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Pierre Larmande

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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⟩
Journal articles lirmm-03615366v1
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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⟩
Journal articles lirmm-03615370v1
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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
Frontiers in Public Health, 2020, 8, pp.563247. ⟨10.3389/fpubh.2020.563247⟩
Journal articles hal-02968260v1
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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⟩
Journal articles lirmm-03615375v1

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

Venice Juanillas , Alexis Dereeper , Nicolas Beaume , Gaetan Droc , Joshua Dizon
GigaScience, 2019, 8 (12), ⟨10.1093/gigascience/giz156⟩
Journal articles lirmm-03615381v1

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

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

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⟩
Journal articles lirmm-03615384v1
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Gigwa v2-Extended and improved genotype investigator

Guilhem Sempere , Adrien Petel , Mathieu Rouard , Julien Frouin , Yann Hueber
GigaScience, 2019, 8 (5), ⟨10.1093/gigascience/giz051⟩
Journal articles hal-02627410v1
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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
Bioinformatics, 2019, 35 (20), pp.4147-4155. ⟨10.1093/bioinformatics/btz190⟩
Journal articles hal-02626802v1
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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
PLoS ONE, 2018, 13 (11), pp.e0198270. ⟨10.1371/journal.pone.0198270⟩
Journal articles lirmm-01964772v1

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
Current Biology - CB, 2018, 28 (14), pp.2274-2282. e6. ⟨10.1016/j.cub.2018.05.066⟩
Journal articles hal-03958213v1
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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
Database -Weston-, 2018, 2018, pp.#bay088. ⟨10.1093/database/bay088⟩
Journal articles lirmm-01964769v1
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AgroPortal: A vocabulary and ontology repository for agronomy

Clement Jonquet , Anne Toulet , Elizabeth Arnaud , Sophie Aubin , Esther Dzale Yeumo
Computers and Electronics in Agriculture, 2018, 144, pp.126-143. ⟨10.1016/j.compag.2017.10.012⟩
Journal articles lirmm-01679502v1
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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⟩
Journal articles lirmm-01652022v2
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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
Future Generation Computer Systems, 2017, 75, pp.284-298. ⟨10.1016/j.future.2017.01.012⟩
Journal articles hal-01516082v1
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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⟩
Journal articles hal-01411532v1
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Gigwa—Genotype investigator for genome- wide analyses

Guilhem Sempéré , Florian Philippe , Alexis Dereeper , Manuel Ruiz , Gautier Sarah
GigaScience, 2016, 5 (1), pp.1-9. ⟨10.1186/s13742-016-0131-8⟩
Journal articles hal-01411506v1
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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
Current Plant Biology, 2016, 7-8, pp.6-9. ⟨10.1016/j.cpb.2016.12.002⟩
Journal articles hal-02631148v1
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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⟩
Journal articles hal-01268129v1

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
Plant Biotechnology Journal, 2012, 10 (5), pp.555-68. ⟨10.1111/j.1467-7652.2012.00689.x⟩
Journal articles hal-00821958v1
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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⟩
Journal articles hal-01218997v1
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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
Nucleic Acids Research, 2008, 36 (Database issue), pp.D1022-7. ⟨10.1093/nar/gkm762⟩
Journal articles hal-00464031v1
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OryGenesDB: a database for rice reverse genetics

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

Pierre Larmande , Bertrand Pitollat , Ndomassi Tando , Yann Pomie , Bill Happi
SWAT4HCLS - 13th Semantic Web Applications and Tools for Health Care and Life Sciences Conference, Feb 2023, Basel, Switzerland
Conference papers hal-04005132v1
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DLinker Results for OAEI 2022

Happi Bill Gates , Géraud Fokou Pelap , Danai Symeonidou , Pierre Larmande
17th International Workshop on Ontology Matching, OM 2022, Oct 2022, Online, France. pp.166-173
Conference papers hal-03967103v1
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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⟩
Conference papers hal-03443436v1
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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
Conference papers hal-03107587v1

