Cyril Pommier
Présentation
Cyril Pommier is a bio-informatician with a multidisciplinary background in molecular biology and computer science. He worked four years on genomic databases and has been working since 2007 on plant data management in global data federations with a focus on crops phenomic. He builds bridges between plant experimentation in the field, molecular biology and computer science from information system development to data management frameworks. He is now in charge of data and federation in the URGI PlantBioinfoPF, an INRAE bioinformatic platform part of ELIXIR-fr. Cyril Pommier is also co leader of the Plant community of ELIXIR (https://elixir-europe.org/communities/plant-sciences), the European Infrastructure for life science and co leader the Information System of Phenom-EMPHASIS, the national infrastructure for plant phenotyping. He is leading the building of data repositories (https://doi.org/10.34133/2019/1671403), data portals (https://urgi.versailles.inrae.fr/faidare/) and co leads international plant data standards (MIAPPE https://www.miappe.org , BrAPI https://www.brapi.org).
Publications
Publications
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Plant Science Data Integration, from Building Community Standards to Defining a Consistent Data LifecycleTowards Responsible Plant Data Linkage: Data Challenges for Agricultural Research and Development, Springer International Publishing, pp.149-160, 2023, ⟨10.1007/978-3-031-13276-6_8⟩ |
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Mining plant genomic and genetic data using the GnpIS information systemAalt 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⟩ |
Whole genome sequencing projects of the plant pathogenic fungi Botrytis Cinerea and Sclerotinia SclerotiorumMacromolecules 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 |
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Ontology mapping for wheat trait information managementSéminaire résidentiel INRAE Semantic Linked Data, 2023 |
ELIXIR Plant sciences 2020-2023 RoadmapAutre publication scientifique hal-03254504v1 |
Plant phenotyping data standards to enable sharing and integration2025 North American Plant Phenotyping Network Annual Conference, NAPPN, Feb 2025, Saint Louis (Missouri), United States |
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Find Genomic, Genetic and Phenomic Data for Wheat Using the WheatIS Data Discovery ToolPAG 32, Jan 2025, San Diego (CA), United States |
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Genetic Resources Data Exchange and Findability for the French Plant Genebanks Using BrAPIPAG 32, Jan 2025, San Diego (CA), United States |
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Les services de FAIRification des données à l’URGI : cas d’utilisation par des projets/consortium nationaux et internationauxRéunion annuelle de l'IFB, Dec 2025, Paris, France |
FAIR Plant Phenomics Data Management Tools and Guidelines.Plant and Animal Genome, Jan 2024, San Diego, United States |
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Plant phenotyping data standards to enable sharing and integrationPhenoharmonis 2024, Bioversity; Digitag; INRAE; Phenome, May 2024, Montpelier, France |
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Plant phenotyping data management from phenomics to integration for analysis and PGR characterizations: challenges and solutions from INRAE, ELIXIR and EMPHASISTowards Data Linkage: Data Standardization for Agricultural Research., NARO, Oct 2024, Tsukuba, Japan |
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Long Term Plant Phenomic Data Sharing in Generic Data Repositories (Zenodo, Dataverse, e!Dale) Using MIAPPEPlant and Animal Genome (PAG), Jan 2024, San Diego (CA), United States |
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Les outils de gestion de données de phénotypage soutenus par INRAEAG RARE, INRAE, May 2023, Toulouse, France |
Plant science data management and integration: the heterogeneity and dispersion challengeApplied Bioinformatics in Life Sciences (4th edition), Mar 2022, Louvain, Belgium |
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Plant Phenomics data management challenges and solutions based on the Minimum Information About Plant Phenotyping Experiments (MIAPPE)Ontologies Community of Practice, CGIAR, Nov 2020, Webinar, France |
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Phenotype and genotype data sharingPAG XXVII - Plant and Animal Genome Conference, Jan 2019, San Diego, Californie, United States. pp.24 Slides |
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Developing infrastructures for FAIR data in plant biologyGatersleben Research Conference - Applied Bioinformatics for crops (GRC2019), IPK, Mar 2019, Gatersleben, Germany |
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The Vitis Ontology: sustainable and FAIR (Findable, Accessible, Interoperable, Reusable) for consistent and complete data description through biologist friendly ontologiesThe First Annual Meeting of COST Action CA17111 INTEGRAPE 2019, Mar 2019, Chania, Greece, 26-28 March 2019, Greece |
