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European projects

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64

Curriculum vitæ Cyril Pommier


Plant research data engineer.


Journal articles19 documents

  • Elizabeth Arnaud, Marie-Angélique Laporte, Soonho Kim, Céline Aubert, Sabina Leonelli, et al.. The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems. Gene Expression Patterns, Elsevier, 2020, pp.100105. ⟨10.1016/j.patter.2020.100105⟩. ⟨hal-02949637⟩
  • Evangelia Papoutsoglou, Daniel Faria, Daniel Arend, Elizabeth Arnaud, Ioannis Athanasiadis, et al.. Enabling reusability of plant phenomic datasets with MIAPPE 1.1. New Phytologist, Wiley, 2020, 227 (1), pp.260-273. ⟨10.1111/nph.16544⟩. ⟨hal-02949641⟩
  • Pascal Neveu, Anne Tireau, Nadine Hilgert, Vincent Negre, Jonathan Mineau-Cesari, et al.. Dealing with multi-source and multi-scale information in plant phenomics: the ontology-driven Phenotyping Hybrid Information System. New Phytologist, Wiley, 2019, 221 (1), pp.588-601. ⟨10.1111/nph.15385⟩. ⟨hal-02627721⟩
  • Anthony Bernard, Teresa Barreneche, Marine Delmas, Sophie Durand, Cyril Pommier, et al.. The walnut genetic resources of INRA: chronological phenotypic data and ontology. BMC Research Notes, BioMed Central, 2019, 12 (1), pp.662. ⟨10.1186/s13104-019-4678-1⟩. ⟨hal-02626113⟩
  • Rafael Abbeloos, Jan Erik Backlund, Martin Basterrechea Salido, Guillaume Bauchet, Omar Benites-Alfaro, et al.. BrAPI - an Application Programming Interface for Plant Breeding Applications.. Bioinformatics, Oxford University Press (OUP), 2019, 35 (20), pp.4147-4155. ⟨10.1093/bioinformatics/btz190⟩. ⟨hal-02626802⟩
  • Joëlle Amselem, Guillaume Cornut, Nathalie Choisne, Michael Alaux, Françoise Alfama Depauw, et al.. RepetDB: a unified resource for transposable element references. Mobile DNA, BioMed Central, 2019, 10, pp.1-8. ⟨10.1186/s13100-019-0150-y⟩. ⟨hal-02625212⟩
  • Cyril Pommier, Célia Michotey, Guillaume Cornut, Pierre Roumet, Eric Duchêne, et al.. Applying FAIR principles to plant phenotypic data management in GnpIS. Plant Phenomics, Science Partner Journals, 2019, 2019, pp.1-15. ⟨10.34133/2019/1671403⟩. ⟨hal-02624031⟩
  • Pawel Krajewski, Dijun Chen, Hanna Cwiek, Aalt D. J. van Dijk, Fabio Fiorani, et al.. Corrigendum: Towards recommendations for metadata and data handling in plant phenotyping. Journal of Experimental Botany, Oxford University Press (OUP), 2018, 69 (7), pp.1819-1819. ⟨10.1093/jxb/ery006⟩. ⟨hal-02620800⟩
  • Michael Alaux, Jane Rogers, Thomas Letellier, Raphaël Flores, Françoise Alfama, et al.. Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data. Genome Biology, BioMed Central, 2018, 19 (1), pp.905-911. ⟨10.1186/s13059-018-1491-4⟩. ⟨hal-02278879⟩
