Cyril Pommier Plant research data engineer.

Identifiants chercheurs

IdHAL :

cyril-pommier

ORCID :

0000-0002-9040-8733

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

Article dans une revue (29)

Wheat historical phenotypic data from European genebanks as an important resource for research and breeding Erwan Le Floch,Anne-Françoise Adam-Blondon,Michael Alaux,Etienne Bardet,Noor Baset al. Scientific Data , 2026, ⟨10.1038/s41597-026-06908-x⟩ Article dans une revue (data paper) hal-05549503v2
Strengthening bioinformatics education: e-learning initiatives across ELIXIR Nodes and Communities Monique Zahn-Zabala,Minna Ahokas,Bérénice Batut,Sebastian Beier,Alexander Botzkiet al. F1000Research, 2025, 14, pp.1422. ⟨10.12688/f1000research.173116.1⟩ Article dans une revue hal-05441563v1
Reassessing data management in increasingly complex phenotypic datasets Cyril Pommier,Isabelle Alic,Llorenç Cabrera-Bosquet,Xavier Draye,Neveu Pascalet al. Trends in Plant Science, In press, 12p. ⟨10.1016/j.tplants.2025.09.001⟩ Article dans une revue hal-05301975v1
BrAPI v2: real-world applications for data integration and collaboration in the breeding and genetics community Peter Selby,Rafael Abbeloos,Anne-Francoise Adam-Blondon,Francisco J. Agosto-Pérez,Michael Alauxet al. Database - The journal of Biological Databases and Curation, 2025, 2025, pp.baaf048. ⟨10.1093/database/baaf048⟩ Article dans une revue hal-05290990v1
Mapping bread wheat trait ontologies for semantic interoperability Claire Nédellec,Sophie Aubin,Clara Sauvion,Liliana Ibanescu,Sonia Bravoet al. F1000Research, 2024, pp.1102. ⟨10.12688/f1000research.154860.1⟩ Article dans une revue hal-04717147v1
SyntenyViewer: a comparative genomics-driven translational research tool Raphael Flores,Cécile Huneau,Laura Burlot,Mathilde Lainé,Erik Kimmelet al. Database - The journal of Biological Databases and Curation, 2023, 2023, ⟨10.1093/database/baad027⟩ Article dans une revue hal-04099923v1
The FAIR Cookbook - the essential resource for and by FAIR doers Philippe Rocca-Serra,Wei Gu,Vassilios Ioannidis,Tooba Abbassi-Daloii,Salvador Capella-Gutierrezet al. Scientific Data , 2023, 10 (1), pp.292. ⟨10.1038/s41597-023-02166-3⟩ Article dans une revue hal-04538400v1
ELIXIR biovalidator for semantic validation of life science metadata Isuru Liyanage,Tony Burdett,Bert Droesbeke,Karoly Erdos,Rolando Fernandezet al. Bioinformatics, 2022, 38 (11), pp.3141-3142. ⟨10.1093/bioinformatics/btac195⟩ Article dans une revue hal-04312070v1
Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR Sebastian Beier,Anne Fiebig,Cyril Pommier,Isuru Liyanage,Matthias Langeet al. F1000Research, 2022, 11, pp.231. ⟨10.12688/f1000research.109080.1⟩ Article dans une revue hal-04456815v1
Editorial: Phenotyping; From Plant, to Data, to Impact and Highlights of the International Plant Phenotyping Symposium - IPPS 2018 Cyril Pommier,Trevor Garnett,Carolyn Lawrence-Dill,Tony Pridmore,Michelle Wattet al. Frontiers in Plant Science, 2020, 11, ⟨10.3389/fpls.2020.618342⟩ Article dans une revue hal-03219213v1
Enabling reusability of plant phenomic datasets with MIAPPE 1.1 Evangelia Papoutsoglou,Daniel Faria,Daniel Arend,Elizabeth Arnaud,Ioannis Athanasiadiset al. New Phytologist, 2020, 227 (1), pp.260-273. ⟨10.1111/nph.16544⟩ Article dans une revue hal-02949641v1
The ontologies community of practice: A CGIAR initiative for big data in agrifood systems Elizabeth Arnaud,Marie-Angélique Laporte,Soonho Kim,Céline Aubert,Sabina Leonelliet al. Patterns, 2020, 1 (7), pp.100105. ⟨10.1016/j.patter.2020.100105⟩ Article dans une revue hal-02949637v1
Dealing with multi-source and multi-scale information in plant phenomics: the ontology-driven Phenotyping Hybrid Information System Pascal Neveu,Anne Tireau,Nadine Hilgert,Vincent Negre,Jonathan Mineau-Cesariet al. New Phytologist, 2019, 221 (1), pp.588-601. ⟨10.1111/nph.15385⟩ Article dans une revue hal-02627721v1
The walnut genetic resources of INRA: chronological phenotypic data and ontology Anthony Bernard,Teresa Barreneche,Marine Delmas,Sophie Durand,Cyril Pommieret al. BMC Research Notes, 2019, 12 (1), pp.662. ⟨10.1186/s13104-019-4678-1⟩ Article dans une revue (data paper) hal-02626113v1