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Data standards for plant phenotyping: MIAPPE and its implementations26. Plant and Animal Genome Conference (PAG XXVI), Jan 2018, San Diego, United States. pp.24 slides |
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Phenome-Emphasis-Elixir: phenotyping data management and integration12. International Conference on Grapevine Breeding and Genetics, Jul 2018, Bordeaux, France. pp.16 |
Developing grapevine FAIR DataPAG Conference 2018, Jan 2018, San Diego, United States |
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BreedWheat GWAS data in GnpIS information systemEucarpia Cereal Section - Breeding cereals for sustainable agriculture, Mar 2018, Clermont-Ferrand, France |
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FAIR Data publication for phenomics dataIntegrative Bioinformatics Symposium 2018, BBSRC Rothamsted Research. GBR., Jun 2018, Rothamsted, United Kingdom. pp.52 slides + 40 slides |
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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 |
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Improving the « FAIRness » of Inra’s data for plant biology and breedingPAG XXVI - Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.14 slides |
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The IWGSC Data repository and wheat data resources hosted at URGI: Overview and perspectivesPAG XXVI - Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.32 slides |
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Exemples d’outils et services pour la gestion et le partage des données à l’InraJournée "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 |
EMBI-EBI Industry Workshop: Ontologies in Agriculture, Food and NutritionOntologies in Agriculture, Food and Nutrition, European Molecular Biology Laboratory (EMBL). GBR., Apr 2017, Cambridge, United Kingdom |
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Distributed plant phenotyping data integration: challenges and feedback from French and international consortiumsData Scientist Big Data Plant Breeding, Wageningen University and Research Centre (WUR). NLD., Dec 2017, Wageningen, Netherlands |
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Findable, Accessible, Interoperable and Reusable data linked to genetic resources for plant biology and breeding at INRA4. International Symposium on Genomics of Plant Genetic Resources, Sep 2017, Giessen, Germany. pp.17 slides |
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Reusing the NCBO BioPortal technology for agronomy to build AgroPortalICBO 2016 - 7th International Conference on Biomedical Ontologies, P. Jaiswal; R. Hoehndorf, Aug 2016, Corvallis, OR, United States |
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Contribution to a European roadmap for data standardisation in Plant Science at URGI-INRAPlant Biology Europe EPSO / FESBP 2016 Congress, Jun 2016, Prague, Czech Republic |
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Exposing French agronomic resources as Linked Open DataIN-OLIVE, Jun 2016, Montpellier, France |
Exposing French agronomic resources as Linked Open DataSWAT4LS: Semantic Web Applications and Tools for Life Sciences, Dec 2015, Cambridge, United Kingdom |
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Phenotypic Data Exchange and Processing Using ISA-Tab Standard: transPLANT Project Use Case with GnpIS.Ephesis and Bii23. Plant and Animal Genome (PAG), Jan 2015, San Diego, United States |
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Grape@GnpIS: Overview of the GnpIS grape genomics and genetics integrative resource23. Plant and Animal Genome (PAG XXIII), Jan 2015, San Diego, United States. pp.24 slides |
GnpIS-Asso : A Generic Database for Managing and Exploiting Plant Genetic Association Studies Results Using High Throughput Genotyping and Phenotyping Data23. Plant and Animal Genome, Jan 2015, San Diego, United States |
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Towards efficient data integration and knowledge management in the Agronomic domainAPIA: Applications Pratiques de l'Intelligence Artificielle, Institut National de Recherche en Informatique et en Automatique (INRIA). FRA., Jul 2015, Rennes, France. pp.117-124 |
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URGI plant and fungi platform: distributed resources through GMOD toolsPlant and Animal Genome conference XXII, GMOD session, Jan 2014, San Diego, United States |
Open data for grapevine biology11. International Congress on Grapevine Breeding and Genetics, Jul 2014, Pékin, China |
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Plant biology open data interoperability in the big data eraPlant Biology Europe EPSO/FEPBS 2014, Jun 2014, Dublin, Germany |
Information system for phenotype data: trait, trials and genotypes identification and integration22. Conference Plant and Animal Genome, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI). GBR., Jan 2014, San Diego, United States |
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A generic tool for managing and exploiting genetic association studies results using high throughput genotyping and phenotypingPlant Genomics Seminar 2012, Apr 2012, Pont-Royal en Provence, France |
