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1. GenomeDiver: a platform for phenotype-guided medical genomic diagnosis

Author

Pearson, Nathaniel M., Stolte, Christian, Shi, Kevin, Beren, Faygel, Abul-Husn, Noura S., Bertier, Gabrielle, Brown, Kaitlyn, Diaz, George A., Odgis, Jacqueline A., Suckiel, Sabrina A., Horowitz, Carol R., Wasserstein, Melissa, Gelb, Bruce D., Kenny, Eimear E., Gagnon, Charles, Jobanputra, Vaidehi, Bloom, Toby, and Greally, John M.

Published
2021
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2. GUÍA: a digital platform to facilitate result disclosure in genetic counseling

Author

Suckiel, Sabrina A., Odgis, Jaqueline A., Gallagher, Katie M., Rodriguez, Jessica E., Watnick, Dana, Bertier, Gabrielle, Sebastin, Monisha, Yelton, Nicole, Maria, Estefany, Lopez, Jessenia, Ramos, Michelle, Kelly, Nicole, Teitelman, Nehama, Beren, Faygel, Kaszemacher, Tom, Davis, Kojo, Laguerre, Irma, Richardson, Lynne D., Diaz, George A., Pearson, Nathaniel M., Ellis, Stephen B., Stolte, Christian, Robinson, Mimsie, Kovatch, Patricia, Horowitz, Carol R., Gelb, Bruce D., Greally, John M., Bauman, Laurie J., Zinberg, Randi E., Abul-Husn, Noura S., Wasserstein, Melissa P., and Kenny, Eimear E.

Published
2021
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3. Correction to: The NYCKidSeq project: study protocol for a randomized controlled trial incorporating genomics into the clinical care of diverse New York City children

Author

Odgis, Jacqueline A., Gallagher, Katie M., Suckiel, Sabrina A., Donohue, Katherine E., Ramos, Michelle A., Kelly, Nicole R., Bertier, Gabrielle, Blackburn, Christina, Brown, Kaitlyn, Fielding, Lena, Lopez, Jessenia, Aguiniga, Karla Lopez, Maria, Estefany, Rodriguez, Jessica E., Sebastin, Monisha, Teitelman, Nehama, Watnick, Dana, Yelton, Nicole M., Abhyankar, Avinash, Abul-Husn, Noura S., Baum, Aaron, Bauman, Laurie J., Beal, Jules C., Bloom, Toby, Cunningham-Rundles, Charlotte, Diaz, George A., Dolan, Siobhan, Ferket, Bart S., Jobanputra, Vaidehi, Kovatch, Patricia, McDonald, Thomas V., McGoldrick, Patricia E., Rhodes, Rosamond, Rinke, Michael L., Robinson, Mimsie, Rubinstein, Arye, Shulman, Lisa H., Stolte, Christian, Wolf, Steven M., Yozawitz, Elissa, Zinberg, Randi E., Greally, John M., Gelb, Bruce D., Horowitz, Carol R., Wasserstein, Melissa P., and Kenny, Eimear E.

Published
2021
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4. Implications of secondary findings for clinical contexts

Author

Morrison, Michael, primary, Teare, Harriet, additional, Bertier, Gabrielle, additional, Buchanan, James, additional, Bylstra, Yasmin, additional, Gaff, Clara, additional, Jackson, Leigh, additional, Kato, Kazuto, additional, Kaufmann, Elke, additional, Kelly, Susan, additional, Lázaro-Muñoz, Gabriel, additional, Leitsalu, Liis, additional, Milani, Lili, additional, Schaefer, G. Owen, additional, Schickhardt, Christoph, additional, Shabani, Mahsa, additional, Tutty, Erin, additional, Winkler, Eva C., additional, and Wordsworth, Sarah, additional

Published
2020
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5. Contributors

Author

Berg, Jonathan S., primary, Bertier, Gabrielle, additional, Bowling, Kevin M., additional, Brothers, Kyle B., additional, Buchanan, James, additional, Buyx, Alena, additional, Bylstra, Yasmin, additional, De Clercq, Eva, additional, Cooper, Gregory M., additional, Erdmann†, Pia, additional, Foreman, Ann Katherine Major, additional, Gaff, Clara, additional, Jackson, Leigh, additional, Kato, Kazuto, additional, Kaufmann, Elke, additional, Kelly, Susan, additional, Knoppers, Bartha Maria, additional, Langanke, Martin, additional, Lázaro-Muñoz, Gabriel, additional, Leitsalu, Liis, additional, Liedtke, Wenke, additional, Mertz, Marcel, additional, Milani, Lili, additional, Morrison, Michael, additional, Richter, Gesine, additional, Schaefer, G. Owen, additional, Schickhardt, Christoph, additional, Schleidgen, Sebastian, additional, Shabani, Mahsa, additional, Teare, Harriet, additional, Thompson, Michelle L., additional, Thorogood, Adrian, additional, Tutty, Erin, additional, Williams, Janet L., additional, Winkler, Eva C., additional, Wordsworth, Sarah, additional, and Zawati, Ma’n, additional

Published
2020
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12. Additional file 1 of The NYCKidSeq project: study protocol for a randomized controlled trial incorporating genomics into the clinical care of diverse New York City children