BrAPI - an Application Programming Interface for Plant Breeding Applications. Rafael Abbeloos,Jan Erik Backlund,Martin Basterrechea Salido,Guillaume Bauchet,Omar Benites-Alfaroet al. Bioinformatics, 2019, 35 (20), pp.4147-4155. ⟨10.1093/bioinformatics/btz190⟩ Article dans une revue hal-02626802v1
RepetDB: a unified resource for transposable element references Joëlle Amselem,Guillaume Cornut,Nathalie Choisne,Michael Alaux,Françoise Alfama Depauwet al. Mobile DNA, 2019, 10, pp.1-8. ⟨10.1186/s13100-019-0150-y⟩ Article dans une revue hal-02625212v1
Applying FAIR principles to plant phenotypic data management in GnpIS Cyril Pommier,Célia Michotey,Guillaume Cornut,Pierre Roumet,Eric Duchêneet al. Plant Phenomics, 2019, 2019, pp.1-15. ⟨10.34133/2019/1671403⟩ Article dans une revue hal-02624031v1
Corrigendum: Towards recommendations for metadata and data handling in plant phenotyping Pawel Krajewski,Dijun Chen,Hanna Cwiek,Aalt D. J. van Dijk,Fabio Fioraniet al. Journal of Experimental Botany, 2018, 69 (7), pp.1819-1819. ⟨10.1093/jxb/ery006⟩ Article dans une revue hal-02620800v1
Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data Michael Alaux,Jane Rogers,Thomas Letellier,Raphaël Flores,Françoise Alfamaet al. Genome Biology, 2018, 19 (1), pp.905-911. ⟨10.1186/s13059-018-1491-4⟩ Article dans une revue hal-02278879v1
Developing data interoperability using standards: A wheat community use case Esther Dzale Yeumo,Michaël Alaux,Elizabeth Arnaud,Sophie Aubin,Ute Baumannet al. F1000Research, 2017, 6 (1843), pp.1843. ⟨10.12688/f1000research.12234.1⟩ Article dans une revue lirmm-01652022v2
TransPLANT resources for triticeae genomic data Manuel Spannagl,Michael M. Alaux,Matthias Lange,Dan M. Bolser,Kai Christian Baderet al. PLANT GENOME, 2016, 9 (1), 13 p. ⟨10.3835/plantgenome2015.06.0038⟩ Article dans une revue hal-02635899v1
Towards an open grapevine information system Anne-Françoise Adam-Blondon,Michael Alaux,Cyril Pommier,D Cantu,Z-M Chenget al. Horticulture research, 2016, 3, pp.16056. ⟨10.1038/hortres.2016.56⟩ Article dans une revue (article de synthèse) hal-01404714v1
Measures for interoperability of phenotypic data: minimum information requirements and formatting Thomas Altmann,Daniel Arend,Elizabeth Arnaud,Dijun Chen,Guillaume Cornutet al. Plant Methods, 2016, 12, pp.1-18. ⟨10.1186/s13007-016-0144-4⟩ Article dans une revue hal-02640958v1
Towards recommendations for metadata and data handling in plant phenotyping Pawel Krajewski,Dijun Chen,Hanna Cwiek,Aalt D. J. van Dijk,Fabio Fioraniet al. Journal of Experimental Botany, 2015, 66 (18), pp.5417-5427. ⟨10.1093/jxb/erv271⟩ Article dans une revue hal-02636470v1
GnpIS: an information system to integrate genetic and genomic data from plants and fungi Delphine D. Steinbach,Michael M. Alaux,Joelle J. Amselem,Nathalie Choisne,Sophie S. Durandet al. Database - The journal of Biological Databases and Curation, 2013, 2013, pp.1-9. ⟨10.1093/database/bat058⟩ Article dans une revue hal-02648084v1
The Ectocarpus Genome and Brown Algal Genomics The Ectocarpus Genome Consortium J. Mark Cock,Lieven Sterck,Sophia Ahmed,Andrew E. Allen,Grigoris Amoutziaset al. Advances in Botanical Research, 2012, 64, pp.141 - 184. ⟨10.1016/B978-0-12-391499-6.00005-0⟩ Article dans une revue hal-02649287v1
The $Ectocarpus$ genome and the independent evolution of multicellularity in brown algae J. Mark Cock,Lieven Sterck,Pierre Rouzé,Delphine Scornet,Andrew E. Allenet al. Nature, 2010, 465 (7298), pp.617-621. ⟨10.1038/nature09016⟩ Article dans une revue cea-00906990v1
GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts. S. Aubourg,V. Brunaud,C. Bruyere,M. Cock,R. Cookeet al. Nucleic Acids Research, 2005, 33, pp.D641-D646 Article dans une revue hal-00313737v1
GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts Sebastien Aubourg,Veronique Brunaud,Clémence Bruyère,J. Mark Cock,Richard Cookeet al. Nucleic Acids Research, 2005, 33, pp.D641-D646. ⟨10.1093/nar/gki115⟩ Article dans une revue hal-01189162v1