  • Esther Yeumo, Michaël Alaux, Elizabeth Arnaud, Sophie Aubin, Ute Baumann, et al.. Developing data interoperability using standards: A wheat community use case. F1000Research, Faculty of 1000, 2017, 6 (1843), pp.1843. ⟨10.12688/f1000research.12234.1⟩. ⟨lirmm-01652022v2⟩
  • Thomas Altmann, Daniel Arend, Elizabeth Arnaud, Dijun Chen, Guillaume Cornut, et al.. Measures for interoperability of phenotypic data: minimum information requirements and formatting. Plant Methods, BioMed Central, 2016, 12, pp.1-18. ⟨10.1186/s13007-016-0144-4⟩. ⟨hal-02640958⟩
  • Anne-Françoise Adam-Blondon, Michael Alaux, Cyril Pommier, D Cantu, Z-M Cheng, et al.. Towards an open grapevine information system. Horticulture research, Nature Publishing Group, 2016, 3, pp.16056. ⟨10.1038/hortres.2016.56⟩. ⟨hal-01404714⟩
  • Manuel Spannagl, Michael Alaux, Matthias Lange, Dan M. Bolser, Kai Christian Bader, et al.. TransPLANT resources for triticeae genomic data. PLANT GENOME, 2016, 9 (1), 13 p. ⟨10.3835/plantgenome2015.06.0038⟩. ⟨hal-02635899⟩
  • Pawel Krajewski, Dijun Chen, Hanna Cwiek, Aalt D. J. van Dijk, Fabio Fiorani, et al.. Towards recommendations for metadata and data handling in plant phenotyping. Journal of Experimental Botany, Oxford University Press (OUP), 2015, 66 (18), pp.5417-5427. ⟨10.1093/jxb/erv271⟩. ⟨hal-02636470⟩
  • Delphine Steinbach, Michael Alaux, Joelle Amselem, Nathalie Choisne, Sophie Durand, et al.. GnpIS: an information system to integrate genetic and genomic data from plants and fungi. Database - The journal of Biological Databases and Curation, Oxford University Press, 2013, 2013, pp.1-9. ⟨10.1093/database/bat058⟩. ⟨hal-02648084⟩
  • J. Mark Cock, Lieven Sterck, Sophia Ahmed, Andrew E. Allen, Grigoris Amoutzias, et al.. The Ectocarpus Genome and Brown Algal Genomics The Ectocarpus Genome Consortium. Advances in Botanical Research, Elsevier, 2012, 64, pp.141 - 184. ⟨10.1016/B978-0-12-391499-6.00005-0⟩. ⟨hal-02649287⟩
  • J. Mark Cock, Lieven Sterck, Pierre Rouzé, Delphine Scornet, Andrew E. Allen, et al.. The $Ectocarpus$ genome and the independent evolution of multicellularity in brown algae. Nature, Nature Publishing Group, 2010, 465 (7298), pp.617-621. ⟨10.1038/nature09016⟩. ⟨cea-00906990⟩
  • S. Aubourg, V. Brunaud, C. Bruyere, M. Cock, R. Cooke, et al.. GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts.. Nucleic Acids Research, Oxford University Press, 2005, 33, pp.D641-D646. ⟨hal-00313737⟩
  • Sebastien Aubourg, Veronique Brunaud, Clémence Bruyère, Marc Cock, Richard Cooke, et al.. GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts. Nucleic Acids Research, Oxford University Press, 2005, 33, pp.D641-D646. ⟨10.1093/nar/gki115⟩. ⟨hal-01189162⟩