Author

Odgis, Jacqueline A., Gallagher, Katie M., Suckiel, Sabrina A., Donohue, Katherine E., Ramos, Michelle A., Kelly, Nicole R., Bertier, Gabrielle, Blackburn, Christina, Brown, Kaitlyn, Fielding, Lena, Jessenia Lopez, Aguiniga, Karla Lopez, Estefany Maria, Rodriguez, Jessica E., Sebastin, Monisha, Nehama Teitelman, Watnick, Dana, Yelton, Nicole M., Abhyankar, Avinash, Abul-Husn, Noura S., Baum, Aaron, Bauman, Laurie J., Beal, Jules C., Bloom, Toby, Cunningham-Rundles, Charlotte, Diaz, George A., Dolan, Siobhan, Ferket, Bart S., Vaidehi Jobanputra, Kovatch, Patricia, McDonald, Thomas V., McGoldrick, Patricia E., Rhodes, Rosamond, Rinke, Michael L., Mimsie Robinson, Rubinstein, Arye, Shulman, Lisa H., Stolte, Christian, Wolf, Steven M., Yozawitz, Elissa, Zinberg, Randi E., Greally, John M., Gelb, Bruce D., Horowitz, Carol R., Wasserstein, Melissa P., and Kenny, Eimear E.

Abstract

Additional file 1. SPIRIT checklist.

Published
2021
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13. The NYCKidSeq project: study protocol for a randomized controlled trial incorporating genomics into the clinical care of diverse New York City children

Author

Odgis, Jacqueline A., primary, Gallagher, Katie M., additional, Suckiel, Sabrina A., additional, Donohue, Katherine E., additional, Ramos, Michelle A., additional, Kelly, Nicole R., additional, Bertier, Gabrielle, additional, Blackburn, Christina, additional, Brown, Kaitlyn, additional, Fielding, Lena, additional, Lopez, Jessenia, additional, Aguiniga, Karla Lopez, additional, Maria, Estefany, additional, Rodriguez, Jessica E., additional, Sebastin, Monisha, additional, Teitelman, Nehama, additional, Watnick, Dana, additional, Yelton, Nicole M., additional, Abhyankar, Avinash, additional, Abul-Husn, Noura S., additional, Baum, Aaron, additional, Bauman, Laurie J., additional, Beal, Jules C., additional, Bloom, Toby, additional, Cunningham-Rundles, Charlotte, additional, Diaz, George A., additional, Dolan, Siobhan, additional, Ferket, Bart S., additional, Jobanputra, Vaidehi, additional, Kovatch, Patricia, additional, McDonald, Thomas V., additional, McGoldrick, Patricia E., additional, Rhodes, Rosamond, additional, Rinke, Michael L., additional, Robinson, Mimsie, additional, Rubinstein, Arye, additional, Shulman, Lisa H., additional, Stolte, Christian, additional, Wolf, Steven M., additional, Yozawitz, Elissa, additional, Zinberg, Randi E., additional, Greally, John M., additional, Gelb, Bruce D., additional, Horowitz, Carol R., additional, Wasserstein, Melissa P., additional, and Kenny, Eimear E., additional

Published
2021
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14. Transcriptome and genome sequencing uncovers functional variation in humans

Author

Lappalainen, Tuuli, Sammeth, Michael, Friedländer, Marc R., ʼt Hoen, Peter A. C., Monlong, Jean, Rivas, Manuel A., Gonzàlez-Porta, Mar, Kurbatova, Natalja, Griebel, Thasso, Ferreira, Pedro G., Barann, Matthias, Wieland, Thomas, Greger, Liliana, van Iterson, Maarten, Almlöf, Jonas, Ribeca, Paolo, Pulyakhina, Irina, Esser, Daniela, Giger, Thomas, Tikhonov, Andrew, Sultan, Marc, Bertier, Gabrielle, MacArthur, Daniel G., Lek, Monkol, Lizano, Esther, Buermans, Henk P. J., Padioleau, Ismael, Schwarzmayr, Thomas, Karlberg, Olof, Ongen, Halit, Kilpinen, Helena, Beltran, Sergi, Gut, Marta, Kahlem, Katja, Amstislavskiy, Vyacheslav, Stegle, Oliver, Pirinen, Matti, Montgomery, Stephen B., Donnelly, Peter, McCarthy, Mark I., Flicek, Paul, Strom, Tim M., Lehrach, Hans, Schreiber, Stefan, Sudbrak, Ralf, Carracedo, Ángel, Antonarakis, Stylianos E., Häsler, Robert, Syvänen, Ann-Christine, van Ommen, Gert-Jan, Brazma, Alvis, Meitinger, Thomas, Rosenstiel, Philip, Guigó, Roderic, Gut, Ivo G., Estivill, Xavier, and Dermitzakis, Emmanouil T.

