The workshop established metabolite identification as the critical area, where a maximal impact of computational metabolomics and data management on other fields could be achieved. In particular, the existing four ELIXIR Use Cases, where the metabolomics community - both industry and academia - would benefit most, and which could be exhaustively mapped onto the current five ELIXIR Platforms were discussed. This opinion article is a call for support for a new ELIXIR metabolomics Use Case, which aligns with and complements the existing and planned ELIXIR Platforms and Use Cases. The meeting was funded by PhenoMeNal, European Commission's Horizon2020 programme, grant agreement number 654241 Sí
HAL - UPEC / UPEM; H... arrow_drop_down Europe PubMed CentralArticle . 2017 . Peer-reviewedFull-Text: http://europepmc.org/articles/PMC5627583Data sources: PubMed CentralRecolector de Ciencia Abierta, RECOLECTAArticle . 2017Data sources: Recolector de Ciencia Abierta, RECOLECTAFlore (Florence Research Repository)Article . 2017Data sources: Flore (Florence Research Repository)Oxford University Research Archive; F1000ResearchOther literature type . Article . 2017 . 2018 . Peer-reviewedLicense: CC BYSpiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital RepositorySpiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital Repositoryadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 25 citations 25 popularity Top 10% influence Average impulse Top 10% Powered by BIP!visibility 34visibility views 34 download downloads 65 Powered bymore_vert HAL - UPEC / UPEM; H... arrow_drop_down Europe PubMed CentralArticle . 2017 . Peer-reviewedFull-Text: http://europepmc.org/articles/PMC5627583Data sources: PubMed CentralRecolector de Ciencia Abierta, RECOLECTAArticle . 2017Data sources: Recolector de Ciencia Abierta, RECOLECTAFlore (Florence Research Repository)Article . 2017Data sources: Flore (Florence Research Repository)Oxford University Research Archive; F1000ResearchOther literature type . Article . 2017 . 2018 . Peer-reviewedLicense: CC BYSpiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital RepositorySpiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital Repositoryadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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description Publicationkeyboard_double_arrow_right Article , Other literature type 2020 Luxembourg, Italy, France, United Kingdom, Italy, France, Germany, Spain EnglishPublisher:Public Library of Science (PLoS) Funded by:EC | ELIXIR-EXCELERATEEC| ELIXIR-EXCELERATEGurwitz, Kim T; Singh Gaur, Prakash; Bellis, Louisa J; Larcombe, Lee; Alloza, Eva; Balint, Balint Laszlo; Botzki, Alexander; Dimec, Jure; Dominguez Del Angel, Victoria; Fernandes, Pedro L; Korpelainen, Eija; Krause, Roland; Kuzak, Mateusz; Le Pera, Loredana; Leskošek, Brane; Lindvall, Jessica M; Marek, Diana; Martinez, Paula A; Muyldermans, Tuur; Nygård, Ståle; Palagi, Patricia M; Peterson, Hedi; Psomopoulos, Fotis; Spiwok, Vojtech; Van Gelder, Celia WG; Via, Allegra; Vidak, Marko; Wibberg, Daniel; Morgan, Sarah L; Rustici, Gabriella;ELIXIR is a pan-European intergovernmental organisation for life science that aims to coordinate bioinformatics resources in a single infrastructure across Europe; bioinformatics training is central to its strategy, which aims to develop a training community that spans all ELIXIR member states. In an evidence-based approach for strengthening bioinformatics training programmes across Europe, the ELIXIR Training Platform, led by the ELIXIR EXCELERATE Quality and Impact Assessment Subtask in collaboration with the ELIXIR Training Coordinators Group, has implemented an assessment strategy to measure quality and impact of its entire training portfolio. Here, we present ELIXIR’s framework for assessing training quality and impact, which includes the following: specifying assessment aims, determining what data to collect in order to address these aims, and our strategy for centralised data collection to allow for ELIXIR-wide analyses. In addition, we present an overview of the ELIXIR training data collected over the past 4 years. We highlight the importance of a coordinated and consistent data collection approach and the relevance of defining specific metrics and answer scales for consortium-wide analyses as well as for comparison of data across iterations of the same course. ELIXIR-EXCELERATE is funded by the European Commission within the Research Infrastructures programme of Horizon 2020, grant agreement number 676559 (https://ec.europa.eu/programmes/horizon2020/en/area/researchinfrastructures). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7377377Data sources: PubMed CentralServeur académique lausannoisArticle . 2020License: CC BYData sources: Serveur académique lausannoisPLoS Computational Biology; Publications at Bielefeld University; Recolector de Ciencia Abierta, RECOLECTA; CNR ExploRAOther literature type . Article . 