Chapitre d'ouvrage (3)

Plant Science Data Integration, from Building Community Standards to Defining a Consistent Data Lifecycle Cyril Pommier,Frederik Coppens,Hanna Ćwiek-Kupczyńska,Daniel Faria,Sebastian Beieret al. Towards 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-03896793v1
Mining plant genomic and genetic data using the GnpIS information system Anne-Francoise Adam-Blondon,Michael Alaux,Sophie Durand,Thomas Letellier,Guillaume Merceronet al. 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⟩ Chapitre d'ouvrage hal-03206731v1
Whole genome sequencing projects of the plant pathogenic fungi Botrytis Cinerea and Sclerotinia Sclerotiorum Sabine, Helma Fillinger,Joelle J. Amselem,Francois Artiguenave,Arnaud Billault,Mathias Choqueret al. 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 Chapitre d'ouvrage hal-02820038v1

Autre publication scientifique (2)

Ontology mapping for wheat trait information management Claire Nédellec,Sophie Aubin,Liliana Ibanescu,Clara Sauvion,Sonia Bravoet al. Séminaire résidentiel INRAE Semantic Linked Data, 2023 Autre publication scientifique hal-04420465v1
ELIXIR Plant sciences 2020-2023 Roadmap Cyril Pommier,Kristina Gruden,Astrid Junker,Frederik Coppens,Richard Finkerset al. 2021, ⟨10.7490/f1000research.1118482.1⟩ Autre publication scientifique hal-03254504v1

Communication dans un congrès (41)

