المؤلفون: Pelayo, Sylvie, Kaipio, Johanna

المساهمون: CHU Lille, Université de Lille, METRICS : Evaluation des technologies de santé et des pratiques médicales - ULR 2694, Aalto University

مصطلحات موضوعية: Mesh:Medical Informatics/organization & administration, Mesh:User-Computer Interface, Mesh:Alert Fatigue, Mesh:Health Personnel, Mesh:Electronic Health Records/organization & administration, Mesh:Health Information Interoperability, Mesh:Humans

الوصف: OBJECTIVE: To summarize significant research contributions published in 2017 on Human Factors and Organizational Issues (HFOI) in medical informatics. METHODS: An extensive search using PubMed/Medline and Web of Science® RESULTS: The five best papers offer a glimpse of the quality and breadth of the work being conducted in the HFOI community. CONCLUSIONS: The selection of the HFOI section of the 2018 IMIA Yearbook highlights a growing number of high quality studies. There are especially more studies interested in testing Human Factors and Ergonomics methods and demonstrating the benefits. ; 27

وصف الملف: application/octet-stream; application/rdf+xml; charset=utf-8; application/pdf

العلاقة: Yearbook of medical informatics; Yearb Med Inform; http://hdl.handle.net/20.500.12210/17090.2Test

الإتاحة: https://doi.org/20.500.12210/17090.2Test
https://hdl.handle.net/20.500.12210/17090.2Test

المؤلفون: Volant, Stevenn, Lechat, Pierre, Woringer, Perrine, Motreff, Laurence, Campagne, Pascal, Malabat, Christophe, Kennedy, Sean, Ghozlane, Amine

المساهمون: Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur Paris (IP)-Centre National de la Recherche Scientifique (CNRS), Pôle Biomics (C2RT), Centre de Ressources et de Recherche Technologique - Center for Technological Resources and Research (C2RT), Institut Pasteur Paris (IP)-Institut Pasteur Paris (IP), Institut Pasteur

المصدر: ISSN: 1471-2105 ; BMC Bioinformatics ; https://pasteur.hal.science/pasteur-02951458Test ; BMC Bioinformatics, 2020, 21 (1), pp.345. ⟨10.1186/s12859-020-03666-4⟩.

مصطلحات موضوعية: Differential analysis, Metagenomics, Visualization, Web application, MESH: Body Fluids, MESH: Child, Preschool, MESH: Metagenome, MESH: Metagenomics, MESH: Microbiota, MESH: RNA, Ribosomal, 16S, MESH: Software, MESH: Statistics as Topic, MESH: User-Computer Interface, MESH: Workflow, MESH: Classification, MESH: Feces, MESH: Humans, MESH: Internet, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology

الوصف: International audience ; Comparing the composition of microbial communities among groups of interest (e.g., patients vs healthy individuals) is a central aspect in microbiome research. It typically involves sequencing, data processing, statistical analysis and graphical display. Such an analysis is normally obtained by using a set of different applications that require specific expertise for installation, data processing and in some cases, programming skills.

العلاقة: info:eu-repo/semantics/altIdentifier/pmid/32778056; pasteur-02951458; https://pasteur.hal.science/pasteur-02951458Test; https://pasteur.hal.science/pasteur-02951458/documentTest; https://pasteur.hal.science/pasteur-02951458/file/s12859-020-03666-4.pdfTest; PUBMED: 32778056; PUBMEDCENTRAL: PMC7430814

الإتاحة: https://doi.org/10.1186/s12859-020-03666-4Test
https://pasteur.hal.science/pasteur-02951458Test
https://pasteur.hal.science/pasteur-02951458/documentTest
https://pasteur.hal.science/pasteur-02951458/file/s12859-020-03666-4.pdfTest

المؤلفون: Marcilly, Romaric, Douze, Laura, Bousquet, Cédric, Pelayo, Sylvia

المساهمون: Centre Hospitalier Régional Universitaire CHU Lille (CHRU Lille), Evaluation des technologies de santé et des pratiques médicales - ULR 2694 (METRICS), Université de Lille-Centre Hospitalier Régional Universitaire CHU Lille (CHRU Lille), Centre d'Investigation Clinique - Innovation Technologique de Lille - CIC 1403 - CIC 9301 (CIC Lille), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lille-Centre Hospitalier Régional Universitaire CHU Lille (CHRU Lille), Laboratoire d'Informatique Médicale et Ingénierie des Connaissances en e-Santé (LIMICS), Université Paris 13 (UP13)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)

المصدر: ISSN: 0926-9630.

