
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⟩
Chapitre d'ouvrage
hal-03896793
v1
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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⟩
Chapitre d'ouvrage
hal-03206731
v1
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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
Chapitre d'ouvrage
hal-02820038
v1
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Ontology mapping for wheat trait information managementSéminaire résidentiel INRAE Semantic Linked Data, 2023
Autre publication scientifique
hal-04420465
v1
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ELIXIR Plant sciences 2020-2023 RoadmapAutre publication scientifique hal-03254504 v1 |
Plant phenotyping data standards to enable sharing and integration2025 North American Plant Phenotyping Network Annual Conference, NAPPN, Feb 2025, Saint Louis (Missouri), United States
Communication dans un congrès
hal-04967423
v1
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FAIR Plant Phenomics Data Management Tools and Guidelines.Plant and Animal Genome, Jan 2024, San Diego, United States
Communication dans un congrès
hal-04425516
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Plant phenotyping data standards to enable sharing and integrationPhenoharmonis 2024, Bioversity; Digitag; INRAE; Phenome, May 2024, Montpelier, France
Communication dans un congrès
hal-04967400
v1
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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
Communication dans un congrès
hal-04967207
v1
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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
Communication dans un congrès
hal-04425548
v1
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Les outils de gestion de données de phénotypage soutenus par INRAEAG RARE, INRAE, May 2023, Toulouse, France
Communication dans un congrès
hal-04314299
v1
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Plant science data management and integration: the heterogeneity and dispersion challengeApplied Bioinformatics in Life Sciences (4th edition), Mar 2022, Louvain, Belgium
Communication dans un congrès
hal-03851454
v1
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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
Communication dans un congrès
hal-04314409
v1
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Developing infrastructures for FAIR data in plant biologyGatersleben Research Conference - Applied Bioinformatics for crops (GRC2019), IPK, Mar 2019, Gatersleben, Germany
Communication dans un congrès
hal-03316569
v1
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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
Communication dans un congrès
hal-02789384
v1
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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
Communication dans un congrès
hal-02947459
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Data standards for plant phenotyping: MIAPPE and its implementations26. Plant and Animal Genome Conference (PAG XXVI), Jan 2018, San Diego, Californie, United States. pp.24 slides
Communication dans un congrès
hal-02789754
v1
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Phenome-Emphasis-Elixir: phenotyping data management and integrationInterenational Grape Genetics and Breeding Symposium, Jul 2018, Bordeaux, France. pp.16
Communication dans un congrès
hal-02789613
v1
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Developing grapevine FAIR DataPAG Conference 2018, Jan 2018, San Diego, United States
Communication dans un congrès
hal-02738117
v1
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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
Communication dans un congrès
hal-02790227
v1
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BreedWheat GWAS data in GnpIS information systemEucarpia Cereal Section - Breeding cereals for sustainable agriculture, Mar 2018, Clermont-Ferrand, France
Communication dans un congrès
hal-02340450
v1
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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
Communication dans un congrès
hal-02787988
v1
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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
Communication dans un congrès
hal-01779751
v1
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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
Communication dans un congrès
hal-02788401
v1
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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
Communication dans un congrès
hal-02787834
v1
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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
Communication dans un congrès
hal-02785564
v1
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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
Communication dans un congrès
hal-02791168
v1
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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
Communication dans un congrès
hal-02788362
v1
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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
Communication dans un congrès
hal-02794139
v1
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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
Communication dans un congrès
hal-01398251
v1
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Exposing French agronomic resources as Linked Open DataIN-OLIVE, Jun 2016, Montpellier, France
Communication dans un congrès
hal-01411759
v1
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Exposing French agronomic resources as Linked Open DataSWAT4LS: Semantic Web Applications and Tools for Life Sciences, Dec 2015, Cambridge, United Kingdom
Communication dans un congrès
lirmm-01274884
v1
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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
Communication dans un congrès
hal-02739236
v1
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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, Californie, United States. pp.24 slides
Communication dans un congrès
hal-02741780
v1
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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
Communication dans un congrès
hal-01174322
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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
Communication dans un congrès
hal-01176903
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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 (CA), United States
Communication dans un congrès
hal-02796293
v1
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Open data for grapevine biologyXI. International Congress on Grapevine Breeding and Genetics, Jul 2014, Pékin, China
Communication dans un congrès
hal-01352690
v1
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Plant biology open data interoperability in the big data eraPlant Biology Europe EPSO/FEPBS 2014, Jun 2014, Dublin, Germany
Communication dans un congrès
hal-02801067
v1
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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
Communication dans un congrès
hal-02795958
v1
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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
Communication dans un congrès
hal-01268379
v1
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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
Communication dans un congrès
hal-01019754
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AGENT Guidelines for dataflow2025
Pré-publication, Document de travail
hal-04822902
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BioHackEU22 Project 22: Plant data exchange and standard interoperability2023
Pré-publication, Document de travail
hal-04020940
v1
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PHENET-EMPHASIS Data Management TrainingDoctoral. Data Management training, Paris, France. 2024, 1 p
Cours
hal-04822964
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FAIR data PLANT PHENO 2023École thématique. FAIR data PLANT PHENO 2023, Paris, France. 2023
Cours
hal-04459199
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Plant Data Managment for Phenotyping ExperimentsÉcole thématique. France. 2020
Cours
hal-03102944
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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
Poster de conférence
hal-04927258
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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⟩
Poster de conférence
hal-04428391
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Research Data Management Toolkit (RDMkit): guidelines for plant phenotyping data management and sharing7th International Plant Phenotyping Symposium, Sep 2022, Wageningen, Netherlands. , 2022, ⟨10.5281/zenodo.7148792⟩
Poster de conférence
hal-03800325
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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⟩
Poster de conférence
lirmm-02351000
v1
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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
Poster de conférence
hal-02788853
v1
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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
Poster de conférence
hal-01606277
v1
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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
Poster de conférence
hal-02795537
v1
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PHENOME: French Plant Phenomic CenterRecent progress in drought tolerance from genetics to modelling, Jun 2015, Montpellier, France. 2015
Poster de conférence
hal-02744329
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PHENOME: French Plant Phenomic CenterEPPN Plant Phenotyping Symposium, Nov 2015, Barcelona, Spain. 2015
Poster de conférence
hal-01229565
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PHENOME: French Plant Phenomic Center9th International Wheat Conference, Sep 2015, Sydney, Australia. 2015
Poster de conférence
hal-02800017
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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
Poster de conférence
lirmm-01274725
v1
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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
Poster de conférence
hal-02801654
v1
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Wheat Crop Ontology: A Species Specific Trait Ontology. Use Case: The URGI Information SystemPlant and Animal Genome, Jan 2013, San Diego, United States. 2013
Poster de conférence
hal-02810186
v1
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