Cyril Pommier

Plant research data engineer.
102
Documents
Identifiants chercheurs

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).

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Publications

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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 Bas et al.

Scientific Data , In press, ⟨10.1038/s41597-026-06908-x⟩

Article dans une revue (data paper) hal-05549503v1
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Strengthening bioinformatics education: e-learning initiatives across ELIXIR Nodes and Communities

Monique Zahn-Zabala , Minna Ahokas , Bérénice Batut , Sebastian Beier , Alexander Botzki et 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 Pascal et al.

Trends in Plant Science, In press, 12p. ⟨10.1016/j.tplants.2025.09.001⟩

Article dans une revue hal-05301975v1
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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 Alaux et al.

Database - The journal of Biological Databases and Curation, In press, 2025, pp.baaf048. ⟨10.1093/database/baaf048⟩

Article dans une revue hal-05290990v1
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Mapping bread wheat trait ontologies for semantic interoperability

Claire Nédellec , Sophie Aubin , Clara Sauvion , Liliana Ibanescu , Sonia Bravo et al.

F1000Research, 2024, pp.1102. ⟨10.12688/f1000research.154860.1⟩

Article dans une revue hal-04717147v1
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SyntenyViewer: a comparative genomics-driven translational research tool

Raphael Flores , Cécile Huneau , Laura Burlot , Mathilde Lainé , Erik Kimmel et 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-Gutierrez et al.

Scientific Data , 2023, 10 (1), pp.292. ⟨10.1038/s41597-023-02166-3⟩

Article dans une revue hal-04538400v1
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ELIXIR biovalidator for semantic validation of life science metadata

Isuru Liyanage , Tony Burdett , Bert Droesbeke , Karoly Erdos , Rolando Fernandez et 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 Lange et al.

F1000Research, 2022, 11, pp.231. ⟨10.12688/f1000research.109080.1⟩

Article dans une revue hal-04456815v1
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The ontologies community of practice: A CGIAR initiative for big data in agrifood systems

Elizabeth Arnaud , Marie-Angélique Laporte , Soonho Kim , Céline Aubert , Sabina Leonelli et al.

Patterns, 2020, 1 (7), pp.100105. ⟨10.1016/j.patter.2020.100105⟩

Article dans une revue hal-02949637v1

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 Watt et al.

Frontiers in Plant Science, 2020, 11, ⟨10.3389/fpls.2020.618342⟩

Article dans une revue hal-03219213v1
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Enabling reusability of plant phenomic datasets with MIAPPE 1.1

Evangelia Papoutsoglou , Daniel Faria , Daniel Arend , Elizabeth Arnaud , Ioannis Athanasiadis et al.

New Phytologist, 2020, 227 (1), pp.260-273. ⟨10.1111/nph.16544⟩

Article dans une revue hal-02949641v1
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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-Cesari et al.

New Phytologist, 2019, 221 (1), pp.588-601. ⟨10.1111/nph.15385⟩

Article dans une revue hal-02627721v1
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The walnut genetic resources of INRA: chronological phenotypic data and ontology

Anthony Bernard , Teresa Barreneche , Marine Delmas , Sophie Durand , Cyril Pommier et al.

BMC Research Notes, 2019, 12 (1), pp.662. ⟨10.1186/s13104-019-4678-1⟩

Article dans une revue (data paper) hal-02626113v1
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BrAPI - an Application Programming Interface for Plant Breeding Applications.

Rafael Abbeloos , Jan Erik Backlund , Martin Basterrechea Salido , Guillaume Bauchet , Omar Benites-Alfaro et al.

Bioinformatics, 2019, 35 (20), pp.4147-4155. ⟨10.1093/bioinformatics/btz190⟩

Article dans une revue hal-02626802v1
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RepetDB: a unified resource for transposable element references

Joëlle Amselem , Guillaume Cornut , Nathalie Choisne , Michael Alaux , Françoise Alfama Depauw et al.

Mobile DNA, 2019, 10, pp.1-8. ⟨10.1186/s13100-019-0150-y⟩

Article dans une revue hal-02625212v1
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Applying FAIR principles to plant phenotypic data management in GnpIS

Cyril Pommier , Célia Michotey , Guillaume Cornut , Pierre Roumet , Eric Duchêne et 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 Fiorani et al.