Published
2013
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15. GenomeDiver: A platform for phenotype-guided medical genomic diagnosis

Author

Pearson, Nathaniel, primary, Stolte, Christian, additional, Shi, Kevin, additional, Beren, Faygel, additional, Abul-Husn, Noura S., additional, Bertier, Gabrielle, additional, Brown, Kaitlyn, additional, Odgis, Jacqueline A., additional, Suckiel, Sabrina A., additional, Horowitz, Carol R., additional, Wasserstein, Melissa, additional, Gelb, Bruce D., additional, Kenny, Eimear E., additional, Gagnon, Charles, additional, Jobanputra, Vaidehi, additional, Bloom, Toby, additional, and Greally, John M., additional

Published
2020
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16. The NYCKidSeq project: study protocol for a randomized controlled trial incorporating genomics into the clinical care of diverse New York City children

Author

Odgis, Jacqueline A, primary, Gallagher, Katie M., additional, Suckiel, Sabrina A., additional, Donohue, Katherine E., additional, Ramos, Michelle A., additional, Kelly, Nicole R., additional, Bertier, Gabrielle, additional, Blackburn, Christina, additional, Brown, Kaitlyn, additional, Fielding, Lena, additional, Lopez, Jessenia, additional, Aguiniga, Karla Lopez, additional, Maria, Estefany, additional, Rodriguez, Jessica E., additional, Sebastin, Monisha, additional, Teitelman, Nehama, additional, Watnick, Dana, additional, Yelton, Nicole M., additional, Abhyankar, Avinash, additional, Abul-Husn, Noura S., additional, Baum, Aaron, additional, Bauman, Laurie J., additional, Beal, Jules C., additional, Bloom, Toby, additional, Cunningham-Rundles, Charlotte, additional, Diaz, George A., additional, Dolan, Siobhan, additional, Ferket, Bart S., additional, Jobanputra, Vaidehi, additional, Kovatch, Patricia, additional, McDonald, Thomas V., additional, McGoldrick, Patricia E., additional, Rhodes, Rosamond, additional, Rinke, Michael L., additional, Robinson, Mimsie, additional, Rubinstein, Arye, additional, Shulman, Lisa H., additional, Stolte, Christian, additional, Wolf, Steven M., additional, Yozawitz, Elissa, additional, Zinberg, Randi E., additional, Greally, John M., additional, Gelb, Bruce D., additional, Horowitz, Carol R., additional, Wasserstein, Melissa P., additional, and Kenny, Eimear E., additional

Published
2020
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17. GUÍA: a digital platform to facilitate result disclosure in genetic counseling

Author

Suckiel, Sabrina A., primary, Odgis, Jaqueline A., additional, Gallagher, Katie M., additional, Rodriguez, Jessica E., additional, Watnick, Dana, additional, Bertier, Gabrielle, additional, Sebastin, Monisha, additional, Yelton, Nicole, additional, Maria, Estefany, additional, Lopez, Jessenia, additional, Ramos, Michelle, additional, Kelly, Nicole, additional, Teitelman, Nehama, additional, Beren, Faygel, additional, Kaszemacher, Tom, additional, Davis, Kojo, additional, Laguerre, Irma, additional, Richardson, Lynne D., additional, Diaz, George A., additional, Pearson, Nathaniel M., additional, Ellis, Stephen B., additional, Stolte, Christian, additional, Robinson, Mimsie, additional, Kovatch, Patricia, additional, Horowitz, Carol R., additional, Gelb, Bruce D., additional, Greally, John M., additional, Bauman, Laurie J., additional, Zinberg, Randi E., additional, Abul-Husn, Noura, additional, Wasserstein, Melissa P., additional, and Kenny, Eimear E., additional

Published
2020
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18. The NYCKidSeq project: study protocol for a randomized controlled trial incorporating genomics into the clinical care of diverse New York City children

Author

Odgis, Jacqueline A., primary, Gallagher, Katie M., additional, Suckiel, Sabrina A., additional, Donohue, Katherine E., additional, Ramos, Michelle A., additional, Kelly, Nicole R., additional, Bertier, Gabrielle, additional, Blackburn, Christina, additional, Brown, Kaitlyn, additional, Fielding, Lena, additional, Lopez, Jessenia, additional, Aguiniga, Karla Lopez, additional, Maria, Estefany, additional, Rodriguez, Jessica E., additional, Sebastin, Monisha, additional, Teitelman, Nehama, additional, Watnick, Dana, additional, Yelton, Nicole M., additional, Abhyankar, Avinash, additional, Abul-Husn, Noura S., additional, Baum, Aaron, additional, Bauman, Laurie J., additional, Beal, Jules C., additional, Bloom, Toby, additional, Cunningham-Rundles, Charlotte, additional, Diaz, George A., additional, Dolan, Siobhan, additional, Ferket, Bart S., additional, Jobanputra, Vaidehi, additional, Kovatch, Patricia, additional, McDonald, Thomas V., additional, McGoldrick, Patricia E., additional, Rhodes, Rosamond, additional, Rinke, Michael L., additional, Robinson, Mimsie, additional, Rubinstein, Arye, additional, Shulman, Lisa H., additional, Stolte, Christian, additional, Wolf, Steven M., additional, Yozawitz, Elissa, additional, Zinberg, Randi E., additional, Greally, John M., additional, Gelb, Bruce D., additional, Horowitz, Carol R., additional, Wasserstein, Melissa P., additional, and Kenny, Eimear E., additional

Published
2020
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19. Comment évaluer la FAIRness pour améliorer les processus de récompense du partage de la donnée? Une étape au travers d'une grille d'évaluation plus exhaustive

