Pierre Larmande

73
Documents

Présentation

My research aims to model the complexity of biological data in order to extract knowledge that can be used to identify the molecular mechanisms controlling the expression of phenotypes in plants in a context of environmental adaptation. I am particularly interested in tropical cereals (Asian and African rice, millet, sorghum). My main research interests are Data integration, Semantic Web, plant-ontologies, semantic data linking, Knowledge management and Big Data for plant genomics. I am is the lead PI of the Agronomic Linked Data project (AgroLD), which is a Knowledge Graph database that consists of data integrated from a variety of plant resources and ontologies. For more info visit my homepage

Domaines de recherche

Bio-informatique [q-bio.QM]

Compétences

Knowledge Graphs Functional Genomics Data Integration AI Ontology-based data representation

Publications

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Publications

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A Unified approach to publish semantic annotations of agricultural documents as knowledge graphs

Nadia Yacoubi Ayadi , Stephan Bernard , Robert Bossy , Marine Courtin , Bill Gates Happi Happi et al.
Smart Agricultural Technology, 2024, 8, pp.43. ⟨10.1016/j.atech.2024.100484⟩
Article dans une revue hal-04495022 v1
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PyRice: a Python package for querying Oryza sativa databases

Quan Do , Ho Bich Hai , Pierre Larmande
Bioinformatics, 2021, 37 (7), pp.1037-1038. ⟨10.1093/bioinformatics/btaa694⟩
Article dans une revue lirmm-03615370 v1

OryzaGP 2021 update: a rice gene and protein dataset for named-entity recognition

Pierre Larmande , Yusha Liu , Xinzhi Yao , Jingbo Xia
Genomics & Informatics, 2021, 19 (3), pp.e27. ⟨10.5808/gi.21015⟩
Article dans une revue lirmm-03615366 v1
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COMOKIT: A Modeling Kit to Understand, Analyze, and Compare the Impacts of Mitigation Policies Against the COVID-19 Epidemic at the Scale of a City

Benoit Gaudou , Nghi Quang Huynh , Damien Philippon , Arthur Brugière , Kevin Chapuis et al.
Frontiers in Public Health, 2020, 8, pp.563247. ⟨10.3389/fpubh.2020.563247⟩
Article dans une revue (article de synthèse) hal-02968260 v1
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Enabling a fast annotation process with the Table2Annotation tool

Pierre Larmande , Kazim Muhammed Jibril
Genomics & Informatics, 2020, 18 (2), pp.e19. ⟨10.5808/GI.2020.18.2.e19⟩
Article dans une revue lirmm-03615375 v1

Progress in single-access information systems for wheat and rice crop improvement

Armin Scheben , Chon-Kit Kenneth Chan , Locedie Mansueto , Ramil Mauleon , Pierre Larmande et al.
Briefings in Bioinformatics, 2019, 20 (2), pp.565-571. ⟨10.1093/bib/bby016⟩
Article dans une revue hal-02962718 v1

Corrigendum to: Rice Galaxy: an open resource for plant science

Venice Juanillas , Alexis Dereeper , Nicolas Beaume , Gaetan Droc , Joshua Dizon et al.
GigaScience, 2019, 8 (12), ⟨10.1093/gigascience/giz156⟩
Article dans une revue lirmm-03615381 v1
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Gigwa v2-Extended and improved genotype investigator

Guilhem Sempere , Adrien Petel , Mathieu Rouard , Julien Frouin , Yann Hueber et al.
GigaScience, 2019, 8 (5), ⟨10.1093/gigascience/giz051⟩
Article dans une revue hal-02627410 v1
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OryzaGP: rice gene and protein dataset for named-entity recognition

Pierre Larmande , Huy Do , Yue Wang
Genomics & Informatics, 2019, 17 (2), pp.e17. ⟨10.5808/GI.2019.17.2.e17⟩
Article dans une revue lirmm-03615384 v2
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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-02626802 v1
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Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy

Aravind Venkatesan , Gildas Tagny Ngompe , Nordine El Hassouni , Imène Chentli , Valentin Guignon et al.
PLoS ONE, 2018, 13 (11), pp.e0198270. ⟨10.1371/journal.pone.0198270⟩
Article dans une revue lirmm-01964772 v1