Journal of Experimental Botany, 2018, 69 (7), pp.1819-1819. ⟨10.1093/jxb/ery006⟩

Article dans une revue hal-02620800v1
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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 Alfama et al.

Genome Biology, 2018, 19 (1), pp.905-911. ⟨10.1186/s13059-018-1491-4⟩

Article dans une revue hal-02278879v1
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Developing data interoperability using standards: A wheat community use case

Esther Dzale Yeumo , Michaël Alaux , Elizabeth Arnaud , Sophie Aubin , Ute Baumann et al.

F1000Research, 2017, 6 (1843), pp.1843. ⟨10.12688/f1000research.12234.1⟩

Article dans une revue lirmm-01652022v2
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Towards an open grapevine information system

Anne-Françoise Adam-Blondon , Michael Alaux , Cyril Pommier , D Cantu , Z-M Cheng et al.

Horticulture research, 2016, 3, pp.16056. ⟨10.1038/hortres.2016.56⟩

Article dans une revue (article de synthèse) hal-01404714v1
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TransPLANT resources for triticeae genomic data

Manuel Spannagl , Michael M. Alaux , Matthias Lange , Dan M. Bolser , Kai Christian Bader et al.

PLANT GENOME, 2016, 9 (1), 13 p. ⟨10.3835/plantgenome2015.06.0038⟩

Article dans une revue hal-02635899v1
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Measures for interoperability of phenotypic data: minimum information requirements and formatting

Thomas Altmann , Daniel Arend , Elizabeth Arnaud , Dijun Chen , Guillaume Cornut et 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 Fiorani et al.

Journal of Experimental Botany, 2015, 66 (18), pp.5417-5427. ⟨10.1093/jxb/erv271⟩

Article dans une revue hal-02636470v1
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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. Durand et 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 Amoutzias et 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
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The $Ectocarpus$ genome and the independent evolution of multicellularity in brown algae

J. Mark Cock , Lieven Sterck , Pierre Rouzé , Delphine Scornet , Andrew E. Allen et 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. Cooke et al.

Nucleic Acids Research, 2005, 33, pp.D641-D646

Article dans une revue hal-00313737v1
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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 Cooke et al.

Nucleic Acids Research, 2005, 33, pp.D641-D646. ⟨10.1093/nar/gki115⟩

Article dans une revue hal-01189162v1

Plant Science Data Integration, from Building Community Standards to Defining a Consistent Data Lifecycle

Cyril Pommier , Frederik Coppens , Hanna Ćwiek-Kupczyńska , Daniel Faria , Sebastian Beier et 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
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Mining plant genomic and genetic data using the GnpIS information system

Anne-Francoise Adam-Blondon , Michael Alaux , Sophie Durand , Thomas Letellier , Guillaume Merceron et 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 Choquer et 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

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
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Find Genomic, Genetic and Phenomic Data for Wheat Using the WheatIS Data Discovery Tool

Michael Alaux , Mario Caccamo , Sarah Dyer , David Edwards , Raphaël Flores et al.

PAG 32, Jan 2025, San Diego (CA), United States

Communication dans un congrès hal-05528830v1
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Genetic Resources Data Exchange and Findability for the French Plant Genebanks Using BrAPI

Michael Alaux , Anne-Françoise Adam-Blondon , Alice Boizet , Raphael Flores , Nicolas Francillonne et al.

PAG 32, Jan 2025, San Diego (CA), United States

Communication dans un congrès hal-05528802v1
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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 Flores et 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
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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
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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
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Developing infrastructures for FAIR data in plant biology

Cyril Pommier , Guillaume Cornut , Michael Alaux , Windpouire Esther Dzale Yeumo , Raphaël Flores et al.

Gatersleben Research Conference - Applied Bioinformatics for crops (GRC2019), IPK, Mar 2019, Gatersleben, Germany

Communication dans un congrès hal-03316569v1
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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
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Data standards for plant phenotyping: MIAPPE and its implementations

Cyril Pommier , Guillaume Cornut , Thomas Letellier , Célia Michotey , Pascal Neveu et al.