Author

David, Romain, Mabile, Laurence, Yahia, Mohamed, Cambon-Thomsen, Anne, Archambeau, Anne-Sophie, Bezuidenhout, Louise, Bekaert, Sofie, Bertier, Gabrielle, Bravo, Elena, Carpenter, Jane, Cohen-Nabeiro, Anna, Delavaud, Aurélie, De Rosa, Michele, Dollé, Laurent, Grattarola, Florencia, Murphy, Fiona, Pamerlon, Sophie, Specht, Alison, Tassé, Anne-Marie, Thomsen, Mogens, Zilioli, Martina, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Epidémiologie et analyses en santé publique : risques, maladies chroniques et handicaps (LEASP), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Charles Gerhardt Montpellier - Institut de Chimie Moléculaire et des Matériaux de Montpellier (ICGM ICMMM), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut de Chimie du CNRS (INC), Global Biodiversity Information Facility France (GBIF France), University of Oxford [Oxford], Universiteit Gent = Ghent University [Belgium] (UGENT), Department of Biology [Montréal], McGill University = Université McGill [Montréal, Canada], Istituto Superiore di Sanita [Rome], The University of Sydney, Fondation pour la recherche sur la Biodiversité (FRB), Biothèque Wallonia-Bruxelles, Bioinformatics and Sequence Analysis (BONSAI), Centre National de la Recherche Scientifique (CNRS)-Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Murphy Mitchell Consulting LTD, University of Lincoln, Institut de Recherche pour le Développement (IRD), Centre de Synthèse et d’Analyse sur la Biodiversité (CESAB), Public Population Project in Genomics and Society (P3G), Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Istituto per il Rilevamento Elettromagnetico dell'Ambiente [Napoli] (IREA-CNR), Consiglio Nazionale delle Ricerche [Napoli] (CNR), RDA USA, Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Charles Gerhardt Montpellier - Institut de Chimie Moléculaire et des Matériaux de Montpellier (ICGM), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Global Biodiversity Information Facility (GBIF), University of Oxford, Universiteit Gent = Ghent University (UGENT), Istituto Superiore di Sanità (ISS), Université de Lille, Sciences et Technologies-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), and Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
reusable, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], interoperable, Findable, accessible, interoperable, reusable, FAIRness literacy, Findable, FAIRness literacy, [INFO.INFO-ET]Computer Science [cs]/Emerging Technologies [cs.ET], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], accessible, [SDE.ES]Environmental Sciences/Environmental and Society
Abstract

The SHARC (SHAring Reward & Credit) interest group (IG) is an interdisciplinary group set up in the framework of RDA (Research Data Alliance) to improve crediting and rewarding mechanisms in the sharing process throughout the data life cycle. Notably, one of the objectives is to promote data sharing activities in research assessment schemes at national and European levels. To this aim,the RDA-SHARC IG is developing assessment grids using criteria to establish if data are compliant to the FAIR principles (findable /accessible / interoperable / reusable). The grid is aiming to be extensive, generic and trans-disciplinary. It is meant to be used by evaluators to assess the quality of the sharing practice of the researcher/scientist over a given period, taking into account the means & support available over that period. The grid displays a mind-mapped tree-graph structure based on previous works on FAIR data management (Reymonet et al., 2018; Wilkinson et al., 2016; Wilkinson et al., 2018; and E.U.Guidelines about FAIRness Data Management Plans). The criteria used are based on the work from FORCE 11*, and the Open Science Career Assessment Matrix designed by the EC Working group on Rewards under Open science. The criteria are organised in 5 clusters: ‘Motivations for sharing’; ‘Findable’, ‘Accessible’, ‘Interoperable’ and ‘Reusable’. For each criterion, 4 graduations are proposed (‘Never / Not Assessable’; ‘If mandatory’; ‘Sometimes’; ‘Always’). Only one value must be selected per criterion. Evaluation should be done by cluster; the final overall assessment will be based on the sum of the number of each ticked value / total number of criteria in each cluster; the ‘motivations for sharing’ should be appreciated qualitatively in the final interpretation. The final goals are to develop a graduated assessment of the researcher FAIRness literacy and help identifying needs to build FAIRness guidelines to improve the sharing capacity of researchers.

Published
2019

20. How to assess FAIRness to improve crediting and rewarding processes for data sharing? A step forward towards an extensive assessment grid

Author

David, Romain, Mabile, Laurence, Yahia, Mohamed, Cambon-Thomsen, Anne, Archambeau, Anne-Sophie, Bezuidenhout, Louise, Bekaert, Sofie, Bertier, Gabrielle, Bravo, Elena, Carpenter, Jane, Cohen-Nabeiro, Anna, Delavaud, Aurélie, Dollé, Laurent, de Rosa, Michele, Murphy, Fiona, Grattarola, Florencia, Pamerlon, Sophie, Specht, Alison, Tassé, Anne-Marie, Thomsen, Mogens, Zilioli, Martina, David, Romain, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Epidémiologie et analyses en santé publique : risques, maladies chroniques et handicaps (LEASP), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Charles Gerhardt Montpellier - Institut de Chimie Moléculaire et des Matériaux de Montpellier (ICGM), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Global Biodiversity Information Facility France (GBIF France), Global Biodiversity Information Facility (GBIF), University of Oxford, Universiteit Gent = Ghent University (UGENT), Department of Biology [Montréal], McGill University = Université McGill [Montréal, Canada], Istituto Superiore di Sanita [Rome], The University of Sydney, Fondation pour la recherche sur la Biodiversité (FRB), Biothèque Wallonia-Bruxelles, Bioinformatics and Sequence Analysis (BONSAI), Université de Lille, Sciences et Technologies-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Murphy Mitchell Consulting LTD, University of Lincoln, Institut de Recherche pour le Développement (IRD), Centre de Synthèse et d’Analyse sur la Biodiversité (CESAB), Public Population Project in Genomics and Society (P3G), Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Istituto per il Rilevamento Elettromagnetico dell'Ambiente [Napoli] (IREA-CNR), Consiglio Nazionale delle Ricerche [Napoli] (CNR), and RDA USA