Conference papers28 documents

  • Eric Duchêne, Cyril Pommier. The Vitis Ontology: sustainable and FAIR (Findable, Accessible, Interoperable, Reusable) for consistent and complete data description through biologist friendly ontologies. The First Annual Meeting of COST Action CA17111 INTEGRAPE 2019, Mar 2019, Chania, Greece, 26-28 March 2019, Greece. ⟨hal-02947459⟩
  • Cyril Pommier. Phenotype and genotype data sharing: From data standard to publication and data discovery. PAG XXVII - Plant and Animal Genome Conference, Jan 2019, San Diego, Californie, United States. pp.24 Slides. ⟨hal-02789384⟩
  • Cyril Pommier. Standards for distributed Plant Phenotyping data integration: challenges and solutions.. COST FA1306 "The quest for tolerant varieties - Phenotyping at plant and cellular level" - WG1 Meeting "Phenotyping: from the lab to the field", Mar 2018, Leuven, Belgium. pp.67 slides. ⟨hal-01779751⟩
  • Cyril Pommier. FAIR Data publication for phenomics data. Integrative Bioinformatics Symposium 2018, BBSRC Rothamsted Research. GBR., Jun 2018, Rothamsted, United Kingdom. pp.52 slides + 40 slides. ⟨hal-02787988⟩
  • Michael Alaux, Cyril Pommier, Esther Dzale Yeumo, Sophie Durand, Raphaël Flores, et al.. Improving the « FAIRness » of Inra’s data for plant biology and breeding. PAG XXVI - Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.14 slides. ⟨hal-02790227⟩
  • Michael Alaux, Jane Rogers, Thomas Letellier, Raphaël Flores, Cyril Pommier, et al.. The IWGSC Data repository and wheat data resources hosted at URGI: Overview and perspectives. PAG XXVI - Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.32 slides. ⟨hal-02788401⟩
  • Cyril Pommier, Guillaume Cornut, Thomas Letellier, Célia Michotey, Pascal Neveu, et al.. Data standards for plant phenotyping: MIAPPE and its implementations. 26. Plant and Animal Genome Conference (PAG XXVI), Jan 2018, San Diego, Californie, United States. pp.24 slides. ⟨hal-02789754⟩
  • Cyril Pommier, Eric Duchêne, Thierry Lacombe, Timothée Flutre, Michael Alaux, et al.. Developing grapevine FAIR Data. PAG Conference 2018, Jan 2018, San Diego, United States. ⟨hal-02738117⟩
  • Anne-Francoise Adam-Blondon, Cyril Pommier, Llorenç Cabrera Bosquet. Phenome-Emphasis-Elixir: phenotyping data management and integration. Interenational Grape Genetics and Breeding Symposium, Jul 2018, Bordeaux, France. pp.16. ⟨hal-02789613⟩
  • Mathilde Lainé, Thomas Letellier, Raphaël Flores, Nacer Mohellibi, Cyril Pommier, et al.. BreedWheat GWAS data in GnpIS information system. Eucarpia Cereal Section - Breeding cereals for sustainable agriculture, Mar 2018, Clermont-Ferrand, France. ⟨hal-02340450⟩
  • Cyril Pommier, Windpouire Esther Dzale Yeumo. Exemples d’outils et services pour la gestion et le partage des données à l’Inra. Journée "Bonnes pratiques et outils liés à la mise en place d’une base de données recherche", Centre National de la Recherche Scientifique (CNRS). FRA., Dec 2017, Paris, France. pp.40 slides. ⟨hal-02785564⟩
  • Cyril Pommier. Distributed plant phenotyping data integration: challenges and feedback from French and international consortiums. Data Scientist Big Data Plant Breeding, Wageningen University and Research Centre (WUR). NLD., Dec 2017, Wageningen, Netherlands. ⟨hal-02788362⟩
  • Cyril Pommier. EMBI-EBI Industry Workshop: Ontologies in Agriculture, Food and Nutrition: Speaker. Ontologies in Agriculture, Food and Nutrition, European Molecular Biology Laboratory (EMBL). GBR., Apr 2017, Cambridge, United Kingdom. ⟨hal-02787834⟩
  • Sophie Durand, Windpouire Esther Dzale Yeumo, Cyril Pommier, Michael Alaux, Guillaume Cornut, et al.. Findable, Accessible, Interoperable and Reusable data linked to genetic resources for plant biology and breeding at INRA. 4. International Symposium on Genomics of Plant Genetic Resources, Sep 2017, Giessen, Germany. pp.17 slides. ⟨hal-02791168⟩
  • Aravind Venkatesan, Nordine El Hassouni, Florian Phillipe, Cyril Pommier, Hadi Quesneville, et al.. Exposing French agronomic resources as Linked Open Data. IN-OLIVE, Jun 2016, Montpellier, France. ⟨hal-01411759⟩