26. Plant and Animal Genome Conference (PAG XXVI), Jan 2018, San Diego, United States. pp.24 slides

Communication dans un congrès hal-02789754v1
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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 Alaux et al.

PAG Conference 2018, Jan 2018, San Diego, United States

Communication dans un congrès hal-02738117v1

BreedWheat GWAS data in GnpIS information system

Mathilde Lainé , Thomas Letellier , Raphaël Flores , Nacer Mohellibi , Cyril Pommier et al.

Eucarpia Cereal Section - Breeding cereals for sustainable agriculture, Mar 2018, Clermont-Ferrand, France

Communication dans un congrès hal-02340450v1
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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
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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
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Improving the « FAIRness » of Inra’s data for plant biology and breeding

Michael Alaux , Cyril Pommier , Esther Dzale Yeumo , Sophie Durand , Raphaël Flores et al.

PAG XXVI - Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.14 slides

Communication dans un congrès hal-02790227v1
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The IWGSC Data repository and wheat data resources hosted at URGI: Overview and perspectives

Michael Alaux , Jane Rogers , Thomas Letellier , Raphaël Flores , Cyril Pommier et al.

PAG XXVI - Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.32 slides

Communication dans un congrès hal-02788401v1
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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

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

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
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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 Cornut et al.

4. International Symposium on Genomics of Plant Genetic Resources, Sep 2017, Giessen, Germany. pp.17 slides

Communication dans un congrès hal-02791168v1
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Reusing the NCBO BioPortal technology for agronomy to build AgroPortal

Clement Jonquet , Anne Toulet , Elizabeth Arnaud , Sophie Aubin , Esther Dzalé-Yeumo et 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
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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. Durand et al.

Plant Biology Europe EPSO / FESBP 2016 Congress, Jun 2016, Prague, Czech Republic

Communication dans un congrès hal-02794139v1
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Exposing French agronomic resources as Linked Open Data

Aravind Venkatesan , Nordine El Hassouni , Florian Phillipe , Cyril Pommier , Hadi Quesneville et 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 Quesneville et al.

SWAT4LS: Semantic Web Applications and Tools for Life Sciences, Dec 2015, Cambridge, United Kingdom

Communication dans un congrès lirmm-01274884v1
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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 Michotey et al.

23. Plant and Animal Genome (PAG), Jan 2015, San Diego, United States

Communication dans un congrès hal-02739236v1
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Grape@GnpIS: Overview of the GnpIS grape genomics and genetics integrative resource

Nacer Mohellibi , Nathalie Choisne , Aminah A. Keliet , Daphné Verdelet , Françoise Alfama et 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 Mohellibi et al.

23. Plant and Animal Genome, Jan 2015, San Diego, United States

Communication dans un congrès hal-01174322v1
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Towards efficient data integration and knowledge management in the Agronomic domain

Aravind Venkatesan , Nordine El Hassouni , Florian Phillipe , Cyril Pommier , Hadi Quesneville et 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
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URGI plant and fungi platform: distributed resources through GMOD tools

Joelle J. Amselem , Michael M. Alaux , Nathalie Choisne , Olivier Inizan , Nicolas Lapalu et al.

Plant and Animal Genome conference XXII, GMOD session, Jan 2014, San Diego, United States

Communication dans un congrès hal-02796293v1

Open data for grapevine biology

Anne-Francoise Adam-Blondon , Eric Duchêne , Sophie Durand , Jérôme Grimplet , Thierry Lacombe et al.

11. International Congress on Grapevine Breeding and Genetics, Jul 2014, Pékin, China

Communication dans un congrès hal-01352690v1
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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 Pommier et 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. Keliet et 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 Causse et al.

Plant Genomics Seminar 2012, Apr 2012, Pont-Royal en Provence, France

Communication dans un congrès hal-01268379v1
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URGI genome annotation system:an integrated system for structural and functional genome annotation

Joelle J. Amselem , Michael Alaux , Nathalie Choisne , Nicolas Lapalu , Baptiste Brault et 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
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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
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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
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URGI – A scientific facility dedicated to plant bioinformatics

Mariène Wan , Françoise Alfama , Johann Confais , Nicolas Francillonne , Christina Gacic et al.