Subjects
reusable, [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], Findable, accessible, [SDE.ES]Environmental Sciences/Environmental and Society, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, interoperable, [INFO.INFO-ET] Computer Science [cs]/Emerging Technologies [cs.ET], [SDV.EE.ECO] Life Sciences [q-bio]/Ecology, environment/Ecosystems, [INFO.INFO-DB] Computer Science [cs]/Databases [cs.DB], FAIRness literacy, [INFO.INFO-ET]Computer Science [cs]/Emerging Technologies [cs.ET], [SDE.ES] Environmental Sciences/Environmental and Society, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

Le poster a été déposé dans Zenodo; International audience; The SHARC (SHAring Reward & Credit) interest group (IG) is an interdisciplinary group set up in the framework of RDA (Research Data Alliance) to improve crediting and rewarding mechanisms in the sharing process throughout the data life cycle. Notably, one of the objectives is to promote data sharing activities in research assessment schemes at national and European levels. To this aim, the RDA-SHARC IG is developing assessment grids using criteria to establish if data are compliant to the FAIR principles (findable /accessible / interoperable / reusable).The grid is aiming to be extensive, generic and trans-disciplinary. It is meant to be used by evaluators to assess the quality of the sharing practice of the researcher/scientist over a given period, taking into account the means & support available over that period. The grid displays a mind-mapped tree-graph structure based on previous works on FAIR data management (Reymonet et al., 2018; Wilkinson et al., 2016; Wilkinson et al., 2018; and E.U.Guidelines about FAIRness Data Management Plans). The criteria used are based on the work from FORCE 11*, and the Open Science Career Assessment Matrix designed by the EC Working group on Rewards under Open science. The criteria are organised in 5 clusters: ‘Motivations for sharing’; ‘Findable’, ‘Accessible’, ‘Interoperable’ and ‘Reusable’. For each criterion, 4 graduations are proposed (‘Never / Not Assessable’; ‘If mandatory’; ‘Sometimes’; ‘Always’). Only one value must be selected per criterion. Evaluation should be done by cluster; the final overall assessment will be based on the sum of the number of each ticked value / total number of criteria in each cluster; the ‘motivations for sharing’ should be appreciated qualitatively in the final interpretation. The final goals are to develop a graduated assessment of the researcher FAIRness literacy and help identifying needs to build FAIRness guidelines to improve the sharing capacity of researchers.

Published
2019

21. Comment opérationnaliser et évaluer la prise en compte du concept 'FAIR' dans le partage des données: vers une grille simplifiée d'évaluation du respect des critères FAIR

Author

David, Romain, Mabile, Laurence, Yahia, Mohamed, Cambon-Thomsen, Anne, Archambeau, Anne-Sophie, Bezuidenhout, Louise, Bekaert, Sofie, Bertier, Gabrielle, Bravo, Elena, Carpenter, Jane, Cohen-Nabeiro, Anna, Delavaud, Aurélie, De Rosa, Michele, Dollé, Laurent, Grattarola, Florencia, Murphy, Fiona, Pamerlon, Sophie, Specht, Alison, Tassé, Anne-Marie, Thomsen, Mogens, and Zilioli, Martina

Subjects
Data sharing, Research Data Alliance, MaDICS, rewarding, credits, data, accessible, Interoperable formats, FAIR criteria
Abstract

SHARC (SHAring Reward & Credit) est un groupe d'intérêt scientifique interdisciplinaire créé dans le cadre de RDA (Research Data Alliance) dans le but de faciliter le partage des données de recherche (et des ressources) par la valorisation de l'ensemble des activités pré-requises à ce partage, tout au long du cycle de vie des données. Dans ce cadre, un sous-groupe de travail SHARC élabore des grilles d'évaluation des chercheurs afin de mesurer leur niveau de prise en compte des principes FAIR dans la gestion de leurs données. La grille d'évaluation présentée dans ce poster est destinée à être complétée par tout scientifique produisant et / ou utilisant des données. Il s'agit d'un résumé d'une grille d'évaluation plus étendue conçue pour un partage optimal des données (non encore mise en œuvre pour le moment par la plupart des scientifiques). L'évaluation est basée sur les critères de conformité FAIR. Pour remplir cet objectif, la grille affiche le minimum de critères qui doivent absolument être appliqués par les chercheurs pour attester de leur pratique FAIR. Ces critères sont organisés en 5 groupes: «Motivations de partage»; "Trouvable", "Accessible", "Interopérable" et "Réutilisable". Pour chaque critère, 4 degrés d'évaluation sont proposés ("Jamais / Non évaluable"; "Si obligatoire"; "Parfois"; "Toujours"). Au moins un degré mais un seul doit être sélectionné par critère. L'évaluation doit être effectuée pour chaque catégorie F / A / I / R; L'évaluation finale est la somme de chaque degré coché rapportée au nombre total de critères dans chaque catégorie F / A / I / R. Des règles d'interprétation prenant en compte les «motivations du partage» sont proposées.