2020 . Peer-reviewedLicense: CC BYRecolector de Ciencia Abierta, RECOLECTAOther literature type . Article . 2020License: CC BYData sources: Recolector de Ciencia Abierta, RECOLECTAUPCommons. Portal del coneixement obert de la UPCOther literature type . Article . 2020License: CC BYData sources: UPCommons. Portal del coneixement obert de la UPCOpen Repository and Bibliography - LuxembourgArticle . 2020Data sources: Open Repository and Bibliography - Luxembourgadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 6 citations 6 popularity Top 10% influence Average impulse Top 10% Powered by BIP!visibility 125visibility views 125 download downloads 204 Powered bymore_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7377377Data sources: PubMed CentralServeur académique lausannoisArticle . 2020License: CC BYData sources: Serveur académique lausannoisPLoS Computational Biology; Publications at Bielefeld University; Recolector de Ciencia Abierta, RECOLECTA; CNR ExploRAOther literature type . Article . 2020 . Peer-reviewedLicense: CC BYRecolector de Ciencia Abierta, RECOLECTAOther literature type . Article . 2020License: CC BYData sources: Recolector de Ciencia Abierta, RECOLECTAUPCommons. Portal del coneixement obert de la UPCOther literature type . Article . 2020License: CC BYData sources: UPCommons. Portal del coneixement obert de la UPCOpen Repository and Bibliography - LuxembourgArticle . 2020Data sources: Open Repository and Bibliography - Luxembourgadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2020 France EnglishPublisher:Public Library of Science (PLoS) Funded by:EC | ELIXIR-EXCELERATE, ANR | IFB (ex Renabi-IFB)EC| ELIXIR-EXCELERATE ,ANR| IFB (ex Renabi-IFB)Chennen, Kirsley; Weber, Thomas; Lornage, Xavière; Kress, Arnaud; Böhm, Johann; Thompson, Julie; Laporte, Jocelyn; Poch, Olivier;pmc: PMC7394404
pmid: 32735577
International audience; The diffusion of next-generation sequencing technologies has revolutionized research and diagnosis in the field of rare Mendelian disorders, notably via whole-exome sequencing (WES). However, one of the main issues hampering achievement of a diagnosis via WES analyses is the extended list of variants of unknown significance (VUS), mostly composed of missense variants. Hence, improved solutions are needed to address the challenges of identifying potentially deleterious variants and ranking them in a prioritized short list. We present MISTIC (MISsense deleTeriousness predICtor), a new prediction tool based on an original combination of two complementary machine learning algorithms using a soft voting system that integrates 113 missense features, ranging from multi-ethnic minor allele frequencies and evolutionary conservation, to physiochemical and biochemical properties of amino acids. Our approach also uses training sets with a wide spectrum of variant profiles, including both high-confidence positive (deleterious) and negative (benign) variants. Compared to recent state-of-the-art prediction tools in various benchmark tests and independent evaluation scenarios, MISTIC exhibits the best and most consistent performance, notably with the highest AUC value (> 0.95). Importantly, MISTIC maintains its high performance in the specific case of discriminating deleterious variants from benign variants that are rare or population-specific. In a clinical context, MISTIC drastically reduces the list of VUS (<30%) and significantly improves the ranking of "causative" deleterious variants. Pre-computed MISTIC scores for all possible human missense variants are available at http://lbgi.fr/mistic.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7394404Data sources: PubMed CentralHAL-Inserm; Hal-DiderotArticle . 2020add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 13 citations 13 popularity Top 10% influence Average impulse Top 10% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7394404Data sources: PubMed CentralHAL-Inserm; Hal-DiderotArticle . 2020add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2020Embargo end date: 01 Jan 2020 FrancePublisher:arXiv Funded by:ANR | PHENOME, ANR | FooSIN, ANR | FRIMOUSS +3 projectsANR| PHENOME ,ANR| FooSIN ,ANR| FRIMOUSS ,EC| EOSC-Life ,ANR| METABOHUB ,EC| EPPN2020Authors: Jacob, Daniel; David, Romain; Aubin, Sophie; Gibon, Yves;Jacob, Daniel; David, Romain; Aubin, Sophie; Gibon, Yves;International audience; Making data compliant with the FAIR Data principles (Findable, Accessible, Interoperable, Reusable) is still a challenge for many researchers, who are not sure which criteria should be met first and how. Illustrated from experimental data tables associated with a Design of Experiments, we propose an approach that can serve as a model for a research data management that allows researchers to disseminate their data by satisfying the main FAIR criteria without insurmountable efforts. More importantly, this approach aims to facilitate the FAIRification process by providing researchers with tools to improve their data management practices.