The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes

Philippe Cubry , Christine Tranchant-Dubreuil , Anne-Céline Thuillet , Cécile Monat , Marie-Noelle Ndjiondjop et al.
Current Biology, 2018, 28 (14), pp.2274-2282. e6. ⟨10.1016/j.cub.2018.05.066⟩
Article dans une revue hal-03958213 v1
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AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

Lisa Harper , Jacqueline Campbell , Ethalinda K S Cannon , Sook Jung , Monica Poelchau et al.
Database -Weston-, 2018, 2018, pp.#bay088. ⟨10.1093/database/bay088⟩
Article dans une revue lirmm-01964769 v1
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AgroPortal: A vocabulary and ontology repository for agronomy

Clement Jonquet , Anne Toulet , Elizabeth Arnaud , Sophie Aubin , Esther Dzale Yeumo et al.
Computers and Electronics in Agriculture, 2018, 144, pp.126-143. ⟨10.1016/j.compag.2017.10.012⟩
Article dans une revue lirmm-01679502 v1
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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-01652022 v2
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Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities

Sarah Cohen-Boulakia , Khalid Belhajjame , Olivier Collin , Jérôme Chopard , Christine Froidevaux et al.
Future Generation Computer Systems, 2017, 75, pp.284-298. ⟨10.1016/j.future.2017.01.012⟩
Article dans une revue hal-01516082 v1
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AgroLD API. Une architecture orientée services pour l'extraction de connaissances dans la base de données liées AgroLD

Gildas Tagny Ngompe , Aravind Venkatesan , Nordine El Hassouni , Manuel Ruiz , Pierre Larmande
Revue des Sciences et Technologies de l'Information - Série ISI : Ingénierie des Systèmes d'Information, 2016, 21 (5-6), pp.133-158. ⟨10.3166/isi.21.5-6.133-157⟩
Article dans une revue hal-01411532 v1
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Gigwa—Genotype investigator for genome- wide analyses

Guilhem Sempéré , Florian Philippe , Alexis Dereeper , Manuel Ruiz , Gautier Sarah et al.
GigaScience, 2016, 5 (1), pp.1-9. ⟨10.1186/s13742-016-0131-8⟩
Article dans une revue hal-01411506 v1
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The South Green portal: a comprehensive resource for tropical and Mediterranean crop genomics

Valentin Guignon , Yann Hueber , Mathieu Rouard , Stéphanie Bocs , David Couvin et al.
Current Plant Biology, 2016, 7-8, pp.6-9. ⟨10.1016/j.cpb.2016.12.002⟩
Article dans une revue hal-02631148 v1
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Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases

Julien Wollbrett , Pierre Larmande , Frédéric F. de Lamotte , Manuel Ruiz
BMC Bioinformatics, 2013, 14, ⟨10.1186/1471-2105-14-126⟩
Article dans une revue hal-01268129 v1

In-depth molecular and phenotypic characterization in a rice insertion line library facilitates gene identification through reverse and forward genetics approaches.

Mathias Lorieux , Mélisande Blein , Jaime Lozano , Mathieu Bouniol , Gaétan Droc et al.
Plant Biotechnology Journal, 2012, 10 (5), pp.555-68. ⟨10.1111/j.1467-7652.2012.00689.x⟩
Article dans une revue istex hal-00821958 v1
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OryGenesDB 2008 update: a database interoperability for functional genomics of rice.