Published
2018
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22. Operationalizing and evaluating the FAIRness concept for a good quality of data sharing in Research: the RDA-SHARC-IG (SHAring Rewards and Credit Interest Group)

Author

David, Romain, Mabile, Laurence, Yahia, Mohamed, Cambon-Thomsen, Anne, Archambeau, Anne-Sophie, Bezuidenhout, Louise, Bekaert, Sofie, Bertier, Gabrielle, Bravo, Elena, Carpenter, Jane, Cohen-Nabeiro, Anna, Delavaud, Aurélie, De Rosa, Michele, Dollé, Laurent, Grattarola, Florencia, Murphy, Fiona, Pamerlon, Sophie, Specht, Alison, Tassé, Anne-Marie, Thomsen, Mogens, Zilioli, Martina, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Institut Charles Gerhardt Montpellier - Institut de Chimie Moléculaire et des Matériaux de Montpellier (ICGM ICMMM), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut de Chimie du CNRS (INC), Department of Clinical Genetics/EMGO Institute for Health and Care research, Patrimoine naturel (PatriNat), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Agence Française pour la Biodiversité (AFB), University of Oxford [Oxford], Universiteit Gent = Ghent University [Belgium] (UGENT), Department of Biology [Montréal], McGill University = Université McGill [Montréal, Canada], Istituto Superiore di Sanita [Rome], The University of Sydney, Fondation pour la recherche sur la Biodiversité (FRB), Bioinformatics and Sequence Analysis (BONSAI), Centre National de la Recherche Scientifique (CNRS)-Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Sciences et Technologies-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Biothèque Wallonia-Bruxelles, University of Lincoln, Murphy Mitchell Consulting LTD, Institut de Recherche pour le Développement (IRD), Public Population Project in Genomics and Society (P3G), Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Institut National de la Santé et de la Recherche Médicale (INSERM), CNR-IREA Milan, icube strasbourg / bureau de MaDICS, Université de Toulouse (UT), Institut Charles Gerhardt Montpellier - Institut de Chimie Moléculaire et des Matériaux de Montpellier (ICGM), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), University of Oxford, Universiteit Gent = Ghent University (UGENT), Istituto Superiore di Sanità (ISS), Université de Lille, Sciences et Technologies-Inria Lille - Nord Europe, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 (CRIStAL), Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centrale Lille-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM), and David, Romain

Subjects
MaDICS, [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], accessible, [SDE.ES]Environmental Sciences/Environmental and Society, rewarding, credits, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, data, [INFO.INFO-ET] Computer Science [cs]/Emerging Technologies [cs.ET], [SDV.EE.ECO] Life Sciences [q-bio]/Ecology, environment/Ecosystems, Data sharing, Research Data Alliance, Interoperable formats, [INFO.INFO-DB] Computer Science [cs]/Databases [cs.DB], [INFO.INFO-ET]Computer Science [cs]/Emerging Technologies [cs.ET], [SDE.ES] Environmental Sciences/Environmental and Society, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], 10. No inequality, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

The RDA-SHARC (SHAring Reward & Credit) interest group is an interdisciplinary volunteer member-based group set up as part of RDA (Research Data Alliance) to unpack and improve crediting and rewarding mechanisms in the sharing process throughout the data life cycle. Background and objectives of this group are reported here. Notably, one of the objectives is to promote the inclusion of data sharing activities in the research (& researchers) assessment scheme at national and European levels. To this aim, the RDA-SHARC-IG is developing two assessment grids using criteria to establish if data are compliant to the F.A.I.R principles (findable /accessible / interoperable / reusable) based on previous works on FAIR data management (Reymonet et al., 2018; Wilkinson et al., 2018; and E.U.Guidelines*): 1/ The self-assessment grid to be used by a scientist as a ‘checklist’ to identify her/his own activities and to pinpoint the hurdles that hinder efficient sharing and reuse of his/her data by all potential users. 2/ The two-level grid (quick/extensive) to be used by the evaluator to assess the quality of the researcher/scientist sharing practice, over a given period, taking into account the means & support available over that period. Assessment criteria are classified according their importance with regards to FAIRness (essential / recommended / desirable) meanwhile good practices are recommended for critical steps. To implement a highly fair assessment of the sharing process, appropriate criteria must be selected in order to design optimal generic assessment grids. This process requires participation, time and input from volunteer scientists data producers/users from various fields.