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URGI genome annotation system:an integrated system for structural and functional genome annotation12. Edition du colloque JOBIM : Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2011, Paris, France. 2 p |
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AGENT Guidelines for dataflow2025 |
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BioHackEU22 Project 22: Plant data exchange and standard interoperability2023 |
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PHENET-EMPHASIS Data Management TrainingDoctoral. Data Management training, Paris, France. 2024, 1 p |
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FAIR data PLANT PHENO 2023École thématique. FAIR data PLANT PHENO 2023, Paris, France. 2023 |
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Plant Data Managment for Phenotyping ExperimentsÉcole thématique. France. 2020 |
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From hurdles to harmony: FAIR data management for plant phenotyping in EMPHASIS and ELIXIR communitiesEuropean Plant Phenomics Symposium (EPPS), Sep 2025, Bonn, Germany |
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Forest Tree data in FAIDARE, a plant data discovery portalPlant and Animal Genome (PAG), Jan 2025, San Diego (CA), United States |
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URGI – A scientific facility dedicated to plant bioinformaticsJOBIM 2025, Jul 2025, Bordeaux (France), France |
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Learning path development for plant data managementELIXIR All Hands 2023, Jun 2023, Dublin, Ireland. f1000research.com, https://doi.org/10.7490/f1000research.1119444.1, 2023, ⟨10.7490/f1000research.1119444.1⟩ |
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Research Data Management Toolkit (RDMkit): guidelines for plant phenotyping data management and sharing7. International Plant Phenotyping Symposium (IPPS 2022), Sep 2022, Wageningen, Netherlands. , 2022, ⟨10.5281/zenodo.7148792⟩ |
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D2KAB project taking off: Data to Knowledge in Agronomy and Biodiversity14th Research Data Alliance Plenary Conference (RDA P14), Best poster award, Oct 2019, Helsinki, Finland. , 2019, ⟨10.5281/zenodo.3520300⟩ |
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PHIS, a plant science ontology-driven Phenotyping Hybrid Information SystemNETTAB 2018: Building a FAIR Bioinformatics environment, Oct 2018, Genova, Italy. , 1 p., 2018 |
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Findable, Accessible, Interoperable and Reusable data linked to genetic resources for plant biology and breeding at INRACrop diversification in a changing world : Mobilizing the green gold of plant genetic resources, May 2017, Montpellier, France. , 2017, EUCARPIA Genetic Resources 2017 |
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PHENOME: French Plant Phenomic CenterRecent progress in drought tolerance from genetics to modelling, Jun 2015, Montpellier, France. 2015 |
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Forest tree GnpIS: an information system dedicated to forest tree genetics, genomics and phenomics35. New Phytologist Symposium, Jun 2015, Boston, United States. 2015 |
PHENOME: French Plant Phenomic Center9th International Wheat Conference, Sep 2015, Sydney, Australia. 2015 |
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Data integration in the agronomic domain : national and international data discovery systemJOBIM: Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. , Post-105 (#59), 2015 |
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PHENOME: French Plant Phenomic CenterEPPN Plant Phenotyping Symposium, Nov 2015, Barcelona, Spain. 2015 |
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BreedWheat genotyping and phenotyping data in GnpIS information systemJOBIM 2015 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. 2015 |
Wheat Crop Ontology: A Species Specific Trait Ontology. Use Case: The URGI Information SystemPlant and Animal Genome, Jan 2013, San Diego, United States. 2013 |
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ELIXIR-CONVERGE D5.5 Report on the remaining four DMP processesELIXIR. 2023 |
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D4.5:Data policy rulesINRAE. 2021, 10p |
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EU Project N° 739514 Acronym EMPHASIS-PREP Full title Preparation for EMPHASIS: European Infrastructure for multi-scale Plant Phenomics and Simulation for food security in a changing climate Project website emphasis.plant-phenotyping.euINRAE. 2019 |
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RDF Query interface from BrAPI web service sourceINRAE. 2017, https://rd-alliance.org/sites/default/files/attachment/Creation%20of%20a%20Query%20interface%20for%20phenotyping%20data%20Final%20Report.pdf |
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Projet Coll-GATE[Contract] 2015 |
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Rapport d'étape chantier entrepôt et annuaire institutionnels pour les données de la recherche[0] 2014, 18 p |
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Rapport de synthèse du chantier DOI[0] 2014, 47 p |