Gaëtan Droc , Christophe Périn , Sebastien Fromentin , Pierre Larmande
Nucleic Acids Research, 2009, 37 (Database issue), pp.D992-D995. ⟨10.1093/nar/gkn821⟩
Article dans une revue hal-01218997 v1
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Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library

Pierre Larmande , Céline Gay , Mathias Lorieux , Christophe Périn , Matthieu Bouniol et al.
Nucleic Acids Research, 2008, 36 (Database issue), pp.D1022-7. ⟨10.1093/nar/gkm762⟩
Article dans une revue hal-00464031 v1
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OryGenesDB: a database for rice reverse genetics

Gaëtan Droc , Manuel Ruiz , Pierre Larmande , Andy Pereira , Pietro Piffanelli et al.
Nucleic Acids Research, 2006, 34, pp.D736-D740. ⟨10.1093/nar/gkj012⟩
Article dans une revue hal-01218996 v1
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AgroLD: a Knowledge Graph for the Plant Sciences

Pierre Larmande , Bertrand Pitollat , Ndomassi Tando , Yann Pomie , Bill Happi et al.
16th Semantic Web Applications and Tools for Health Care and Life Science (SWAT4HCLS), Andra Waagmeester; Andrea Splendiani; M. Scott Marshall, Feb 2025, Barcelone, Spain
Communication dans un congrès ird-04932817 v1
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The Wheat and Rice Genomics Scientific Literature Knowledge Graphs

Nadia Yacoubi Ayadi , Franck Michel , Robert Bossy , Marine Courtin , Bill Gates Happi Happi et al.
Semantic Web Technologies for Health Care and Life Science (SWAT4HCLS), Andra Waagmeester; M. Scott Marshall; Andrea Splendiani, Feb 2025, Barcelone, Spain
Communication dans un congrès ird-04932752 v1
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AgroLD: a Knowledge Graph for the Plant Sciences

Pierre Larmande , Bertrand Pitollat , Ndomassi Tando , Yann Pomie , Bill Gates Happi Happi et al.
SWAT4HCLS - 14th Semantic Web Applications and Tools for Health Care and Life Sciences Conference, Feb 2023, Basel, Switzerland. pp.167-168
Communication dans un congrès hal-04005132 v1
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DLinker Results for OAEI 2022

Bill Gates Happi Happi , Géraud Fokou Pelap , Danai Symeonidou , Pierre Larmande
OM 2022 - 17th International Workshop on Ontology Matching, Oct 2022, Online, France. pp.166-173
Communication dans un congrès hal-03967103 v1
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AgroLD: A knowledge graph for the plant sciences

Pierre Larmande , Konstantin Todorov
ISWC 2021 - 20th International Semantic Web Conference, Oct 2021, Virtual, France. pp.496-510, ⟨10.1007/978-3-030-88361-4_29⟩
Communication dans un congrès hal-03443436 v1
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AgroLD: une base de connaissances pour l'étude du phénome des plantes cultivées

Pierre Larmande , Tagny Gildas , Manuel Ruiz
EGC 2021 - 21e Conférence Extraction et Gestion des Connaissances, Jan 2021, Montpellier (virtuel), France. pp.461-468
Communication dans un congrès hal-03107587 v1
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Candidate gene prioritization using graph embedding

Quan Do , Pierre Larmande
IEEE-RIVF 2020, Apr 2020, Ho Chi Minh City, Vietnam
Communication dans un congrès hal-02461886 v1

Candidate gene prioritization using graph embedding

Quan Do , Pierre Larmande
RIVF 2020 - International Conference on Computing and Communication Technologies, Oct 2020, Ho Chi Minh City, France. pp.1-6, ⟨10.1109/RIVF48685.2020.9140776⟩
Communication dans un congrès lirmm-03615404 v1
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AgroLD: un graphe de connaissances pour la caractérisation des mécanismes moléculaires complexes impactant le phénome des plantes

Pierre Larmande , Gildas Tagny , Manuel Ruiz
30es Journées Francophones d'Ingénierie des Connaissances, IC 2019, AFIA, Jul 2019, Toulouse, France. pp.217-218
Communication dans un congrès hal-02329684 v1
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Comparative study of Named-Entity Recognition methods in the agronomical domain

Huy Do , Hanh Tran , Quang Khoat Than , Pierre Larmande
CiCling, Mar 2018, Hanoi, Vietnam
Communication dans un congrès hal-01711331 v1
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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
Communication dans un congrès hal-02789754 v1
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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-01398251 v1
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Development of a knowledge system for Big Data: Case study to plant phenotyping data

