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Cyril Pommier

Plant research data engineer.
32
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).
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

hadi-quesneville
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SyntenyViewer: a comparative genomics-driven translational research tool

Raphael Flores , Cécile Huneau , Laura Burlot , Mathilde Lainé , Erik Kimmel
Database - The journal of Biological Databases and Curation, 2023, 2023, ⟨10.1093/database/baad027⟩
Article dans une revue hal-04099923v1
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RepetDB: a unified resource for transposable element references

Joëlle Amselem , Guillaume Cornut , Nathalie Choisne , Michael Alaux , Françoise Alfama Depauw
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
Plant Phenomics, 2019, 2019, pp.1-15. ⟨10.34133/2019/1671403⟩
Article dans une revue hal-02624031v1
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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
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
F1000Research, 2017, 6 (1843), pp.1843. ⟨10.12688/f1000research.12234.1⟩
Article dans une revue lirmm-01652022v2
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TransPLANT resources for triticeae genomic data

Manuel Spannagl , Michael M. Alaux , Matthias Lange , Dan M. Bolser , Kai Christian Bader
PLANT GENOME, 2016, 9 (1), 13 p. ⟨10.3835/plantgenome2015.06.0038⟩
Article dans une revue hal-02635899v1
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Towards an open grapevine information system

Anne-Françoise Adam-Blondon , Michael Alaux , Cyril Pommier , D Cantu , Z-M Cheng
Horticulture research, 2016, 3, pp.16056. ⟨10.1038/hortres.2016.56⟩
Article dans une revue hal-01404714v1
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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
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
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
Nature, 2010, 465 (7298), pp.617-621. ⟨10.1038/nature09016⟩
Article dans une revue cea-00906990v1
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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
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
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Developing infrastructures for FAIR data in plant biology

Cyril Pommier , Guillaume Cornut , Michael Alaux , Windpouire Esther Dzale Yeumo , Raphaël Flores
Gatersleben Research Conference - Applied Bioinformatics for crops (GRC2019), IPK, Mar 2019, Gatersleben, Germany
Communication dans un congrès hal-03316569v1

Developing grapevine FAIR Data

Cyril Pommier , Eric Duchêne , Thierry Lacombe , Timothée Flutre , Michael Alaux
PAG Conference 2018, Jan 2018, San Diego, United States
Communication dans un congrès hal-02738117v1
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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
PAG XXVI - Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.32 slides
Communication dans un congrès hal-02788401v1

BreedWheat GWAS data in GnpIS information system

Mathilde Lainé , Thomas Letellier , Raphaël Flores , Nacer Mohellibi , Cyril Pommier
Eucarpia Cereal Section - Breeding cereals for sustainable agriculture, Mar 2018, Clermont-Ferrand, France
Communication dans un congrès 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
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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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
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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Exposing French agronomic resources as Linked Open Data

Aravind Venkatesan , Nordine El Hassouni , Florian Phillipe , Cyril Pommier , Hadi Quesneville
IN-OLIVE, Jun 2016, Montpellier, France
Communication dans un congrès 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
Plant Biology Europe EPSO / FESBP 2016 Congress, Jun 2016, Prague, Czech Republic
Communication dans un congrès hal-02794139v1
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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
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

Exposing French agronomic resources as Linked Open Data

Aravind Venkatesan , Nordine El Hassouni , Florian Philippe , Cyril Pommier , Hadi Quesneville
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
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
23. Plant and Animal Genome (PAG XXIII), Jan 2015, San Diego, Californie, United States. pp.24 slides
Communication dans un congrès hal-02741780v1
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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
Plant Biology Europe EPSO/FEPBS 2014, Jun 2014, Dublin, Germany
Communication dans un congrès hal-02801067v1
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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
Plant and Animal Genome conference XXII, GMOD session, Jan 2014, San Diego (CA), United States
Communication dans un congrès hal-02796293v1

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
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
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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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
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

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

Florian Philippe , Aravind Venkatesan , Nordine El Hassouni , Cyril Pommier , Manuel Ruiz
JOBIM: Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. , Post-105 (#59), 2015
Poster de conférence lirmm-01274725v1
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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
JOBIM 2015 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. 2015
Poster de conférence hal-02801654v1
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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
35. New Phytologist Symposium, Jun 2015, Boston, United States. 2015
Poster de conférence hal-02795537v1

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
Plant and Animal Genome, Jan 2013, San Diego, United States. 2013
Poster de conférence hal-02810186v1