  • Clement Jonquet, Anne Toulet, Elizabeth Arnaud, Sophie Aubin, Esther Dzalé-Yeumo, et al.. Reusing the NCBO BioPortal technology for agronomy to build AgroPortal. ICBO: International Conference on Biomedical Ontologies, Aug 2016, Corvallis, OR, United States. ⟨hal-01398251⟩
  • Cyril Pommier, Michael Alaux, Windpouire Esther Dzale Yeumo, Guillaume Cornut, Sophie Durand, et al.. Contribution to a European roadmap for data standardisation in Plant Science at URGI-INRA. Plant Biology Europe EPSO / FESBP 2016 Congress, Jun 2016, Prague, Czech Republic. ⟨hal-02794139⟩
  • Aravind Venkatesan, Nordine El Hassouni, Florian Philippe, Cyril Pommier, Hadi Quesneville, et al.. Exposing French agronomic resources as Linked Open Data. SWAT4LS: Semantic Web Applications and Tools for Life Sciences, Dec 2015, Cambridge, United Kingdom. ⟨lirmm-01274884⟩
  • Aravind Venkatesan, Nordine El Hassouni, Florian Phillipe, Cyril Pommier, Hadi Quesneville, et al.. Towards efficient data integration and knowledge management in the Agronomic domain. APIA: Applications Pratiques de l'Intelligence Artificielle, Institut National de Recherche en Informatique et en Automatique (INRIA). FRA., Jul 2015, Rennes, France. pp.117-124. ⟨hal-01176903⟩
  • Delphine Steinbach, Guillaume Merceron, Célia Michotey, Raphaël-Gauthier Flores, Nacer Mohellibi, et al.. GnpIS-Asso : A Generic Database for Managing and Exploiting Plant Genetic Association Studies Results Using High Throughput Genotyping and Phenotyping Data. 23. Plant and Animal Genome, Jan 2015, San Diego, United States. ⟨hal-01174322⟩
  • Cyril Pommier, Pawel Krajewski, Thomas Letellier, Hanna Cwiek, Célia Michotey, et al.. Phenotypic Data Exchange and Processing Using ISA-Tab Standard: transPLANT Project Use Case with GnpIS.Ephesis and Bii. 23. Plant and Animal Genome (PAG), Jan 2015, San Diego, United States. ⟨hal-02739236⟩
  • Nacer Mohellibi, Nathalie Choisne, Aminah Keliet, Daphné Verdelet, Françoise Alfama, et al.. Grape@GnpIS: Overview of the GnpIS grape genomics and genetics integrative resource. 23. Plant and Animal Genome (PAG XXIII), Jan 2015, San Diego, Californie, United States. pp.24 slides. ⟨hal-02741780⟩
  • Anne-Francoise Adam-Blondon, Eric Duchêne, Sophie Durand, Jérôme Grimplet, Thierry Lacombe, et al.. Open data for grapevine biology. XI. International Congress on Grapevine Breeding and Genetics, Jul 2014, Pékin, China. ⟨hal-01352690⟩
  • Anne-Francoise Adam-Blondon, Sophie Durand, Erik Kimmel, Raphaël-Gauthier Flores, Cyril Pommier, et al.. Plant biology open data interoperability in the big data era. Plant Biology Europe EPSO/FEPBS 2014, Jun 2014, Dublin, Germany. ⟨hal-02801067⟩
  • Cyril Pommier, Michael Alaux, Sophie Durand, Raphaël-Gauthier Flores, Aminah Keliet, et al.. Information system for phenotype data: trait, trials and genotypes identification and integration. 22. Conference Plant and Animal Genome, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI). GBR., Jan 2014, San Diego, United States. ⟨hal-02795958⟩
  • Joelle Amselem, Michael Alaux, Nathalie Choisne, Olivier Inizan, Nicolas Lapalu, et al.. URGI plant and fungi platform: distributed resources through GMOD tools. Plant and Animal Genome conference XXII, GMOD session, Jan 2014, San Diego (CA), United States. ⟨hal-02796293⟩
  • Célia Michotey, Frédéric Sapet, Pierre Dubreuil, Jacques Le Gouis, Mathilde Causse, et al.. A generic tool for managing and exploiting genetic association studies results using high throughput genotyping and phenotyping. Plant Genomics Seminar 2012, Apr 2012, Pont-Royal en Provence, France. ⟨hal-01268379⟩
  • Joelle Amselem, Michael Alaux, Nathalie Choisne, Nicolas Lapalu, Baptiste Brault, et al.. URGI genome annotation system:an integrated system for structural and functional genome annotation. 12. Edition du colloque JOBIM : Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2011, Paris, France. 2 p. ⟨hal-01019754⟩