Luyen Le Ngoc , Anne Tireau , Aravind Venkatesan , Pascal Neveu , Pierre Larmande
WIMS: Web Intelligence, Mining and Semantics, Mines Ales, Jun 2016, Nimes, France. pp.1-9, ⟨10.1145/2912845.2912869⟩
Communication dans un congrès hal-01411565 v1
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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-01411759 v1

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-01274884 v1

Ontology-based services and knowledge management in the Agronomic Domain

Pierre Larmande
RDA: Research Data Alliance, Sep 2015, Paris, France
Communication dans un congrès lirmm-01274693 v1
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AgroPortal : a proposition for ontology-based services in the agronomic domain

Clement Jonquet , Esther Dzalé-Yeumo , Elizabeth Arnaud , Pierre Larmande
IN-OVIVE, Jun 2015, Rennes, France
Communication dans un congrès lirmm-01172232 v1
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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-01176903 v1

Towards a multi-scale and formalized representation of protein sequence-structure-function relationships : the nsLTP family as a case of study

Cécile Fleury , Marie Francoise M. F. Gautier , Pierre Larmande , Sabine Pérès , Frédéric F. de Lamotte et al.
JOBIM2010, Sep 2010, Montpellier, France
Communication dans un congrès hal-02753839 v1

Towards a multi-scale and formalized representation of protein sequence-structure-function relationships : the nsLTP family as a case of study

Cécile Fleury , Marie Francoise M. F. Gautier , Pierre Larmande , Sabine Pérès , Frédéric F. de Lamotte et al.
Séminaire Génomique Végétale, Mar 2010, Pont-Royal en Provence, France
Communication dans un congrès hal-02752562 v1

Towards a multi-scale and formalized representation of protein sequence-structure-function relationships : the nsLTP family as a case of study

Cécile Fleury , Marie Francoise M. F. Gautier , Pierre Larmande , Sabine Pérès , Frédéric F. de Lamotte et al.
18. Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Jul 2010, Boston, United States
Communication dans un congrès hal-02753301 v1

A personalized integrated system for functional genomic analysis

Gaëtan Droc , Christophe Perin , Sébastien Fromentin , Pierre Larmande
17. Conference Plant & Animal Genomes, Jan 2009, San Diego, United States
Communication dans un congrès hal-02757250 v1

Integration of Data Sources for Plant Genomics

Pierre Larmande , C. Tranchant-Dubreuil , L. Regnier , Isabelle Mougenot , Thérèse Libourel Rouge
ICEIS'06: 8th International Conference on Enterprise Information Systems, May 2006, Paphos (Cyprus), Cyprus. pp.314-318
Communication dans un congrès lirmm-00093998 v1
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Leveraging ontology structure for machine learning in knowledge graphs

Elliot Hugo Butz , Jérôme Azé , Konstantin Todorov , Antoine Toffano , Pierre Larmande
JOBIM 2024 - 24es Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2024, Toulouse, France
Poster de conférence hal-04636636 v1
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Graph Neural Networks For Biological Knowledge Discovery

Antoine Toffano , Jérôme Azé , Pierre Larmande
JOBIM 2024 - 24es Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2024, Toulouse, France.
Poster de conférence hal-04631478 v1
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Integration of variation data through SPARQL Micro-Services

Frederic Metereau , Franck Michel , PIERRE LARMANDE , Guilhem Sempere , Catherine Faron
Semantic Web for Health Care and Life Science (SWA4HCLS), Feb 2024, Leiden (DE), Netherlands
Poster de conférence ird-04812730 v1
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The AgroLD project : A Knowledge Graph Database for plant functional genomics

Pierre Larmande , Aravind Venkatesan , Gildas Tagny , Quan Do , Bertrand Pitollat et al.
Fête de la Science - 30 ans du LIRMM, Oct 2022, Montpellier, France.
Poster de conférence hal-04005129 v1
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AgroLD: A Knowledge Graph Database for plant functional genomics

Bertrand Pitollat , Ndomassi Tando , Mathieu Rouard , Gaetan Droc , Aravind Venkatesan et al.
JOBIM 2021, Jul 2021, Paris, France. 2018, ⟨10.1101/325423⟩
Poster de conférence hal-03269813 v1
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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-02351000 v1
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AgroLD indexing tools with ontological annotations