Find Genomic, Genetic and Phenomic Data for Wheat Using the WheatIS Data Discovery Tool Michael Alaux,Mario Caccamo,Sarah Dyer,David Edwards,Raphaël Floreset al. PAG 32, Jan 2025, San Diego (CA), United States Communication dans un congrès hal-05528830v1
Genetic Resources Data Exchange and Findability for the French Plant Genebanks Using BrAPI Michael Alaux,Anne-Françoise Adam-Blondon,Alice Boizet,Raphael Flores,Nicolas Francillonneet al. PAG 32, Jan 2025, San Diego (CA), United States Communication dans un congrès hal-05528802v1
Towards interconnecting external phenotypic data with EURISCO. Kritika Adhikari,Véronique Lefebvre,Ignazio Verde,Michael Alaux,Cyril Pommieret al. 2nd International Workshop on Plant Genetic Resources, PRO-GRACE consortium, Oct 2025, Chania, Greece Communication dans un congrès hal-05600304v1
Plant phenotyping data standards to enable sharing and integration Cyril Pommier 2025 North American Plant Phenotyping Network Annual Conference, NAPPN, Feb 2025, Saint Louis (Missouri), United States Communication dans un congrès hal-04967423v1
Les services de FAIRification des données à l’URGI : cas d’utilisation par des projets/consortium nationaux et internationaux Michaël Alaux,Anne-Françoise Adam-Blondon,Françoise Alfama,Etienne Bardet,Raphaël Floreset al. Réunion annuelle de l'IFB, Dec 2025, Paris, France Communication dans un congrès hal-05530229v1
FAIR Plant Phenomics Data Management Tools and Guidelines. Cyril Pommier Plant and Animal Genome, Jan 2024, San Diego, United States Communication dans un congrès hal-04425516v1
Plant phenotyping data standards to enable sharing and integration Cyril Pommier Phenoharmonis 2024, Bioversity; Digitag; INRAE; Phenome, May 2024, Montpelier, France Communication dans un congrès hal-04967400v1
Plant phenotyping data management from phenomics to integration for analysis and PGR characterizations: challenges and solutions from INRAE, ELIXIR and EMPHASIS Cyril Pommier Towards Data Linkage: Data Standardization for Agricultural Research., NARO, Oct 2024, Tsukuba, Japan Communication dans un congrès hal-04967207v1
Long Term Plant Phenomic Data Sharing in Generic Data Repositories (Zenodo, Dataverse, e!Dale) Using MIAPPE Cyril Pommier,Erwan Le Floch,Daniel Arend,Flora D Anna Plant and Animal Genome (PAG), Jan 2024, San Diego (CA), United States Communication dans un congrès hal-04425548v1
Les outils de gestion de données de phénotypage soutenus par INRAE Cyril Pommier,Anne Delaunay AG RARE, INRAE, May 2023, Toulouse, France Communication dans un congrès hal-04314299v1
Plant science data management and integration: the heterogeneity and dispersion challenge Cyril Pommier Applied Bioinformatics in Life Sciences (4th edition), Mar 2022, Louvain, Belgium Communication dans un congrès hal-03851454v1
Plant Phenomics data management challenges and solutions based on the Minimum Information About Plant Phenotyping Experiments (MIAPPE) Cyril Pommier Ontologies Community of Practice, CGIAR, Nov 2020, Webinar, France Communication dans un congrès hal-04314409v1
Developing infrastructures for FAIR data in plant biology Cyril Pommier,Guillaume Cornut,Michael Alaux,Windpouire Esther Dzale Yeumo,Raphaël Floreset al. Gatersleben Research Conference - Applied Bioinformatics for crops (GRC2019), IPK, Mar 2019, Gatersleben, Germany Communication dans un congrès hal-03316569v1
Phenotype and genotype data sharing Cyril Pommier PAG XXVII - Plant and Animal Genome Conference, Jan 2019, San Diego, Californie, United States. pp.24 Slides Communication dans un congrès hal-02789384v1
The Vitis Ontology: sustainable and FAIR (Findable, Accessible, Interoperable, Reusable) for consistent and complete data description through biologist friendly ontologies Eric Duchêne,Cyril Pommier The First Annual Meeting of COST Action CA17111 INTEGRAPE 2019, Mar 2019, Chania, Greece, 26-28 March 2019, Greece Communication dans un congrès hal-02947459v1