مصطلحات موضوعية: Cognitive work analysis, Information retrieval, MedDRA, Modelling, pharmacovigilance, MESH: Adverse Drug Reaction Reporting Systems, MESH: Drug-Related Side Effects and Adverse Reactions, MESH: Humans, MESH: Information Storage and Retrieval, MESH: Pharmacovigilance, MESH: Specialization, MESH: User-Computer Interface, MESH: Vocabulary, Controlled, [INFO]Computer Science [cs], [INFO.INFO-IR]Computer Science [cs]/Information Retrieval [cs.IR], [SDV.SP.MED]Life Sciences [q-bio]/Pharmaceutical sciences/Medication, [SDV.SP.PHARMA]Life Sciences [q-bio]/Pharmaceutical sciences/Pharmacology

الوصف: International audience ; In the information retrieval task, searching and choosing keywords to form the query is crucial. The present study analyzes and describes the keywords' search strategy into a thesaurus in the field of pharmacovigilance. Two ergonomics experts shadowed 22 pharmacovigilance specialists during their daily work. They focus on the strategies for searching and choosing MedDRA terms to build pharmacovigilance queries. Interviews of four pharmacovigilance specialists completed the observations. Results highlight that, for unusual or complex searches, pharmacovigilance specialists proceed iteratively in three main phases: (i) preparation of a list of terms and of evaluation criteria, (ii) exploration of the MedDRA hierarchy and choice of a term, and (iii) evaluation of the results against the criteria. Overall, the search and the choice of keywords within a thesaurus shares similarity with the information retrieval task and is closely interwoven with the query building process. Based on the results, the paper proposes design specifications for new interfaces supporting the identification of MedDRA terms so that pharmacovigilance reports searches achieve a good level of expressiveness.

العلاقة: info:eu-repo/semantics/altIdentifier/pmid/30741213; hal-04037023; https://hal.science/hal-04037023Test; https://hal.science/hal-04037023/documentTest; https://hal.science/hal-04037023/file/Modeling%20Keyword%20Search%20Strategy%20Analysis%20of%20Pharmacovigilance%20Specialists%27%20Search%20of%20MedDRA%20Terms.pdfTest; PUBMED: 30741213

الإتاحة: https://doi.org/10.3233/978-1-61499-951-5-298Test
https://hal.science/hal-04037023Test
https://hal.science/hal-04037023/documentTest
https://hal.science/hal-04037023/file/Modeling%20Keyword%20Search%20Strategy%20Analysis%20of%20Pharmacovigilance%20Specialists%27%20Search%20of%20MedDRA%20Terms.pdfTest

المؤلفون: Chevenet, François, Castel, Guillaume, Jousselin, Emmanuelle, Gascuel, Olivier

المساهمون: Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Du gène à l'écosystème (MIVEGEC-GeneSys), Pathogènes, Environnement, Santé Humaine (EPATH), Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD France-Sud )-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD France-Sud )-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD France-Sud )-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD France-Sud ), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD France-Sud )-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Bioinformatique évolutive - Evolutionary Bioinformatics, Institut Pasteur Paris (IP)-Centre National de la Recherche Scientifique (CNRS), This work was supported by The PALADIN project (GC), publicly funded through the French National Research Agency under the “Investissements d’avenir” program with the reference ANR-10-LABX-04-01 Labex CEMEB, and coordinated by the University of Montpellier, by the EU-H2020 Virogenesis project (grant number 634650, OG), and by the INCEPTION project (PIA/ANR-16-CONV-0005, OG)., We would like to thank Stéphane Guindon for providing insightful ideas on software and manuscript., ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), European Project: 634650,H2020,H2020-PHC-2014-two-stage,VIROGENESIS(2015)

المصدر: ISSN: 1471-2148 ; BMC Evolutionary Biology ; https://pasteur.hal.science/pasteur-02404219Test ; BMC Evolutionary Biology, 2019, 19 (1), pp.163. ⟨10.1186/s12862-019-1490-4⟩.

