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Cyril Pommier

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Presentation

Plant research data engineer.
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

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.
Gene Expression Patterns, 2020, 1, pp.100105. ⟨10.1016/j.patter.2020.100105⟩
Journal articles hal-02949637v1
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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⟩
Journal articles hal-02949641v1
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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⟩
Journal articles 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⟩
Journal articles hal-02626802v1
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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⟩
Journal articles hal-02627721v1
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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⟩
Journal articles hal-02624031v1
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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⟩
Journal articles hal-02625212v1
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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⟩
Journal articles hal-02278879v1

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⟩
Journal articles hal-02620800v1
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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⟩
Journal articles lirmm-01652022v2
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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⟩
Journal articles hal-02640958v1
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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⟩
Journal articles 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⟩
Journal articles hal-02635899v1

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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles 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⟩
Journal articles cea-00906990v1
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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⟩
Journal articles hal-01189162v1

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
Journal articles hal-00313737v1

Plant science data management and integration: the heterogeneity and dispersion challenge

Cyril Pommier
Applied Bioinformatics in Life Sciences (4th edition), Mar 2022, Louvain, Belgium
Conference papers hal-03851454v1
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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
Conference papers 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
Conference papers hal-02947459v1
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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
Conference papers hal-02789384v1
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Phenome-Emphasis-Elixir: phenotyping data management and integration

Anne-Francoise Adam-Blondon , Cyril Pommier , Llorenç Cabrera Bosquet
Interenational Grape Genetics and Breeding Symposium, Jul 2018, Bordeaux, France. pp.16
Conference papers hal-02789613v1
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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
Conference papers 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
Conference papers hal-01779751v1

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
Conference papers hal-02340450v1
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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
Conference papers hal-02790227v1

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
Conference papers hal-02738117v1
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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, 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 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
Conference papers hal-02788401v1
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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
Conference papers hal-02791168v1

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
Conference papers hal-02787834v1
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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
Conference papers hal-02785564v1

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
Conference papers hal-02788362v1
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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
Conference papers hal-01411759v1
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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
Conference papers hal-02794139v1
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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: International Conference on Biomedical Ontologies, Aug 2016, Corvallis, OR, United States
Conference papers hal-01398251v1
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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
Conference papers 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, Californie, United States. pp.24 slides
Conference papers 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
Conference papers hal-01174322v1

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
Conference papers lirmm-01274884v1
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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
Conference papers hal-01176903v1

Open data for grapevine biology

Anne-Francoise Adam-Blondon , Eric Duchêne , Sophie Durand , Jérôme Grimplet , Thierry Lacombe et al.
XI. International Congress on Grapevine Breeding and Genetics, Jul 2014, Pékin, China
Conference papers hal-01352690v1
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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 N. Lapalu et al.
Plant and Animal Genome conference XXII, GMOD session, Jan 2014, San Diego (CA), United States
Conference papers hal-02796293v1
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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
Conference papers 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
Conference papers 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
Conference papers 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
Conference papers hal-01019754v1
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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.
7th 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 Biodiversity

Sophie Aubin , Anne-Francoise Adam-Blondon , Michael Alaux , Mouhamadou Ba , Stéphan Bernard et al.
RDA P14 2019 - 14th Research Data Alliance Plenary Conference, 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 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
Conference poster 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
Conference poster hal-01606277v1

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
Conference poster hal-01229565v1
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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 V. Jorge et al.
35. 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 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
Conference poster hal-02801654v1
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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
Conference poster hal-02744329v1

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
Conference poster lirmm-01274725v1

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
Conference poster hal-02800017v1

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
Conference poster hal-02810186v1

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⟩
Book sections 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⟩
Book sections 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
Book sections hal-02820038v1