Data standards for plant phenotyping: MIAPPE and its implementations Cyril Pommier,Guillaume Cornut,Thomas Letellier,Célia Michotey,Pascal Neveuet al. 26. Plant and Animal Genome Conference (PAG XXVI), Jan 2018, San Diego, United States. pp.24 slides Communication dans un congrès hal-02789754v1
Phenome-Emphasis-Elixir: phenotyping data management and integration Anne-Francoise Adam-Blondon,Cyril Pommier,Llorenç Cabrera Bosquet 12. International Conference on Grapevine Breeding and Genetics, Jul 2018, Bordeaux, France. pp.16 Communication dans un congrès hal-02789613v1
Developing grapevine FAIR Data Cyril Pommier,Eric Duchêne,Thierry Lacombe,Timothée Flutre,Michael Alauxet al. PAG Conference 2018, Jan 2018, San Diego, United States Communication dans un congrès hal-02738117v1
Improving the « FAIRness » of Inra’s data for plant biology and breeding Michael Alaux,Cyril Pommier,Esther Dzale Yeumo,Sophie Durand,Raphaël Floreset al. PAG XXVI - Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.14 slides Communication dans un congrès hal-02790227v1
BreedWheat GWAS data in GnpIS information system Mathilde Lainé,Thomas Letellier,Raphaël Flores,Nacer Mohellibi,Cyril Pommieret al. Eucarpia Cereal Section - Breeding cereals for sustainable agriculture, Mar 2018, Clermont-Ferrand, France Communication dans un congrès hal-02340450v1
FAIR Data publication for phenomics data Cyril Pommier Integrative Bioinformatics Symposium 2018, BBSRC Rothamsted Research. GBR., Jun 2018, Rothamsted, United Kingdom. pp.52 slides + 40 slides Communication dans un congrès hal-02787988v1
Standards for distributed Plant Phenotyping data integration: challenges and solutions. Cyril Pommier 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-01779751v1
The IWGSC Data repository and wheat data resources hosted at URGI: Overview and perspectives Michael Alaux,Jane Rogers,Thomas Letellier,Raphaël Flores,Cyril Pommieret al. PAG XXVI - Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.32 slides Communication dans un congrès hal-02788401v1
EMBI-EBI Industry Workshop: Ontologies in Agriculture, Food and Nutrition Cyril Pommier Ontologies in Agriculture, Food and Nutrition, European Molecular Biology Laboratory (EMBL). GBR., Apr 2017, Cambridge, United Kingdom Communication dans un congrès hal-02787834v1
Findable, Accessible, Interoperable and Reusable data linked to genetic resources for plant biology and breeding at INRA Sophie Durand,Windpouire Esther Dzale Yeumo,Cyril Pommier,Michael Alaux,Guillaume Cornutet al. 4. International Symposium on Genomics of Plant Genetic Resources, Sep 2017, Giessen, Germany. pp.17 slides Communication dans un congrès hal-02791168v1
Distributed plant phenotyping data integration: challenges and feedback from French and international consortiums Cyril Pommier Data Scientist Big Data Plant Breeding, Wageningen University and Research Centre (WUR). NLD., Dec 2017, Wageningen, Netherlands Communication dans un congrès hal-02788362v1
Exemples d’outils et services pour la gestion et le partage des données à l’Inra Cyril Pommier,Windpouire Esther Dzale Yeumo 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 Communication dans un congrès hal-02785564v1
Contribution to a European roadmap for data standardisation in Plant Science at URGI-INRA Cyril Pommier,Michael M. Alaux,Windpouire Esther Dzale Yeumo,Guillaume Cornut,Sophie S. Durandet al. Plant Biology Europe EPSO / FESBP 2016 Congress, Jun 2016, Prague, Czech Republic Communication dans un congrès hal-02794139v1