مصطلحات موضوعية: Phylogeny, Evolutionary scenario, Ancestral character states, MESH: Albania/epidemiology, MESH: Dengue/epidemiology, MESH: Phylogeny, MESH: Phylogeography, MESH: Software, MESH: User-Computer Interface, MESH: Dengue Virus/genetics, MESH: HIV Infections/epidemiology, MESH: HIV-1/genetics, MESH: Humans, MESH: Phenotype, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy

الوصف: International audience ; Background: Ancestral character states computed from the combination of phylogenetic trees with extrinsic traits are used to decipher evolutionary scenarios in various research fields such as phylogeography, epidemiology, and ecology. Despite the existence of powerful methods and software in ancestral character state inference, difficulties may arise when interpreting the outputs of such inferences. The growing complexity of data (trees, annotations), the diversity of optimization criteria for computing trees and ancestral character states, the combinatorial explosion of potential evolutionary scenarios if some ancestral characters states do not stand out clearly from others, requires the design of new methods to explore associations of phylogenetic trees with extrinsic traits, to ease the visualization and interpretation of evolutionary scenarios. Result: We developed PastView, a user-friendly interface that includes numerical and graphical features to help users to import and/or compute ancestral character states from discrete variables and extract ancestral scenarios as sets of successive transitions of character states from the tree root to its leaves. PastView provides summarized views such as transition maps and integrates comparative tools to highlight agreements or discrepancies between methods of ancestral annotations inference. Conclusion: The main contribution of PastView is to assemble known numerical and graphical methods into a multi-maps graphical user interface dedicated to the computing, searching and viewing of evolutionary scenarios based on phylogenetic trees and ancestral character states. PastView is available publicly as a standalone software on www.pastview.org.

العلاقة: info:eu-repo/semantics/altIdentifier/pmid/31375065; info:eu-repo/grantAgreement//634650/EU/Virus discovery and epidemic tracing from high throughput metagenomic sequencing/VIROGENESIS; pasteur-02404219; https://pasteur.hal.science/pasteur-02404219Test; https://pasteur.hal.science/pasteur-02404219/documentTest; https://pasteur.hal.science/pasteur-02404219/file/document.pdfTest; IRD: fdi:010076565; PRODINRA: 481546; PUBMED: 31375065; PUBMEDCENTRAL: PMC6679476; WOS: 000479274100002

الإتاحة: https://doi.org/10.1186/s12862-019-1490-4Test
https://pasteur.hal.science/pasteur-02404219Test
https://pasteur.hal.science/pasteur-02404219/documentTest
https://pasteur.hal.science/pasteur-02404219/file/document.pdfTest

المؤلفون: Dufresne, Yoann, Lejzerowicz, Franck, Perret-Gentil, Laure Apotheloz, Pawlowski, Jan, Cordier, Tristan

المساهمون: Université de Genève = University of Geneva (UNIGE), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur Paris (IP)-Centre National de la Recherche Scientifique (CNRS), University of California San Diego (UC San Diego), University of California (UC), This work was supported by the Swiss National Science Foundation grant 31003A \ _159709, and the Swiss Network of International Studies project “Monitoring marine biodiversity in the genomic era”.

المصدر: ISSN: 1471-2105 ; BMC Bioinformatics ; https://pasteur.hal.science/pasteur-03263390Test ; BMC Bioinformatics, 2019, 20 (1), pp.88. ⟨10.1186/s12859-019-2663-2⟩.

مصطلحات موضوعية: Amplicon sequencing, High-throughput sequencing, Molecular ecology, Pipeline, Reproducibility, eDNA metabarcoding, MESH: Algorithms, MESH: DNA Barcoding, Taxonomic, MESH: Internet, MESH: Reproducibility of Results, MESH: Software, MESH: User-Computer Interface, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]

الوصف: International audience ; High-throughput amplicon sequencing of environmental DNA (eDNA metabarcoding) has become a routine tool for biodiversity survey and ecological studies. By including sample-specific tags in the primers prior PCR amplification, it is possible to multiplex hundreds of samples in a single sequencing run. The analysis of millions of sequences spread into hundreds to thousands of samples prompts for efficient, automated yet flexible analysis pipelines. Various algorithms and software have been developed to perform one or multiple processing steps, such as paired-end reads assembly, chimera filtering, Operational Taxonomic Unit (OTU) clustering and taxonomic assignment. Some of these software are now well established and widely used by scientists as part of their workflow. Wrappers that are capable to process metabarcoding data from raw sequencing data to annotated OTU-to-sample matrix were also developed to facilitate the analysis for non-specialist users. Yet, most of them require basic bioinformatic or command-line knowledge, which can limit the accessibility to such integrative toolkits. Furthermore, for flexibility reasons, these tools have adopted a step-by-step approach, which can prevent an easy automation of the workflow, and hence hamper the analysis reproducibility.