Stella Zevio , Nordine El Hassouni , Manuel Ruiz , Pierre Larmande
SWAT4LS: Semantic Web Applications and Tools for Life Sciences, Dec 2016, Amsterdam, Netherlands. , 11th Internationale Conference on Semantic Web Applications and Tools for Healthcare and Life Sciences, 2016
Poster de conférence hal-01411713 v1
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Construction d’un gold standard pour les données agronomiques

Imène Chentli , Pierre Larmande , Konstantin Todorov
IC: Ingénierie des Connaissances, Jun 2016, Montpellier, France. , 27es Journées francophones d'Ingénierie des Connaissances, 2016
Poster de conférence hal-01411683 v1
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Integration and Visualization of Epigenome and Mobilome Data in Crops

Dagmara Robakowska Hyzorek , Marie Mirouze , Pierre Larmande
JOBIM: Journées Ouvertes Biologie Informatique Mathématiques, Jun 2016, Lyon, France. , 2016
Poster de conférence hal-01411668 v1
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AgroPortal: an open repository of ontologies and vocabularies for agriculture and nutrition data

Clement Jonquet , Anne Toulet , Elizabeth Arnaud , Sophie Aubin , Esther Dzalé Yeumo et al.
Ben Schaap. GODAN Summit, Sep 2016, New York, NY, United States. , 2016
Poster de conférence hal-01398252 v1
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AgroPortal : A Proposition for Ontology-Based Services in the Agronomic Domain

Clement Jonquet , Esther Dzalé-Yeumo , Elizabeth Arnaud , Pierre Larmande , Anne Toulet et al.
XXIV International Plant & Animal Genome Conference (PAG 2016), Poster session, Jan 2016, San Diego, United States. , P0343, 2016, Systems Biology and Ontologies, Poster session
Poster de conférence lirmm-01397465 v1

South Green bioinformatics platform: Update 2015

A. Armero , Franc-Christophe Baurens , Stephanie Bocs , A. Breil , Frédéric F. de Lamotte et al.
3. Plant Genomics Congress, May 2015, Londres, United Kingdom. Global Engage, 2015, Plant Genomics Congress
Poster de conférence hal-02739966 v1
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Development of a generic indexing tool to optimize the use of biological data

Luyen Le Ngoc , Stéphane Jouannic , Pascal Gantet , Pierre Larmande
JOBIM: Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. , Post-096 (#21), 2015
Poster de conférence lirmm-01274707 v1

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-01274725 v1

Facilitating efficient knowledge management and discovery in the Agronomic Sciences

Aravind Venkatesan , Pierre Larmande , Clement Jonquet , Manuel Ruiz , Patrick Valduriez
4th Research Data Alliance Plenary Meeting (RDA P4), Sep 2014, Amsterdam, Netherlands. , 2014
Poster de conférence lirmm-01071822 v1
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Semantic Annotation Workflow using Bio-Ontologies

Emmanuel Castanier , Clement Jonquet , Soumia Melzi , Pierre Larmande , Manuel Ruiz et al.
Workshop on Crop Ontology and Phenotyping Data Interoperability, Mar 2014, Montpellier, France. , 1 p., 2014
Poster de conférence lirmm-01052546 v1

AgroLD: A Knowledge Graph Database for Plant Functional Genomics

Pierre Larmande , Gildas Tagny Ngompe , Aravind Venkatesan , Manuel Ruiz
Plant Bioinformatics, 2443, Springer US, pp.527-540, 2022, Methods in Molecular Biology, ⟨10.1007/978-1-0716-2067-0_28⟩
Chapitre d'ouvrage lirmm-03615352 v1
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Managing High-Density Genotyping Data with Gigwa

Guilhem Sempéré , Pierre Larmande , Mathieu Rouard
Plant Bioinformatics, 2443, Springer US, pp.415-427, 2022, Methods in Molecular Biology, ⟨10.1007/978-1-0716-2067-0_21⟩
Chapitre d'ouvrage lirmm-03615359 v1