Reusing the NCBO BioPortal technology for agronomy to build AgroPortal Clement Jonquet,Anne Toulet,Elizabeth Arnaud,Sophie Aubin,Esther Dzalé-Yeumoet al. ICBO 2016 - 7th International Conference on Biomedical Ontologies, P. Jaiswal; R. Hoehndorf, Aug 2016, Corvallis, OR, United States Communication dans un congrès hal-01398251v1
Exposing French agronomic resources as Linked Open Data Aravind Venkatesan,Nordine El Hassouni,Florian Phillipe,Cyril Pommier,Hadi Quesnevilleet al. IN-OLIVE, Jun 2016, Montpellier, France Communication dans un congrès hal-01411759v1
Exposing French agronomic resources as Linked Open Data Aravind Venkatesan,Nordine El Hassouni,Florian Philippe,Cyril Pommier,Hadi Quesnevilleet al. SWAT4LS: Semantic Web Applications and Tools for Life Sciences, Dec 2015, Cambridge, United Kingdom Communication dans un congrès lirmm-01274884v1
Phenotypic Data Exchange and Processing Using ISA-Tab Standard: transPLANT Project Use Case with GnpIS.Ephesis and Bii Cyril Pommier,Pawel Krajewski,Thomas Letellier,Hanna Cwiek,Célia Michoteyet al. 23. Plant and Animal Genome (PAG), Jan 2015, San Diego, United States Communication dans un congrès hal-02739236v1
Grape@GnpIS: Overview of the GnpIS grape genomics and genetics integrative resource Nacer Mohellibi,Nathalie Choisne,Aminah A. Keliet,Daphné Verdelet,Françoise Alfamaet al. 23. Plant and Animal Genome (PAG XXIII), Jan 2015, San Diego, United States. pp.24 slides Communication dans un congrès hal-02741780v1
GnpIS-Asso : A Generic Database for Managing and Exploiting Plant Genetic Association Studies Results Using High Throughput Genotyping and Phenotyping Data Delphine Steinbach,Guillaume Merceron,Célia Michotey,Raphaël-Gauthier Flores,Nacer Mohellibiet al. 23. Plant and Animal Genome, Jan 2015, San Diego, United States Communication dans un congrès hal-01174322v1
Towards efficient data integration and knowledge management in the Agronomic domain Aravind Venkatesan,Nordine El Hassouni,Florian Phillipe,Cyril Pommier,Hadi Quesnevilleet al. 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 Communication dans un congrès hal-01176903v1
Open data for grapevine biology Anne-Francoise Adam-Blondon,Eric Duchêne,Sophie Durand,Jérôme Grimplet,Thierry Lacombeet al. 11. International Congress on Grapevine Breeding and Genetics, Jul 2014, Pékin, China Communication dans un congrès hal-01352690v1
URGI plant and fungi platform: distributed resources through GMOD tools Joelle J. Amselem,Michael M. Alaux,Nathalie Choisne,Olivier Inizan,Nicolas Lapaluet al. Plant and Animal Genome conference XXII, GMOD session, Jan 2014, San Diego, United States Communication dans un congrès hal-02796293v1
Plant biology open data interoperability in the big data era Anne-Francoise Adam-Blondon,Sophie S. Durand,Erik Kimmel,Raphaël-Gauthier R.-G. Flores,Cyril Pommieret al. Plant Biology Europe EPSO/FEPBS 2014, Jun 2014, Dublin, Germany Communication dans un congrès hal-02801067v1
Information system for phenotype data: trait, trials and genotypes identification and integration Cyril Pommier,Michael M. Alaux,Sophie S. Durand,Raphaël-Gauthier R.-G. Flores,Aminah A. Kelietet al. 22. 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-02795958v1
A generic tool for managing and exploiting genetic association studies results using high throughput genotyping and phenotyping Célia Michotey,Frédéric Sapet,Pierre Dubreuil,Jacques Le Gouis,Mathilde Causseet al. Plant Genomics Seminar 2012, Apr 2012, Pont-Royal en Provence, France Communication dans un congrès hal-01268379v1
URGI genome annotation system:an integrated system for structural and functional genome annotation Joelle J. Amselem,Michael Alaux,Nathalie Choisne,Nicolas Lapalu,Baptiste Braultet al. 12. Edition du colloque JOBIM : Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2011, Paris, France. 2 p Communication dans un congrès hal-01019754v1