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⟩
Conference papers lirmm-03615404v1
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Candidate gene prioritization using graph embedding

Quan Do , Pierre Larmande
IEEE-RIVF 2020, Apr 2020, Ho Chi Minh City, Vietnam
Conference papers hal-02461886v1
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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
Conference papers hal-02329684v1
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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
Conference papers hal-01711331v1
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Data standards for plant phenotyping: MIAPPE and its implementations

Cyril Pommier , Guillaume Cornut , Thomas Letellier , Célia Michotey , Pascal Neveu
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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Reusing the NCBO BioPortal technology for agronomy to build AgroPortal

Clement Jonquet , Anne Toulet , Elizabeth Arnaud , Sophie Aubin , Esther Dzalé-Yeumo
ICBO 2016 - 7th International Conference on Biomedical Ontologies, P. Jaiswal; R. Hoehndorf, Aug 2016, Corvallis, OR, United States
Conference papers hal-01398251v1
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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⟩
Conference papers hal-01411565v1
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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
Conference papers hal-01411759v1

Ontology-based services and knowledge management in the Agronomic Domain

Pierre Larmande
RDA: Research Data Alliance, Sep 2015, Paris, France
Conference papers lirmm-01274693v1

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
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
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
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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
Conference papers lirmm-01172232v1

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
JOBIM2010, Sep 2010, Montpellier, France
Conference papers hal-02753839v1

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
Séminaire Génomique Végétale, Mar 2010, Pont-Royal en Provence, France
Conference papers hal-02752562v1

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
18. Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Jul 2010, Boston, United States
Conference papers hal-02753301v1

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
Conference papers hal-02757250v1

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
Conference papers lirmm-00093998v1
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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
Fête de la Science - 30 ans du LIRMM, Oct 2022, Montpellier, France.
Conference poster hal-04005129v1
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AgroLD: A Knowledge Graph Database for plant functional genomics

Bertrand Pitollat , Ndomassi Tando , Mathieu Rouard , Gaetan Droc , Aravind Venkatesan
JOBIM 2021, Jul 2021, Paris, France. 2018, ⟨10.1101/325423⟩
Conference poster hal-03269813v1
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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
14th Research Data Alliance Plenary Conference (RDA P14), Best poster award, Oct 2019, Helsinki, Finland. , 2019, ⟨10.5281/zenodo.3520300⟩
Conference poster lirmm-02351000v1
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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
XXIV International Plant & Animal Genome Conference (PAG 2016), Poster session, Jan 2016, San Diego, United States. , P0343, 2016, Systems Biology and Ontologies, Poster session
Conference poster lirmm-01397465v1
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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
Conference poster hal-01411683v1
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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
Conference poster hal-01411668v1
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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
Conference poster hal-01411713v1
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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
Ben Schaap. GODAN Summit, Sep 2016, New York, NY, United States. , 2016
Conference poster hal-01398252v1

South Green bioinformatics platform: Update 2015

A. Armero , Franc-Christophe Baurens , Stephanie Bocs , A. Breil , Frédéric F. de Lamotte
3. Plant Genomics Congress, May 2015, Londres, United Kingdom. Global Engage, 2015, Plant Genomics Congress
Conference poster hal-02739966v1
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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
Conference poster lirmm-01274707v1

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
Conference poster lirmm-01274725v1

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
Conference poster lirmm-01071822v1
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Semantic Annotation Workflow using Bio-Ontologies

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

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⟩
Book sections lirmm-03615352v1
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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⟩
Book sections lirmm-03615359v1
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Intégration de données multi-échelles et extraction de connaissances en agronomie : exemples et perspectives

Pierre Larmande
Bio-informatique [q-bio.QM]. Universite Montpellier, 2020
Habilitation à diriger des recherches tel-02105913v4