GigaScience arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7736789Data sources: PubMed CentralHAL Descartes; Mémoires en Sciences de l'Information et de la Communication; Hal-DiderotArticle . 2020License: CC BYFull-Text: https://hal.inrae.fr/hal-02883355v4/documenthttps://doi.org/10.48550/arxiv...Article . 2020License: arXiv Non-Exclusive DistributionData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 4 citations 4 popularity Top 10% influence Average impulse Average Powered by BIP!visibility 13visibility views 13 Powered bymore_vert GigaScience arrow_drop_down Europe PubMed CentralArticle . 2020Full-Text: http://europepmc.org/articles/PMC7736789Data sources: PubMed CentralHAL Descartes; Mémoires en Sciences de l'Information et de la Communication; Hal-DiderotArticle . 2020License: CC BYFull-Text: https://hal.inrae.fr/hal-02883355v4/documenthttps://doi.org/10.48550/arxiv...Article . 2020License: arXiv Non-Exclusive DistributionData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2019 Denmark, Italy, Norway, Denmark, Netherlands, Denmark, Spain, France, Netherlands, Sweden, Netherlands EnglishPublisher:Springer Science and Business Media LLC Funded by:EC | OLISSIPO, EC | ELIXIR-EXCELERATE, WTEC| OLISSIPO ,EC| ELIXIR-EXCELERATE ,WTJon Ison; Hans Ienasescu; Piotr Jaroslaw Chmura; Emil Karol Rydza; Hervé Ménager; Matúš Kalaš; Veit Schwämmle; Björn Grüning; Niall Beard; Rodrigo Lopez; Séverine Duvaud; Heinz Stockinger; Bengt Persson; Radka Svobodová Vařeková; Tomáš Raček; Jiří Vondrášek; Hedi Peterson; Ahto Salumets; Inge Jonassen; Rob Hooft; Tommi Nyrönen; Alfonso Valencia; Salvador Capella; Josep Lluís Gelpí; Federico Zambelli; Babis Savakis; Brane Leskošek; Kristoffer Rapacki; Christophe Blanchet; Rafael C. Jimenez; Arlindo L. Oliveira; Gert Vriend; Olivier Collin; Jacques van Helden; Peter Løngreen; Søren Brunak;Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue ( https://bio.tools ) of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information. Contains fulltext : 208582.pdf (Publisher’s version ) (Open Access)
NARCIS arrow_drop_down Genome BiologyArticle . 2019Full-Text: http://europepmc.org/articles/PMC6691543Data sources: PubMed CentralRadboud Repository; Genome Biology; Archivio Istituzionale della Ricerca dell'Università degli Studi di MilanoOther literature type . Article . 2019 . Peer-reviewedLicense: CC BYDiposit Digital de la Universitat de Barcelona; Recolector de Ciencia Abierta, RECOLECTAArticle . 2019License: CC BYOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyCopenhagen University Research Information SystemArticle . 2019Data sources: Copenhagen University Research Information SystemUniversity of Southern Denmark Research OutputArticle . 2019Data sources: University of Southern Denmark Research OutputBergen Open Research Archive - UiBArticle . 2019 . Peer-reviewedLicense: CC BYData sources: Bergen Open Research Archive - UiBadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 34 citations 34 popularity Top 1% influence Top 10% impulse Top 10% Powered by BIP!visibility 56visibility views 56 download downloads 103 Powered bymore_vert NARCIS arrow_drop_down Genome BiologyArticle . 2019Full-Text: http://europepmc.org/articles/PMC6691543Data sources: PubMed CentralRadboud Repository; Genome Biology; Archivio Istituzionale della Ricerca dell'Università degli Studi di MilanoOther literature type . Article . 2019 . Peer-reviewedLicense: CC BYDiposit Digital de la Universitat de Barcelona; Recolector de Ciencia Abierta, RECOLECTAArticle . 2019License: CC BYOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyCopenhagen University Research Information SystemArticle . 2019Data sources: Copenhagen University Research Information SystemUniversity of Southern Denmark Research OutputArticle . 2019Data sources: University of Southern Denmark Research OutputBergen Open Research Archive - UiBArticle . 