Pré-publication, Document de travail (2)

AGENT Guidelines for dataflow Anne-Françoise Adam-Blondon,Michael Alaux,Matthijs Brouwer,Paul Kersey,Matthias Langeet al. 2025 Pré-publication, Document de travail hal-04822902v1
BioHackEU22 Project 22: Plant data exchange and standard interoperability Daniel Arend,Sebastian Beier,Laurent Bouri,Marco Brandizi,Donald Hobernet al. 2023 Pré-publication, Document de travail hal-04020940v1

Cours (3)

PHENET-EMPHASIS Data Management Training Cyril Pommier,Isabelle Alic,Sylvain Poque,Sebastian Beier,Farzaneh Kazemipour-Ricciet al. Doctoral. Data Management training, Paris, France. 2024, 1 p Cours hal-04822964v1
FAIR data PLANT PHENO 2023 Cyril Pommier,Célia Michotey,Isabelle Alic École thématique. FAIR data PLANT PHENO 2023, Paris, France. 2023 Cours hal-04459199v1
Plant Data Managment for Phenotyping Experiments Cyril Pommier,Anne-Françoise Adam-Blondon,Célia Michotey École thématique. France. 2020 Cours hal-03102944v1

Logiciel (1)

FAIDARE - FAIR Data-finder for Agronomic REsearch Cyril Pommier,Célia Michotey,Raphaël Flores,Michael Alaux,Guillaume Cornutet al. 2018, ⟨swh:1:dir:23a1de0c4fc2ce7945d06be2edd0086e1f6b0ab8;origin=https://forgemia.inra.fr/urgi-is/data-discovery.git;visit=swh:1:snp:f2b8aaeb16cb22ac2eddbb669cd72ff956e33efd;anchor=swh:1:rev:ccc4e3ae99fb7f063e356919498e8732efc4bfd2⟩ Logiciel hal-04638310v1

Poster de conférence (15)

Forest Tree data in FAIDARE, a plant data discovery portal Maud Marty,Najwa Lakmouri,Cyril Pommier,Célia Michotey Plant and Animal Genome (PAG), Jan 2025, San Diego (CA), United States Poster de conférence hal-04927258v1
From hurdles to harmony: FAIR data management for plant phenotyping in EMPHASIS and ELIXIR communities Farzaneh Kazemipour-Ricci,Isabelle Alic,Cyril Pommier European Plant Phenomics Symposium (EPPS), Sep 2025, Bonn, Germany Poster de conférence hal-05472154v1
URGI – A scientific facility dedicated to plant bioinformatics Mariène Wan,Françoise Alfama,Johann Confais,Nicolas Francillonne,Christina Gacicet al. JOBIM 2025, Jul 2025, Bordeaux (France), France Poster de conférence hal-05186831v1
Learning path development for plant data management Vanita Haurheeram,Célia Michotey,Cyril Pommier,Anne-Françoise Adam-Blondon,Elixir Training Platform ELIXIR 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-04428391v1
Research Data Management Toolkit (RDMkit): guidelines for plant phenotyping data management and sharing Erwan Le Floch,Anne-Françoise Adam-Blondon,Isabelle Alic,Bert Droesbeke,Stijn Dhondtet al. 7. International Plant Phenotyping Symposium (IPPS 2022), Sep 2022, Wageningen, Netherlands. , 2022, ⟨10.5281/zenodo.7148792⟩ Poster de conférence hal-03800325v1
D2KAB project taking off: Data to Knowledge in Agronomy and Biodiversity Sophie Aubin,Anne-Francoise Adam-Blondon,Michael Alaux,Mouhamadou Ba,Stéphan Bernardet al. 14th Research Data Alliance Plenary Conference (RDA P14), Best poster award, Oct 2019, Helsinki, Finland. , 2019, ⟨10.5281/zenodo.3520300⟩ Poster de conférence lirmm-02351000v1
PHIS, a plant science ontology-driven Phenotyping Hybrid Information System Pascal Neveu,Anne Tireau,Nadine Hilgert,Vincent Negre,Jonathan Mineau-Cesariet al. NETTAB 2018: Building a FAIR Bioinformatics environment, Oct 2018, Genova, Italy. , 1 p., 2018 Poster de conférence hal-02788853v1
Findable, Accessible, Interoperable and Reusable data linked to genetic resources for plant biology and breeding at INRA Sophie Durand,Esther Dzale Yeumo,Cyril Pommier,Michaël Alaux,Guillaume Cornutet al. Crop 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-01606277v1
Forest tree GnpIS: an information system dedicated to forest tree genetics, genomics and phenomics Célia Michotey,Christel Anger,François Ehrenmann,Odile Rogier,Véronique Jorgeet al. 35. New Phytologist Symposium, Jun 2015, Boston, United States. 2015 Poster de conférence hal-02795537v1
PHENOME: French Plant Phenomic Center Francois Tardieu,Jacques Le Gouis,Pamela Lucas,Frédéric Baret,Pascal Neveuet al. EPPN Plant Phenotyping Symposium, Nov 2015, Barcelona, Spain. 2015 Poster de conférence hal-01229565v1
Data integration in the agronomic domain : national and international data discovery system Florian Philippe,Aravind Venkatesan,Nordine El Hassouni,Cyril Pommier,Manuel Ruizet al. JOBIM: Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. , Post-105 (#59), 2015 Poster de conférence lirmm-01274725v1
PHENOME: French Plant Phenomic Center Jacques Le Gouis,Pamela Lucas,Frédéric Baret,Pascal Neveu,Cyril Pommieret al. 9th International Wheat Conference, Sep 2015, Sydney, Australia. 2015 Poster de conférence hal-02800017v1
PHENOME: French Plant Phenomic Center Francois F. Tardieu,Jacques Le Gouis,Pamela Lucas,Frédéric Baret,Pascal Neveuet al. Recent progress in drought tolerance from genetics to modelling, Jun 2015, Montpellier, France. 2015 Poster de conférence hal-02744329v1
BreedWheat genotyping and phenotyping data in GnpIS information system Marie Laine,Thomas Letellier,Raphaël-Gauthier R.-G. Flores,Loïc Couderc,Nacer Mohellibiet al. JOBIM 2015 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. 2015 Poster de conférence hal-02801654v1
Wheat Crop Ontology: A Species Specific Trait Ontology. Use Case: The URGI Information System Cyril Pommier,Michael M. Alaux,Erik Kimmel,Delphine Steinbach,Elizabeth Arnaudet al. Plant and Animal Genome, Jan 2013, San Diego, United States. 2013 Poster de conférence hal-02810186v1