العلاقة: info:eu-repo/semantics/altIdentifier/pmid/30782112; pasteur-03263390; https://pasteur.hal.science/pasteur-03263390Test; https://pasteur.hal.science/pasteur-03263390/documentTest; https://pasteur.hal.science/pasteur-03263390/file/s12859-019-2663-2.pdfTest; PUBMED: 30782112; PUBMEDCENTRAL: PMC6381720

الإتاحة: https://doi.org/10.1186/s12859-019-2663-2Test
https://pasteur.hal.science/pasteur-03263390Test
https://pasteur.hal.science/pasteur-03263390/documentTest
https://pasteur.hal.science/pasteur-03263390/file/s12859-019-2663-2.pdfTest

المؤلفون: Pelayo, Sylvie, Kaipio, Johanna

المساهمون: Evaluation des technologies de santé et des pratiques médicales - ULR 2694 (METRICS), Université de Lille-Centre Hospitalier Régional Universitaire CHU Lille (CHRU Lille), Aalto University

المصدر: ISSN: 0943-4747.

مصطلحات موضوعية: MESH: Medical Informatics/organization & administration, MESH: User-Computer Interface, MESH: Alert Fatigue, MESH: Health Personnel, MESH: Electronic Health Records/organization & administration, MESH: Health Information Interoperability, MESH: Humans, [SDV]Life Sciences [q-bio]

الوصف: International audience ; OBJECTIVE: To summarize significant research contributions published in 2017 on Human Factors and Organizational Issues (HFOI) in medical informatics.METHODS: An extensive search using PubMed/Medline and Web of Science®RESULTS: The five best papers offer a glimpse of the quality and breadth of the work being conducted in the HFOI community.CONCLUSIONS: The selection of the HFOI section of the 2018 IMIA Yearbook highlights a growing number of high quality studies. There are especially more studies interested in testing Human Factors and Ergonomics methods and demonstrating the benefits.

العلاقة: info:eu-repo/semantics/altIdentifier/pmid/30157509; hal-02535972; https://hal.univ-lille.fr/hal-02535972Test; https://hal.univ-lille.fr/hal-02535972/documentTest; https://hal.univ-lille.fr/hal-02535972/file/s-0038-1667074.pdfTest; PUBMED: 30157509

الإتاحة: https://doi.org/10.1055/s-0038-1667074Test
https://hal.univ-lille.fr/hal-02535972Test
https://hal.univ-lille.fr/hal-02535972/documentTest
https://hal.univ-lille.fr/hal-02535972/file/s-0038-1667074.pdfTest

المؤلفون: Gurwitz, Kim, T, Aron, Shaun, Panji, Sumir, Maslamoney, Suresh, Fernandes, Pedro L., Judge, David P., Ghouila, Amel, Domelevo Entfellner, Jean-Baka, Guerfali, Fatma Z., Saunders, Colleen, Mansour Alzohairy, Ahmed, Salifu, Samson P., Ahmed, Rehab, Cloete, Ruben, Kayondo, Jonathan, Ssemwanga, Deogratius, Mulder, Nicola

المساهمون: University of Cape Town, University of the Witwatersrand Johannesburg (WITS), Instituto Gulbenkian de Ciência Oeiras (IGC), Fundação Calouste Gulbenkian, Independent bioinformatics training specialist, Cambridge, Laboratoire de Transmission, Contrôle et Immunobiologie des Infections - Laboratory of Transmission, Control and Immunobiology of Infection (LR11IPT02), Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), South African National Bioinformatics Institute (SANBI), University of the Western Cape (UWC), Zagazig University, Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Future Univ Sudan, University of Khartoum, Uganda Virus Research Institute, Research reported in this publication was supported by National Human Genome Research Institute (NHGRI) and the Office of the Director (OD),National Institutes of Health under award number U41HG006941, H3ABioNet Consortium’s Education Training and Working Group as members of the H3Africa Consortium

المصدر: ISSN: 1553-734X.