Poster communications10 documents

  • Sophie Aubin, Anne-Francoise Adam-Blondon, Michael Alaux, Mouhamadou Ba, Stéphan Bernard, et al.. D2KAB project taking off: Data to Knowledge in Agronomy and Biodiversity. 14th RDA Plenary Meeting, Oct 2019, Helsinki, Finland. 2019, ⟨10.5281/zenodo.3520300⟩. ⟨lirmm-02351000⟩
  • Pascal Neveu, Anne Tireau, Nadine Hilgert, Vincent Negre, Jonathan Mineau-Cesari, et al.. PHIS, a plant science ontology-driven Phenotyping Hybrid Information System. NETTAB 2018: Building a FAIR Bioinformatics environment, Oct 2018, Genova, Italy. 1 p., 2018. ⟨hal-02788853⟩
  • Sophie Durand, Esther Dzale Yeumo, Cyril Pommier, Michaël Alaux, Guillaume Cornut, et al.. Findable, Accessible, Interoperable and Reusable data linked to genetic resources for plant biology and breeding at INRA. Crop diversification in a changing world : Mobilizing the green gold of plant genetic resources, May 2017, Montpellier, France. 2017, EUCARPIA Genetic Resources 2017. ⟨hal-01606277⟩
  • Florian Philippe, Aravind Venkatesan, Nordine El Hassouni, Cyril Pommier, Manuel Ruiz, et al.. Data integration in the agronomic domain : national and international data discovery system. JOBIM: Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. 2015. ⟨lirmm-01274725⟩
  • Marie Laine, Thomas Letellier, Raphaël-Gauthier Flores, Loïc Couderc, Nacer Mohellibi, et al.. BreedWheat genotyping and phenotyping data in GnpIS information system. JOBIM 2015 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. 2015. ⟨hal-02801654⟩
  • Francois Tardieu, Jacques Le Gouis, Pamela Lucas, Frédéric Baret, Pascal Neveu, et al.. PHENOME: French Plant Phenomic Center. Recent progress in drought tolerance from genetics to modelling, Jun 2015, Montpellier, France. 2015. ⟨hal-02744329⟩
  • Francois Tardieu, Jacques Le Gouis, Pamela Lucas, Frédéric Baret, Pascal Neveu, et al.. PHENOME: French Plant Phenomic Center. EPPN Plant Phenotyping Symposium, Nov 2015, Barcelona, Spain. 2015. ⟨hal-01229565⟩
  • Jacques Le Gouis, Pamela Lucas, Frédéric Baret, Pascal Neveu, Cyril Pommier, et al.. PHENOME: French Plant Phenomic Center. 9th International Wheat Conference, Sep 2015, Sydney, Australia. 2015. ⟨hal-02800017⟩
  • Célia Michotey, Christel Anger, François Ehrenmann, Odile Rogier, Véronique Jorge, et al.. Forest tree GnpIS: an information system dedicated to forest tree genetics, genomics and phenomics. 35. New Phytologist Symposium, Jun 2015, Boston, United States. 2015. ⟨hal-02795537⟩
  • Cyril Pommier, Michael Alaux, Erik Kimmel, Delphine Steinbach, Elizabeth Arnaud, et al.. Wheat Crop Ontology: A Species Specific Trait Ontology. Use Case: The URGI Information System. Plant and Animal Genome, Jan 2013, San Diego, United States. 2013. ⟨hal-02810186⟩

Book sections2 documents

  • Anne-Francoise Adam-Blondon, Michael Alaux, Sophie Durand, Thomas Letellier, Guillaume Merceron, et al.. Mining plant genomic and genetic data using the GnpIS information system. Aalt D.J van Dijk. Plant Genomics Databases. Methods and Protocols, 1533, Springer, 2017, Methods in Molecular Biology, 978-1-4939-6658-5. ⟨10.1007/978-1-4939-6658-5_5⟩. ⟨hal-03206731⟩
  • Sabine, Helma Fillinger, Joelle Amselem, Francois Artiguenave, Arnaud Billault, Mathias Choquer, et al.. Whole genome sequencing projects of the plant pathogenic fungi Botrytis Cinerea and Sclerotinia Sclerotiorum. Macromolecules and secondary metabolites of grapevine and wine : fruit development, biotic and abiotic stresses, mechanisms of plant defense responses, proteins, glycoproteins, polysaccharides, polyphenolics, aroma compounds and secondar, EDITIONS TEC ET DOC, 2007, 978-2-7430-0965-9. ⟨hal-02820038⟩

Other publications1 document

Reports3 documents

  • Anne-Françoise Adam-Blondon, Claude Pavis, Franciane Nuissier, Thierry Lacombe, Nicolas Guilhot, et al.. Projet Coll-GATE: Collaborative development of a web application for the management of the collections. [Contract] 2015. ⟨hal-02793863⟩
  • Windpouire Esther Dzale Yeumo, Lydie Soler, Michael Alaux, Robert Bossy, Sebastien Carrere, et al.. Rapport de synthèse du chantier DOI. [Autre] 2014, 47 p. ⟨hal-02801364⟩
  • Windpouire Esther Dzale Yeumo, Lydie Soler, Sophie Aubin, Christine Boizot-Szantaï, Patrice Buche, et al.. Rapport d'étape chantier entrepôt et annuaire institutionnels pour les données de la recherche. [Autre] 2014, 18 p. ⟨hal-02801608⟩

Lectures1 document

  • Cyril Pommier, Anne-Françoise Adam-Blondon, Célia Michotey. Plant Data Managment for Phenotyping Experiments: Data standards and use cases for plant scientists and informaticians. École thématique. France. 2020. ⟨hal-03102944⟩