JOBIM 2025, Jul 2025, Bordeaux (France), France

Poster de conférence hal-05186831v1
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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
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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 Dhondt et al.

7. International Plant Phenotyping Symposium (IPPS 2022), Sep 2022, Wageningen, Netherlands. , 2022, ⟨10.5281/zenodo.7148792⟩

Poster de conférence hal-03800325v1
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D2KAB project taking off: Data to Knowledge in Agronomy and Biodiversity

Sophie Aubin , Anne-Francoise Adam-Blondon , Michael Alaux , Mouhamadou Ba , Stéphan Bernard et 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
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PHIS, a plant science ontology-driven Phenotyping Hybrid Information System

Pascal Neveu , Anne Tireau , Nadine Hilgert , Vincent Negre , Jonathan Mineau-Cesari et al.

NETTAB 2018: Building a FAIR Bioinformatics environment, Oct 2018, Genova, Italy. , 1 p., 2018

Poster de conférence hal-02788853v1
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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 Cornut et 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
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PHENOME: French Plant Phenomic Center

Francois F. Tardieu , Jacques Le Gouis , Pamela Lucas , Frédéric Baret , Pascal Neveu et al.

Recent progress in drought tolerance from genetics to modelling, Jun 2015, Montpellier, France. 2015

Poster de conférence hal-02744329v1
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Forest tree GnpIS: an information system dedicated to forest tree genetics, genomics and phenomics

Célia Michotey , Christel Anger , François Ehrenmann , Odile Rogier , Véronique Jorge et al.

35. New Phytologist Symposium, Jun 2015, Boston, United States. 2015

Poster de conférence hal-02795537v1

PHENOME: French Plant Phenomic Center

Jacques Le Gouis , Pamela Lucas , Frédéric Baret , Pascal Neveu , Cyril Pommier et al.

9th International Wheat Conference, Sep 2015, Sydney, Australia. 2015

Poster de conférence hal-02800017v1

Data integration in the agronomic domain : national and international data discovery system

Florian Philippe , Aravind Venkatesan , Nordine El Hassouni , Cyril Pommier , Manuel Ruiz et 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

Francois Tardieu , Jacques Le Gouis , Pamela Lucas , Frédéric Baret , Pascal Neveu et al.

EPPN Plant Phenotyping Symposium, Nov 2015, Barcelona, Spain. 2015

Poster de conférence hal-01229565v1
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BreedWheat genotyping and phenotyping data in GnpIS information system

Marie Laine , Thomas Letellier , Raphaël-Gauthier R.-G. Flores , Loïc Couderc , Nacer Mohellibi et 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 Arnaud et al.

Plant and Animal Genome, Jan 2013, San Diego, United States. 2013

Poster de conférence hal-02810186v1
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ELIXIR-CONVERGE D5.5 Report on the remaining four DMP processes

Laura Portell-Silva , Vanita Haurheeram , Anne-Françoise Adam-Blondon , Salvador Capella-Gutierrez , Marina Popleteeva et al.

ELIXIR. 2023

Rapport (rapport contrat/projet) hal-04503558v1
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D4.5:Data policy rules

François Tardieu , Pascal Neveu , Cyril Pommier

INRAE. 2021, 10p

Rapport hal-04986212v1
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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.eu

Francois Tardieu , Pascal Neveu , Cyril Pommier , Llorenç Cabrera-Bosquet

INRAE. 2019

Rapport (rapport de recherche) hal-04986218v1
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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
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Projet Coll-GATE

Anne-Françoise Adam-Blondon , Claude Pavis , Franciane Nuissier , Thierry Lacombe , Nicolas Guilhot et al.

[Contract] 2015

Rapport (rapport contrat/projet) hal-02793863v1
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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 Buche et al.

[0] 2014, 18 p

Rapport hal-02801608v1
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Rapport de synthèse du chantier DOI

Windpouire Esther Dzale Yeumo , Lydie Soler , Michael M. Alaux , Robert R. Bossy , Sebastien Carrere et al.

[0] 2014, 47 p

Rapport hal-02801364v1