Published
2018

24. Open science precision medicine in Canada: Points to consider

Author

Granados Moreno, Palmira, primary, Ali-Khan, Sarah E., additional, Capps, Benjamin, additional, Caulfield, Timothy, additional, Chalaud, Damien, additional, Edwards, Aled, additional, Gold, E. Richard, additional, Rahimzadeh, Vasiliki, additional, Thorogood, Adrian, additional, Auld, Daniel, additional, Bertier, Gabrielle, additional, Breden, Felix, additional, Caron, Roxanne, additional, César, Priscilla M.D.G., additional, Cook-Deegan, Robert, additional, Doerr, Megan, additional, Duncan, Ross, additional, Issa, Amalia M., additional, Reichman, Jerome, additional, Simard, Jacques, additional, So, Derek, additional, Vanamala, Sandeep, additional, and Joly, Yann, additional

Published
2019
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25. Implémentation clinique du séquençage de nouvelle génération en France et au Québec : une analyse multidisciplinaire des implications pour les politiques publiques

Author

Bertier, Gabrielle and Bertier, Gabrielle

Abstract

La chute des prix des technologies de séquençage de nouvelle génération (NGS) s'est accompagnée de leur utilisation accrue, en recherche et en clinique. L'interprétation toujours meilleure des génomes humains peut permettre le développement de meilleures stratégies de prévention, de diagnostic et de traitement des maladies. Des investissements significatifs ont vu le jour dans de nombreux pays industrialisés en vue de réaliser les promesses de la médecine personnalisée. Cependant, le séquençage du génome complet de patients n'est offert en tant que test clinique que dans un nombre très limité d'établissements de santé dans le monde. La France et le Québec ont investi de manière considérable dans la recherche en génomique. Cependant, des décisions stratégiques doivent encore être prises quant à l'implémentation clinique des technologies NGS dans ces deux juridictions. Dès lors, l'objectif de ce projet est de contribuer à l'ensemble des preuves et faits à la disposition des décideurs publics. Nous avons focalisé notre attention sur deux technologies, le séquençage de l'exome (whole-exome sequencing, WES) et du génome complet (whole-genome sequencing, WGS). Notre objectif était d'établir si l'utilisation efficace et responsable du WES/WGS pouvait être mise en péril par des lacunes dans les politiques publiques ou cadres règlementaires et normatifs applicables. A l'heure actuelle, l'interprétation clinique de la séquence génomique ou exomique d'un patient nécessite l'intervention de nombreuses parties prenantes, y compris des chercheurs qui utilisent des outils, procédés et normes développés dans le cadre de la recherche pour analyser les données NGS. En parallèle, les cadres normatifs existants ont été construits pour accommoder les données génétiques, mais n'abordent pas la question des données génomiques. Notre hypothèse est que ces éléments créent un besoin de standardisation, qui pourrait requérir des adaptations du cadre normatif. Nous avons répondu à trois questi, The decreasing cost of next-generation sequencing (NGS) technologies has resulted in their increased use in research, and in the clinical context. Indeed, the correct interpretation of a human genome can enable better prevention, diagnosis and treatment strategies. Significant public investments in NGS have been made in various developed nations to realise the promise of personalized medicine. Yet, today the sequencing and analysis of a patient’s exome or genome is only offered as a clinical test in a limited number of clinics around the world. France and Quebec have made sizable investments in genomics research, and France announced the launch of a genomic medicine plan in 2016. However, policy decisions still have to be made on the nation-wide clinical implementation of NGS technologies in both jurisdictions. Therefore, this project’s objective was to contribute to the body of evidence available to policymakers in France and Quebec on the clinical implementation of NGS technologies. We focused our attention on two specific NGS technologies, namely Whole Genome Sequencing (WGS), and Whole Exome Sequencing (WES). We specifically aimed to assess if the responsible and efficient use of WES/WGS data in the context of clinical care could be impeded by policy gaps. Currently, the clinical interpretation of a patient’s genome sequence data is done through the intervention of many stakeholders including basic science researchers. These researchers use bioinformatics tools, processes and norms developed for research to filter and analyse patients NGS data. In parallel, existing regulatory and normative frameworks have been developed for the use of genetic data, and include no clear definition of genomic data or genomic technologies. We hypothesised that these elements create a strong need for standardization of practices, and may require adaptations of current regulatory and normative frameworks to the context of NGS. We therefore aimed to answer three research questions: (

Published
2018

26. Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

Author

't Hoen, Peter A C, Friedländer, Marc R, Almlöf, Jonas, Sammeth, Michael, Pulyakhina, Irina, Anvar, Seyed Yahya, Laros, Jeroen F J, Buermans, Henk P J, Karlberg, Olof, Brännvall, Mathias, van Ommen, Gert-Jan B, Estivill, Xavier, Guigó, Roderic, Syvänen, Ann-Christine, Gut, Ivo G, Dermitzakis, Emmanouil T, Antonarakis, Stylianos E, Brazma, Alvis, Flicek, Paul, Schreiber, Stefan, Rosenstiel, Philip, Meitinger, Thomas, Strom, Tim M, Lehrach, Hans, Sudbrak, Ralf, Carracedo, Angel, van Iterson, Maarten, Monlong, Jean, Lizano, Esther, Bertier, Gabrielle, Ferreira, Pedro G, Ribeca, Paolo, Griebel, Thasso, Beltran, Sergi, Gut, Marta, Kahlem, Katja, Lappalainen, Tuuli, Giger, Thomas, Ongen, Halit, Padioleau, Ismael, Kilpinen, Helena, Gonzàlez-Porta, Mar, Kurbatova, Natalja, Tikhonov, Andrew, Greger, Liliana, Barann, Matthias, Esser, Daniela, Häsler, Robert, Wieland, Thomas, Schwarzmayr, Thomas, Sultan, Marc, Amstislavskiy, Vyacheslav, den Dunnen, Johan T, and Antonarakis, Stylianos

