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Cyril Pommier
Plant research data engineer.
87
Documents
Researcher identifiers
cyril-pommier
-
0000-0002-9040-8733
Presentation
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).
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).
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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⟩
Book sections
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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⟩
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hal-03206731v1
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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
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hal-02820038v1
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Ontology mapping for wheat trait information managementSéminaire résidentiel INRAE Semantic Linked Data, 2023
Other publications
hal-04420465v1
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ELIXIR Plant sciences 2020-2023 RoadmapOther publications hal-03254504v1 |
FAIR Plant Phenomics Data Management Tools and Guidelines.Plant and Animal Genome, Jan 2024, San Diego, United States
Conference papers
hal-04425516v1
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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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hal-04425548v1
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Les outils de gestion de données de phénotypage soutenus par INRAEAG RARE, INRAE, May 2023, Toulouse, France
Conference papers
hal-04314299v1
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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
Conference papers
hal-03851454v1
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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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Developing infrastructures for FAIR data in plant biologyGatersleben Research Conference - Applied Bioinformatics for crops (GRC2019), IPK, Mar 2019, Gatersleben, Germany
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hal-03316569v1
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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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hal-02789384v1
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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
Conference papers
hal-02947459v1
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Developing grapevine FAIR DataPAG Conference 2018, Jan 2018, San Diego, United States
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hal-02738117v1
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Phenome-Emphasis-Elixir: phenotyping data management and integrationInterenational Grape Genetics and Breeding Symposium, Jul 2018, Bordeaux, France. pp.16
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hal-02789613v1
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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
Conference papers
hal-02789754v1
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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
Conference papers
hal-02788401v1
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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
Conference papers
hal-02790227v1
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BreedWheat GWAS data in GnpIS information systemEucarpia Cereal Section - Breeding cereals for sustainable agriculture, Mar 2018, Clermont-Ferrand, France
Conference papers
hal-02340450v1
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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
Conference papers
hal-02787988v1
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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
Conference papers
hal-01779751v1
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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
Conference papers
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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
Conference papers
hal-02791168v1
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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
Conference papers
hal-02788362v1
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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
Conference papers
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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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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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Exposing French agronomic resources as Linked Open DataIN-OLIVE, Jun 2016, Montpellier, France
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hal-01411759v1
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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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hal-02739236v1
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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
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hal-02741780v1
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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
Conference papers
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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
Conference papers
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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
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Plant biology open data interoperability in the big data eraPlant Biology Europe EPSO/FEPBS 2014, Jun 2014, Dublin, Germany
Conference papers
hal-02801067v1
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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
Conference papers
hal-02796293v1
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Open data for grapevine biologyXI. International Congress on Grapevine Breeding and Genetics, Jul 2014, Pékin, China
Conference papers
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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
Conference papers
hal-02795958v1
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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
Conference papers
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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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hal-01019754v1
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Mapping bread wheat trait ontologies for semantic interoperability2024
Preprints, Working Papers, ...
hal-04717147v1
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AGENT Guidelines for dataflow2024
Preprints, Working Papers, ...
hal-04822902v1
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BioHackEU22 Project 22: Plant data exchange and standard interoperability2023
Preprints, Working Papers, ...
hal-04020940v1
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PHENET-EMPHASIS Data Management TrainingDoctoral. Data Management training, Paris, France. 2024, 1 p
Lectures
hal-04822964v1
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FAIR data PLANT PHENO 2023École thématique. FAIR data PLANT PHENO 2023, Paris, France. 2023
Lectures
hal-04459199v1
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Plant Data Managment for Phenotyping ExperimentsÉcole thématique. France. 2020
Lectures
hal-03102944v1
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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⟩
Conference poster
hal-04428391v1
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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⟩
Conference poster
hal-03800325v1
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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⟩
Conference poster
lirmm-02351000v1
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PHIS, a plant science ontology-driven Phenotyping Hybrid Information SystemConference poster hal-02788853v1 |
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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
Conference poster
hal-01606277v1
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PHENOME: French Plant Phenomic CenterRecent progress in drought tolerance from genetics to modelling, Jun 2015, Montpellier, France. 2015
Conference poster
hal-02744329v1
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PHENOME: French Plant Phenomic CenterEPPN Plant Phenotyping Symposium, Nov 2015, Barcelona, Spain. 2015
Conference poster
hal-01229565v1
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PHENOME: French Plant Phenomic Center9th International Wheat Conference, Sep 2015, Sydney, Australia. 2015
Conference poster
hal-02800017v1
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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
Conference poster
lirmm-01274725v1
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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
Conference poster
hal-02795537v1
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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
Conference poster
hal-02801654v1
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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
Conference poster
hal-02810186v1
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ELIXIR-CONVERGE D5.5 Report on the remaining four DMP processesELIXIR. 2023
Reports
hal-04503558v1
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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
Reports
hal-04505409v1
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Projet Coll-GATE[Contract] 2015
Reports
hal-02793863v1
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Rapport de synthèse du chantier DOI[0] 2014, 47 p
Reports
hal-02801364v1
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Rapport d'étape chantier entrepôt et annuaire institutionnels pour les données de la recherche[0] 2014, 18 p
Reports
hal-02801608v1
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