2019 . Peer-reviewedLicense: CC BYData sources: Bergen Open Research Archive - UiBadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint , Other literature type 2019 France, Netherlands, Belgium, United States, Luxembourg, France, United States, Spain, DenmarkPublisher:Springer Science and Business Media LLC Funded by:NIH | Unraveling the mammalian ..., EC | SysMedPDNIH| Unraveling the mammalian secretory pathway through systems biology and algorithm development ,EC| SysMedPDLaurent Heirendt; Sylvain Arreckx; Thomas Pfau; Sebastián N. Mendoza; Anne Richelle; Almut Heinken; Hulda S. Haraldsdóttir; Jacek Wachowiak; Sarah M. Keating; Vanja Vlasov; Stefania Magnusdottir; Chiam Yu Ng; German Preciat; Alise Žagare; Siu Hung Joshua Chan; Maike K. Aurich; Catherine M. Clancy; Jennifer Modamio; John T. Sauls; Alberto Noronha; Aarash Bordbar; Benjamin Cousins; Diana C. El Assal; Luis Vitores Valcárcel; Iñigo Apaolaza; Susan Ghaderi; Masoud Ahookhosh; Marouen Ben Guebila; Andrejs Kostromins; Nicolas Sompairac; Hoai M. Le; Ding Ma; Yuekai Sun; Lin Wang; James T. Yurkovich; Miguel A.P. Oliveira; Phan Tu Vuong; Lemmer P. El Assal; Inna Kuperstein; Andrei Zinovyev; H. Scott Hinton; William A. Bryant; Francisco J. Aragón Artacho; Francisco J. Planes; Egils Stalidzans; Alejandro Maass; Santosh Vempala; Michael Hucka; Michael A. Saunders; Costas D. Maranas; Nathan E. Lewis; Thomas Sauter; Bernhard O. Palsson; Ines Thiele; Ronan M. T. Fleming;pmid: 30787451
pmc: PMC6635304
Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental molecular systems biology data and quantitative prediction of physicochemically and biochemically feasible phenotypic states. The COBRA Toolbox is a comprehensive desktop software suite of interoperable COBRA methods. It has found widespread application in biology, biomedicine, and biotechnology because its functions can be flexibly combined to implement tailored COBRA protocols for any biochemical network. This protocol is an update to the COBRA Toolbox v.1.0 and v.2.0. Version 3.0 includes new methods for quality-controlled reconstruction, modeling, topological analysis, strain and experimental design, and network visualization, as well as network integration of chemoinformatic, metabolomic, transcriptomic, proteomic, and thermochemical data. New multi-lingual code integration also enables an expansion in COBRA application scope via high-precision, high-performance, and nonlinear numerical optimization solvers for multi-scale, multi-cellular, and reaction kinetic modeling, respectively. This protocol provides an overview of all these new features and can be adapted to generate and analyze constraint-based models in a wide variety of scenarios. The COBRA Toolbox v.3.0 provides an unparalleled depth of COBRA methods. This study was funded by the National Centre of Excellence in Research (NCER) on Parkinson’s disease, the U.S. Department of Energy, Offices of Advanced Scientific Computing Research and the Biological and Environmental Research as part of the Scientific Discovery Through Advanced Computing program, grant no. DE-SC0010429. This project also received funding from the European Union’s HORIZON 2020 Research and Innovation Programme under grant agreement no. 668738 and the Luxembourg National Research Fund (FNR) ATTRACT program (FNR/A12/01) and OPEN (FNR/O16/11402054) grants. N.E.L. was supported by NIGMS (R35 GM119850) and the Novo Nordisk Foundation (NNF10CC1016517). M.A.P.O. was supported by the Luxembourg National Research Fund (FNR) grant AFR/6669348. A.R. was supported by the Lilly Innovation Fellows Award. F.J.P. was supported by the Minister of Economy and Competitiveness of Spain (BIO2016-77998-R) and the ELKARTEK Programme of the Basque Government (KK-2016/00026). I.A. was supported by a Basque Government predoctoral grant (PRE_2016_2_0044). B.Ø.P. was supported by the Novo Nordisk Foundation through the Center for Biosustainability at the Technical University of Denmark (NNF10CC1016517).