Rapport (7)

ELIXIR-CONVERGE D5.5 Report on the remaining four DMP processes Laura Portell-Silva,Vanita Haurheeram,Anne-Françoise Adam-Blondon,Salvador Capella-Gutierrez,Marina Popleteevaet al. ELIXIR. 2023 Rapport (rapport contrat/projet) hal-04503558v1
D4.5:Data policy rules François Tardieu,Pascal Neveu,Cyril Pommier INRAE. 2021, 10p Rapport hal-04986212v1
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.eu Francois Tardieu,Pascal Neveu,Cyril Pommier,Llorenç Cabrera-Bosquet INRAE. 2019 Rapport (rapport de recherche) hal-04986218v1
RDF Query interface from BrAPI web service source Cyril Pommier,Guillaume Cornut,Michael Alaux,Windpouire Esther Dzale Yeumo INRAE. 2017, https://rd-alliance.org/sites/default/files/attachment/Creation%20of%20a%20Query%20interface%20for%20phenotyping%20data%20Final%20Report.pdf Rapport hal-04505409v1
Projet Coll-GATE Anne-Françoise Adam-Blondon,Claude Pavis,Franciane Nuissier,Thierry Lacombe,Nicolas Guilhotet al. [Contract] 2015 Rapport (rapport contrat/projet) hal-02793863v1
Rapport d'étape chantier entrepôt et annuaire institutionnels pour les données de la recherche Windpouire Esther Dzale Yeumo,Lydie Soler,Sophie Aubin,Christine Boizot-Szantaï,Patrice Bucheet al. [0] 2014, 18 p Rapport hal-02801608v1
Rapport de synthèse du chantier DOI Windpouire Esther Dzale Yeumo,Lydie Soler,Michael M. Alaux,Robert R. Bossy,Sebastien Carrereet al. [0] 2014, 47 p Rapport hal-02801364v1