مصطلحات موضوعية: MESH: Africa, MESH: Computational Biology, MESH: Computer-Assisted Instruction, MESH: Databases, Factual, MESH: Humans, MESH: Internet, MESH: User-Computer Interface, [SDV]Life Sciences [q-bio], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]

الوصف: International audience ; Africa is not unique in its need for basic bioinformatics training for individuals from a diverse range of academic backgrounds. However, particular logistical challenges in Africa, most notably access to bioinformatics expertise and internet stability, must be addressed in order to meet this need on the continent. H3ABioNet (www.h3abionet.org), the Pan African Bioin-formatics Network for H3Africa, has therefore developed an innovative, free-of-charge " Introduction to Bioinformatics " course, taking these challenges into account as part of its educational efforts to provide on-site training and develop local expertise inside its network. A multiple-delivery–mode learning model was selected for this 3-month course in order to increase access to (mostly) African, expert bioinformatics trainers. The content of the course was developed to include a range of fundamental bioinformatics topics at the introductory level. For the first iteration of the course (2016), classrooms with a total of 364 enrolled participants were hosted at 20 institutions across 10 African countries. To ensure that classroom success did not depend on stable internet, trainers pre-recorded their lectures , and classrooms downloaded and watched these locally during biweekly contact sessions. The trainers were available via video conferencing to take questions during contact PLOS Computational Biology | https://doi.org/10.1371/journal.pcbiTest.

العلاقة: info:eu-repo/semantics/altIdentifier/pmid/28981516; pasteur-01635368; https://riip.hal.science/pasteur-01635368Test; https://riip.hal.science/pasteur-01635368/documentTest; https://riip.hal.science/pasteur-01635368/file/Designing.pdfTest; PUBMED: 28981516

الإتاحة: https://doi.org/10.1371/journal.pcbi.1005715Test
https://riip.hal.science/pasteur-01635368Test
https://riip.hal.science/pasteur-01635368/documentTest
https://riip.hal.science/pasteur-01635368/file/Designing.pdfTest

المؤلفون: Lamy, Jean-Baptiste, Duclos, Catherine, Hamek, Saliha, Beuscart-Zéphir, Marie-Catherine, Kerdelhué, Gaetan, Darmoni, Stefan, Favre, Madeleine, Falcoff, Hector, Simon, Christian, Pereira, Suzanne, Serrot, Elisabeth, Mitouard, Thierry, Hardouin, Etienne, Kergosien, Yannick, Venot, Alain

المساهمون: Laboratoire d'Informatique Médicale et de BIOinformatique (LIM&BIO), Université Paris 13 (UP13)

المصدر: ISSN: 0926-9630.

مصطلحات موضوعية: MESH: Computer Graphics, MESH: Drug Information Services, MESH: Electronic Health Records, MESH: France, MESH: Information Storage and Retrieval, MESH: Practice Guidelines as Topic, MESH: Search Engine, MESH: Terminology as Topic, MESH: User-Computer Interface, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie

الوصف: International audience ; Practicing physicians have limited time for consulting medical knowledge and records. We have previously shown that using icons instead of text to present drug monographs may allow contraindications and adverse effects to be identified more rapidly and more accurately. These findings were based on the use of an iconic language designed for drug knowledge, providing icons for many medical concepts, including diseases, antecedents, drug classes and tests. In this paper, we describe a new project aimed at extending this iconic language, and exploring the possible applications of these icons in medicine. Based on evaluators' comments, focus groups of physicians and opinions of academic, industrial and associative partners, we propose iconic applications related to patient records, for example summarizing patient conditions, searching for specific clinical documents and helping to code structured data. Other applications involve the presentation of clinical practice guidelines and improving the interface of medical search engines. These new applications could use the same iconic language that was designed for drug knowledge, with a few additional items that respect the logic of the language.

العلاقة: info:eu-repo/semantics/altIdentifier/pmid/20841669; hal-03810547; https://hal.archives-ouvertes.fr/hal-03810547Test; PUBMED: 20841669

الإتاحة: https://hal.archives-ouvertes.fr/hal-03810547Test

المؤلفون: Yasini, Mobin, Duclos, Catherine, Lamy, Jean-Baptiste, Venot, Alain

المساهمون: Laboratoire d'Informatique Médicale et de BIOinformatique (LIM&BIO), Université Paris 13 (UP13)

المصدر: ISSN: 0926-9630.