Recolector de Cienci... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTAArticle . 2019Full-Text: https://doi.org/10.1038/s41596-018-0098-2Data sources: Recolector de Ciencia Abierta, RECOLECTAOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyeScholarship - University of CaliforniaArticle . 2018Data sources: eScholarship - University of CaliforniaRepositorio Institucional de la Universidad de AlicanteArticle . 2019Data sources: Repositorio Institucional de la Universidad de AlicanteeScholarship - University of CaliforniaArticle . 2019Data sources: eScholarship - University of CaliforniaOpen Repository and Bibliography - LuxembourgArticle . 2019Data sources: Open Repository and Bibliography - Luxembourghttps://doi.org/10.48550/arxiv...Article . 2017License: arXiv Non-Exclusive DistributionData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen bronze 773 citations 773 popularity Top 0.01% influence Top 1% impulse Top 0.01% Powered by BIP!more_vert Recolector de Cienci... arrow_drop_down Recolector de Ciencia Abierta, RECOLECTAArticle . 2019Full-Text: https://doi.org/10.1038/s41596-018-0098-2Data sources: Recolector de Ciencia Abierta, RECOLECTAOnline Research Database In TechnologyArticle . 2019Data sources: Online Research Database In TechnologyeScholarship - University of CaliforniaArticle . 2018Data sources: eScholarship - University of CaliforniaRepositorio Institucional de la Universidad de AlicanteArticle . 2019Data sources: Repositorio Institucional de la Universidad de AlicanteeScholarship - University of CaliforniaArticle . 2019Data sources: eScholarship - University of CaliforniaOpen Repository and Bibliography - LuxembourgArticle . 2019Data sources: Open Repository and Bibliography - Luxembourghttps://doi.org/10.48550/arxiv...Article . 2017License: arXiv Non-Exclusive DistributionData sources: Dataciteadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Preprint 2018 FrancePublisher:Cold Spring Harbor Laboratory Funded by:EC | VIROGENESIS, ANR | INCEPTIONEC| VIROGENESIS ,ANR| INCEPTIONAuthors: Sohta A. Ishikawa; Anna Zhukova; Wataru Iwasaki; Olivier Gascuel;Sohta A. Ishikawa; Anna Zhukova; Wataru Iwasaki; Olivier Gascuel;AbstractThe reconstruction of ancestral scenarios is widely used to study the evolution of characters along phylogenetic trees. One commonly uses the marginal posterior probabilities of the character states, or the joint reconstruction of the most likely scenario. However, marginal reconstructions provide users with state probabilities, which are difficult to interpret and visualize, whereas joint reconstructions select a unique state for every tree node and thus do not reflect the uncertainty of inferences.We propose a simple and fast approach, which is in between these two extremes. We use decision-theory concepts (namely, the Brier score) to associate each node in the tree to a set of likely states. A unique state is predicted in tree regions with low uncertainty, whereas several states are predicted in uncertain regions, typically around the tree root. To visualize the results, we cluster the neighboring nodes associated with the same states and use graph visualization tools. The method is implemented in the PastML program and web server.The results on simulated data demonstrate the accuracy and robustness of the approach. PastML was applied to the phylogeography of Dengue serotype 2 (DENV2), and the evolution of drug resistances in a large HIV data set. These analyses took a few minutes and provided convincing results. PastML retrieved the main transmission routes of human DENV2 and showed the uncertainty of the human-sylvatic DENV2 geographic origin. With HIV, the results show that resistance mutations mostly emerge independently under treatment pressure, but resistance clusters are found, corresponding to transmissions among untreated patients.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6735705Data sources: PubMed CentralbioRxivPreprint . 2018Molecular Biology and EvolutionArticle . 2019 . Peer-reviewedLicense: CC BY NCData sources: CrossrefHAL Descartes; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2019License: CC BY NCadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/379529&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euAccess RoutesGreen hybrid 144 citations 144 popularity Top 1% influence Top 10% impulse Top 1% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2019Full-Text: http://europepmc.org/articles/PMC6735705Data sources: PubMed CentralbioRxivPreprint . 2018Molecular Biology and EvolutionArticle . 2019 . Peer-reviewedLicense: CC BY NCData sources: CrossrefHAL Descartes; Mémoires en Sciences de l'Information et de la CommunicationArticle . 2019License: CC BY NCadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.1101/379529&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2018 France EnglishPublisher:Oxford University Press (OUP) Funded by:EC | PhenoMeNal, WT | Institutional Strategic S...EC| PhenoMeNal ,WT| Institutional Strategic Support Fund Phase2 FY2014/16Cottret, Ludovic; Frainay, Clément; Chazalviel, Maxime; Cabanettes, Floréal; Gloaguen, Yoann; Camenen, Etienne; Merlet, Benjamin; Heux, Stéphanie; Portais, Jean-Charles; Poupin, Nathalie; Vinson, Florence; Jourdan, Fabien;pmc: PMC6030842