Subjects
Male, Small RNA, Sequence analysis, Biomedical Engineering, Bioengineering, Biology, Applied Microbiology and Biotechnology, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, Gene expression, Humans, ddc:576.5, RNA, Messenger, 030304 developmental biology, Genetics, 0303 health sciences, Sequence Analysis, RNA, Gene Expression Profiling, RNA, High-Throughput Nucleotide Sequencing, Reproducibility of Results, Ribosomal RNA, Gene expression profiling, MicroRNAs, 030220 oncology & carcinogenesis, Molecular Medicine, Female, GC-content, Biotechnology
Abstract

RNA sequencing is an increasingly popular technology for genome-wide analysis of transcript sequence and abundance. However, understanding of the sources of technical and interlaboratory variation is still limited. To address this, the GEUVADIS consortium sequenced mRNAs and small RNAs of lymphoblastoid cell lines of 465 individuals in seven sequencing centers, with a large number of replicates. The variation between laboratories appeared to be considerably smaller than the already limited biological variation. Laboratory effects were mainly seen in differences in insert size and GC content and could be adequately corrected for. In small-RNA sequencing, the microRNA (miRNA) content differed widely between samples owing to competitive sequencing of rRNA fragments. This did not affect relative quantification of miRNAs. We conclude that distributing RNA sequencing among different laboratories is feasible, given proper standardization and randomization procedures. We provide a set of quality measures and guidelines for assessing technical biases in RNA-seq data.

Published
2013
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29. Non-invasive Prenatal Testing and the Unveiling of an Impaired Translation Process

Author

Murdoch, Blake, primary, Ravitsky, Vardit, additional, Ogbogu, Ubaka, additional, Ali-Khan, Sarah, additional, Bertier, Gabrielle, additional, Birko, Stanislav, additional, Bubela, Tania, additional, De Beer, Jeremy, additional, Dupras, Charles, additional, Ellis, Meika, additional, Granados Moreno, Palmira, additional, Joly, Yann, additional, Kamenova, Kalina, additional, Master, Zubin, additional, Marcon, Alessandro, additional, Paulden, Mike, additional, Rousseau, François, additional, and Caulfield, Timothy, additional

Published
2017
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37. Operationalizing and evaluating the FAIRness concept for a good quality of data sharing in Research: the RDA-SHARC-IG (SHAring Rewards and Credit Interest Group

Author

David, Romain, Mabile, Laurence, Yahia, Mohamed, Cambon-Thomsen, Anne, Archambeau, Anne-Sophie, Bezuidenhout, Louise, Bekaert, Sofie, Bertier, Gabrielle, Bravo, Elena, Carpenter, Jane, Cohen-Nabeiro, Anna, Delavaud, Aurélie, De Rosa, Michele, Dollé, Laurent, Grattarola, Florencia, Murphy, Fiona, Pamerlon, Sophie, Specht, Alison, Tassé, Anne-Marie, Thomsen, Mogens, and Zilioli, Martina

Subjects
Data sharing, Research Data Alliance, MaDICS, rewarding, credits, data, accessible, Interoperable formats, 10. No inequality
Abstract

The RDA-SHARC (SHAring Reward & Credit) interest group is an interdisciplinary volunteer member-based group set up as part of RDA (Research Data Alliance) to unpack and improve crediting and rewarding mechanisms in the sharing process throughout the data life cycle. Background and objectives of this group are reported here. Notably, one of the objectives is to promote the inclusion of data sharing activities in the research (& researchers) assessment scheme at national and European levels. To this aim, the RDA-SHARC-IG is developing two assessment grids using criteria to establish if data are compliant to the F.A.I.R principles (findable /accessible / interoperable / reusable) based on previous works on FAIR data management (Reymonet et al., 2018; Wilkinson et al., 2018; and E.U.Guidelines*): 1/ The self-assessment grid to be used by a scientist as a ‘checklist’ to identify her/his own activities and to pinpoint the hurdles that hinder efficient sharing and reuse of his/her data by all potential users. 2/ The two-level grid (quick/extensive) to be used by the evaluator to assess the quality of the researcher/scientist sharing practice, over a given period, taking into account the means & support available over that period. Assessment criteria are classified according their importance with regards to FAIRness (essential / recommended / desirable) meanwhile good practices are recommended for critical steps. To implement a highly fair assessment of the sharing process, appropriate criteria must be selected in order to design optimal generic assessment grids. This process requires participation, time and input from volunteer scientists data producers/users from various fields.

38. The role of a bioresource research impact factor as an incentive to share human bioresources.

Author

Cambon-Thomsen, Anne, Thorisson, Gudmundur A, Andrieu, Sandrine, Bertier, Gabrielle, Boeckhout, Martin, Carpenter, Jane, Dagher, Georges, Dalgleish, Raymond, Deschênes, Mylène, di Donato, Jeanne Hélène, Filocamo, Mirella, Goldberg, Marcel, Hewitt, Robert, Hofman, Paul, Kauffmann, Francine, Leitsalu, Liis, Lomba, Irene, Mabile, Laurence, Melegh, Bela, and Metspalu, Andres

Subjects
LETTERS to the editor, PUBLIC health research
Abstract

A letter to the editor is presented in response to article which discusses the role of the bioresource research's impact as an encouragement to share human data such as bioresources.

Published
2011
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