مصطلحات موضوعية: MESH: Access to Information, MESH: Clinical Laboratory Information Systems, MESH: Software, MESH: Software Design, MESH: User-Computer Interface, MESH: Computer Simulation, MESH: Decision Making, Computer-Assisted, MESH: Decision Support Systems, Clinical, MESH: Evidence-Based Medicine, MESH: Guidelines as Topic, MESH: Humans, MESH: Medical Order Entry Systems, MESH: Practice Patterns, Physicians', [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie

الوصف: International audience ; Laboratory tests are not always prescribed appropriately. Guidelines for some important laboratory tests have been developed by expert panels in the Parisian region to maximize the appropriateness of laboratory medicine. However; these recommendations are not frequently consulted by physicians and nurses. We developed a system facilitating consultation of these guidelines, to increase their usability. Elements of information contained in these documents were identified and included in recommendations of different categories. UML modeling was used to represent these categories and their relationships to each other in the guidelines. We used the generated model to implement a computerized interface. The prototype interface, based on web-based technology was found to be rapid and easy to use. By clicking on provided keywords, information about the subject sought is highlighted whilst retaining the entire text of the guideline on-screen.

العلاقة: info:eu-repo/semantics/altIdentifier/pmid/21893797; hal-03810542; https://hal.archives-ouvertes.fr/hal-03810542Test; PUBMED: 21893797

الإتاحة: https://hal.archives-ouvertes.fr/hal-03810542Test

المؤلفون: Pierre Lechat, Laurence Motreff, Amine Ghozlane, Stevenn Volant, Christophe Malabat, Perrine Woringer, Pascal Campagne, Sean Kennedy

المساهمون: Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Pôle Biomics (C2RT), Centre de Ressources et de Recherche Technologique - Center for Technological Resources and Research (C2RT), Institut Pasteur [Paris] (IP)-Institut Pasteur [Paris] (IP), Institut Pasteur, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Institut Pasteur [Paris]

المصدر: BMC Bioinformatics, Vol 21, Iss 1, Pp 1-15 (2020)
BMC Bioinformatics
BMC Bioinformatics, 2020, 21 (1), pp.345. ⟨10.1186/s12859-020-03666-4⟩
BMC Bioinformatics, BioMed Central, 2020, 21 (1), pp.345. ⟨10.1186/s12859-020-03666-4⟩

مصطلحات موضوعية: Source code, Computer science, Statistics as Topic, Biochemistry, Workflow, MESH: Body Fluids, Feces, User-Computer Interface, 0302 clinical medicine, Structural Biology, RNA, Ribosomal, 16S, lcsh:QH301-705.5, media_common, Visualization, 0303 health sciences, Applied Mathematics, Microbiota, MESH: Feces, Classification, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Computer Science Applications, Body Fluids, MESH: RNA, Ribosomal, 16S, MESH: Classification, MESH: Internet, 030220 oncology & carcinogenesis, Child, Preschool, Web application, lcsh:R858-859.7, DNA microarray, MESH: Metagenomics, media_common.quotation_subject, education, Differential analysis, lcsh:Computer applications to medicine. Medical informatics, Set (abstract data type), MESH: Workflow, 03 medical and health sciences, MESH: Software, Humans, MESH: Microbiota, Microbiome, Molecular Biology, MESH: Statistics as Topic, 030304 developmental biology, MESH: User-Computer Interface, User Friendly, Internet, Information retrieval, MESH: Humans, MESH: Child, Preschool, MESH: Metagenome, 16S ribosomal RNA, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, lcsh:Biology (General), Metagenomics, Container (abstract data type), Metagenome, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Software

الوصف: Background Comparing the composition of microbial communities among groups of interest (e.g., patients vs healthy individuals) is a central aspect in microbiome research. It typically involves sequencing, data processing, statistical analysis and graphical display. Such an analysis is normally obtained by using a set of different applications that require specific expertise for installation, data processing and in some cases, programming skills. Results Here, we present SHAMAN, an interactive web application we developed in order to facilitate the use of (i) a bioinformatic workflow for metataxonomic analysis, (ii) a reliable statistical modelling and (iii) to provide the largest panel of interactive visualizations among the applications that are currently available. SHAMAN is specifically designed for non-expert users. A strong benefit is to use an integrated version of the different analytic steps underlying a proper metagenomic analysis. The application is freely accessible at http://shaman.pasteur.frTest/, and may also work as a standalone application with a Docker container (aghozlane/shaman), conda and R. The source code is written in R and is available at https://github.com/aghozlane/shamanTest. Using two different datasets (a mock community sequencing and a published 16S rRNA metagenomic data), we illustrate the strengths of SHAMAN in quickly performing a complete metataxonomic analysis. Conclusions With SHAMAN, we aim at providing the scientific community with a platform that simplifies reproducible quantitative analysis of metagenomic data.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4490f3bad7ceb345f5e42f820eb087e6Test
http://link.springer.com/article/10.1186/s12859-020-03666-4Test