pmid: 29718355
Abstract Metabolism of an organism is composed of hundreds to thousands of interconnected biochemical reactions responding to environmental or genetic constraints. This metabolic network provides a rich knowledge to contextualize omics data and to elaborate hypotheses on metabolic modulations. Nevertheless, performing this kind of integrative analysis is challenging for end users with not sufficiently advanced computer skills since it requires the use of various tools and web servers. MetExplore offers an all-in-one online solution composed of interactive tools for metabolic network curation, network exploration and omics data analysis. In particular, it is possible to curate and annotate metabolic networks in a collaborative environment. The network exploration is also facilitated in MetExplore by a system of interactive tables connected to a powerful network visualization module. Finally, the contextualization of metabolic elements in the network and the calculation of over-representation statistics make it possible to interpret any kind of omics data. MetExplore is a sustainable project maintained since 2010 freely available at https://metexplore.toulouse.inra.fr/metexplore2/.
Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2018Full-Text: http://europepmc.org/articles/PMC6030842Data sources: PubMed CentralInstitutional Repository for Molecular Medicine (MDC)Article . 2018 . Peer-reviewedData sources: Institutional Repository for Molecular Medicine (MDC)HAL Descartes; Mémoires en Sciences de l'Information et de la Communication; HAL-INSA ToulouseArticle . 2018License: CC BY NCFull-Text: https://hal.science/hal-01886470/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen 49 citations 49 popularity Top 10% influence Top 10% impulse Top 1% Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down Europe PubMed CentralArticle . 2018Full-Text: http://europepmc.org/articles/PMC6030842Data sources: PubMed CentralInstitutional Repository for Molecular Medicine (MDC)Article . 2018 . Peer-reviewedData sources: Institutional Repository for Molecular Medicine (MDC)HAL Descartes; Mémoires en Sciences de l'Information et de la Communication; HAL-INSA ToulouseArticle . 2018License: CC BY NCFull-Text: https://hal.science/hal-01886470/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=PMC6030842&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article 2017 France, France, Italy, United KingdomPublisher:American Chemical Society (ACS) Funded by:EC | PhenoMeNal, ANR | METABOHUB, UKRI | MICA: UK MEDical BIOinfor... +5 projectsEC| PhenoMeNal ,ANR| METABOHUB ,UKRI| MICA: UK MEDical BIOinformatics partnership - aggregation, integration, visualisation and analysis of large, complex data (UK MED-BIO). ,UKRI| Open source pipelines for integrated metabolomics analysis by NMR and mass spectrometry ,UKRI| Open source pipelines for integrated metabolomics analysis by NMR and mass spectrometry ,UKRI| Sharing of metabolomics data and their analyses as Galaxy workflows through a UK-China collaboration ,NSERC ,CIHRSchober, D; Jacob, D; Wilson, M; Cruz, JA; Marcu, A; Grant, JR; Moing, A; Deborde, C; De Figueiredo, LF; Haug, K; Rocca-Serra, P; Easton, J; Ebbels, TMD; Hao, J; Ludwig, C; Günther, UL; Rosato, A; Klein, MS; Lewis, IA; Luchinat, C; Jones, AR; Grauslys, A; Larralde, M; Yokochi, M; Kobayashi, N; Porzel, A; Griffin, JL; Viant, MR; Wishart, DS; Steinbeck, C; Salek, RM; Neumann, S;UMR BFP - Equipe Métabolisme; International audience; NMR is a widely used analytical technique with a growing number of repositories available. As a result, demands for a vendor-agnostic, open data format for long-term archiving of NMR data have emerged with the aim to ease and encourage sharing, comparison and reuse of NMR data. Here we present nmrML, an open XML-based exchange and storage format for NMR spectral data. The nmrML format is intended to be fully compatible with existing NMR data for chemical, biochemical and metabolomics experiments. nmrML can capture raw NMR data, spectral data acquisition parameters and, where available, spectral metadata such as chemical structures associated with spectral assignments. The nmrML format is compatible with pure-compound NMR data for reference spectral libraries as well as NMR data from complex bio-mixtures i.e. metabolomics experiments. To facilitate format conversions, we provide nmrML converters for Bruker and Agilent/Varian vendor formats. In addition, easy-to-use web-based spectral viewing, processing and spectral assignment tools that read and write nmrML have been developed. Software libraries and web services for data validation are available for tool developers and end-users. The nmrML format has already been adopted for capturing and disseminating NMR data for small molecules by several open source data processing tools and metabolomics reference spectral libraries, e.g. serving as storage format for the MetaboLights data repository. The nmrML open access data standard has been endorsed by the Metabolomics Standards Initiative (MSI) and we here encourage user participation and feedback to increase usability and make it a successful standard.
Analytical Chemistry arrow_drop_down Spiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital RepositoryOxford University Research Archive; Flore (Florence Research Repository); Analytical ChemistryOther literature type . Article . 2019 . 2017 . 2018 . Peer-reviewedadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess Routeshybrid 47 citations 47 popularity Top 1% influence Top 10% impulse Top 10% Powered by BIP!visibility 14visibility views 14 download downloads 80 Powered bymore_vert Analytical Chemistry arrow_drop_down Spiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital RepositoryOxford University Research Archive; Flore (Florence Research Repository); Analytical ChemistryOther literature type . Article . 2019 . 2017 . 2018 . Peer-reviewedadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Other literature type , Conference object , Article 2017 France Funded by:EC | OpenMinTeDEC| OpenMinTeDAuthors: Chaix, Estelle; Deléger, Louise; Bossy, Robert; Nédellec, Claire;Chaix, Estelle; Deléger, Louise; Bossy, Robert; Nédellec, Claire;pmid: 30910089
pmc: PMC6460834
Introduction Information on food microbial biodiversity is scattered across millions of scientific papers (2 million references in the PubMed bibliographic database in 2017). It is impossible to manually achieve an exhaustive analysis of these documents. Text-mining and knowledge engineering methods can assist the researcher in finding relevant information. Material & MethodsWe propose to study bacterial biodiversity using text-mining tools from the Alvis platform. First, we analyzed terms that designate Microbial and Habitat entities in text. Microorganism names were predicted using the NCBI taxonomy. Habitat entities were detected using the syntactic structure of the terms and the OntoBiotope ontology. This ontology has been specifically enriched for the recognition of food terms in text. In a second time, we predicted links between microorganisms and their habitats (labeled “Lives_in” relationships) using pattern and machine-learning based methods. The results of text-mining predictions are indexed and presented in a semantic search engine. Result The AlvisIR search engine for microbe literature gives online access to 1.2 million PubMed abstracts in 2015, among which 13% are specific to food. This tool makes it possible to use text-mining results to search for information on bacterial biodiversity. It covers all types of microbial habitats to help understand the origin of microbial presence in food. Significance This work presents the first semantic search engine dedicated to better understand microbial food biodiversity from text.
Europe PubMed Centra... arrow_drop_down HAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotConference object . 2017Mémoires en Sciences de l'Information et de la CommunicationConference object . 2017Full-Text: https://hal.science/hal-01602552/documentHAL Descartes; Mémoires en Sciences de l'Information et de la Communication; Hal-DiderotArticle . 2019License: CC BYFull-Text: https://hal.inrae.fr/hal-02628265/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen 10 citations 10 popularity Top 10% influence Average impulse Average Powered by BIP!more_vert Europe PubMed Centra... arrow_drop_down HAL - UPEC / UPEM; HAL-Pasteur; HAL-Inserm; Hal-DiderotConference object . 2017Mémoires en Sciences de l'Information et de la CommunicationConference object . 2017Full-Text: https://hal.science/hal-01602552/documentHAL Descartes; Mémoires en Sciences de l'Information et de la Communication; Hal-DiderotArticle . 2019License: CC BYFull-Text: https://hal.inrae.fr/hal-02628265/documentadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.eudescription Publicationkeyboard_double_arrow_right Article , Other literature type 2017 Netherlands, Netherlands, Italy, United Kingdom, United Kingdom, Netherlands, Netherlands, France, United Kingdom, Spain EnglishPublisher:HAL CCSD Funded by:EC | PhenoMeNalEC| PhenoMeNalvan Rijswijk, M; van Rijswijk, M; Beirnaert, C; Beirnaert, C; Caron, C; Cascante, M; Dominguez, V; Dunn, WB; Ebbels, TMD; Giacomoni, F; Gonzalez-Beltran, A; Hankemeier, T; Haug, K; Haug, K; Izquierdo-Garcia, JL; Jimenez, RC; Jimenez, RC; Jourdan, F; Kale, N; Klapa, MI; Kohlbacher, O; Koort, K; Kultima, K; Le Corguillé, G; Moreno, P; Moschonas, NK; Moschonas, NK; Neumann, S; O'Donovan, C; Reczko, M; Rocca-Serra, P; Rosato, A; Rosato, A; Rosato, A; Salek, RM; Salek, RM; Sansone, S-A; Satagopam, V; Schober, D; Shimmo, R; Spicer, RA; Spicer, RA; Spjuth, O; Spjuth, O; Spjuth, O; Thévenot, EA; Thévenot, EA; Viant, MR; Weber, RJM; Willighagen, EL; Willighagen, EL; Zanetti, G; Steinbeck, C; Steinbeck, C;Metabolomics, the youngest of the major omics technologies, is supported by an active community of researchers and infrastructure developers across Europe. To coordinate and focus efforts around infrastructure building for metabolomics within Europe, a workshop on the "Future of metabolomics in ELIXIR" was organised at Frankfurt Airport in Germany. This one-day strategic workshop involved representatives of ELIXIR Nodes, members of the PhenoMeNal consortium developing an e-infrastructure that supports workflow-based metabolomics analysis pipelines, and experts from the international metabolomics community. The workshop established metabolite identification as the critical area, where a maximal impact of computational metabolomics and data management on other fields could be achieved. In particular, the existing four ELIXIR Use Cases, where the metabolomics community - both industry and academia - would benefit most, and which could be exhaustively mapped onto the current five ELIXIR Platforms were discussed. This opinion article is a call for support for a new ELIXIR metabolomics Use Case, which aligns with and complements the existing and planned ELIXIR Platforms and Use Cases. The meeting was funded by PhenoMeNal, European Commission's Horizon2020 programme, grant agreement number 654241 Sí
HAL - UPEC / UPEM; H... arrow_drop_down Europe PubMed CentralArticle . 2017 . Peer-reviewedFull-Text: http://europepmc.org/articles/PMC5627583Data sources: PubMed CentralRecolector de Ciencia Abierta, RECOLECTAArticle . 2017Data sources: Recolector de Ciencia Abierta, RECOLECTAFlore (Florence Research Repository)Article . 2017Data sources: Flore (Florence Research Repository)Oxford University Research Archive; F1000ResearchOther literature type . Article . 2017 . 2018 . Peer-reviewedLicense: CC BYSpiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital RepositorySpiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital Repositoryadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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For further information contact us at helpdesk@openaire.euAccess RoutesGreen gold 25 citations 25 popularity Top 10% influence Average impulse Top 10% Powered by BIP!visibility 34visibility views 34 download downloads 65 Powered bymore_vert HAL - UPEC / UPEM; H... arrow_drop_down Europe PubMed CentralArticle . 2017 . Peer-reviewedFull-Text: http://europepmc.org/articles/PMC5627583Data sources: PubMed CentralRecolector de Ciencia Abierta, RECOLECTAArticle . 2017Data sources: Recolector de Ciencia Abierta, RECOLECTAFlore (Florence Research Repository)Article . 2017Data sources: Flore (Florence Research Repository)Oxford University Research Archive; F1000ResearchOther literature type . Article . 2017 . 2018 . Peer-reviewedLicense: CC BYSpiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital RepositorySpiral - Imperial College Digital RepositoryArticle . 2017Data sources: Spiral - Imperial College Digital Repositoryadd ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
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