Pierre Larmande
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
Compétences
Publications
Publications
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AgroLD: a Knowledge Graph for the Plant Sciences16th Semantic Web Applications and Tools for Health Care and Life Science (SWAT4HCLS), Andra Waagmeester; Andrea Splendiani; M. Scott Marshall, Feb 2025, Barcelone, Spain |
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Graph Embeddings Meet Link Keys Discovery for Entity MatchingWWW '25: The ACM Web Conference 2025, Apr 2025, Sydney NSW Australia, Australia. pp.3344-3353, ⟨10.1145/3696410.3714581⟩ |
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Evaluating deep learning models for plant protein function predictionJOBIM 2025 - 25es Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2025, Bordeaux, France |
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The Wheat and Rice Genomics Scientific Literature Knowledge GraphsSemantic Web Technologies for Health Care and Life Science (SWAT4HCLS), Andra Waagmeester; M. Scott Marshall; Andrea Splendiani, Feb 2025, Barcelone, Spain |
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AgroLD: a Knowledge Graph for the Plant Sciences14. Semantic Web Applications and Tools for Health Care and Life Sciences Conference (SWAT4HCLS), Feb 2023, Basel, Switzerland. pp.167-168 |
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DLinker Results for OAEI 202217. International Workshop on Ontology Matching (OM2022), Oct 2022, Online, France. pp.166-173 |
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AgroLD: A knowledge graph for the plant sciencesISWC 2021 - 20th International Semantic Web Conference, Oct 2021, Virtual, France. pp.496-510, ⟨10.1007/978-3-030-88361-4_29⟩ |
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AgroLD: une base de connaissances pour l'étude du phénome des plantes cultivéesEGC 2021 - 21e Conférence Extraction et Gestion des Connaissances, Jan 2021, Online, France. pp.461-468 |
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Candidate gene prioritization using graph embeddingRIVF 2020 - International Conference on Computing and Communication Technologies, Oct 2020, Ho Chi Minh City, France. pp.1-6, ⟨10.1109/RIVF48685.2020.9140776⟩ |
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Candidate gene prioritization using graph embeddingIEEE-RIVF 2020, Apr 2020, Ho Chi Minh City, Vietnam |
AgroLD: a Linked Data platform to understand plant genotype-phenotype interactionsInternational Symposium on Integrative Bioinformatics 2019 (IB 2019), INRA, Sep 2019, Paris, France. 1 p |
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AgroLD: un graphe de connaissances pour la caractérisation des mécanismes moléculaires complexes impactant le phénome des plantes30es Journées Francophones d'Ingénierie des Connaissances, IC 2019, AFIA, Jul 2019, Toulouse, France. pp.217-218 |
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Comparative study of Named-Entity Recognition methods in the agronomical domainCiCling, Mar 2018, Hanoi, Vietnam |
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Data standards for plant phenotyping: MIAPPE and its implementations26. Plant and Animal Genome Conference (PAG XXVI), Jan 2018, San Diego, United States. pp.24 slides |
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Reusing the NCBO BioPortal technology for agronomy to build AgroPortalICBO 2016 - 7th International Conference on Biomedical Ontologies, P. Jaiswal; R. Hoehndorf, Aug 2016, Corvallis, OR, United States |
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Development of a knowledge system for Big Data: Case study to plant phenotyping dataWIMS: Web Intelligence, Mining and Semantics, Mines Ales, Jun 2016, Nîmes, France. pp.1-9, ⟨10.1145/2912845.2912869⟩ |
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Exposing French agronomic resources as Linked Open DataIN-OLIVE, Jun 2016, Montpellier, France |
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AgroPortal : a proposition for ontology-based services in the agronomic domainIN-OVIVE, Jun 2015, Rennes, France |
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Towards efficient data integration and knowledge management in the Agronomic domainAPIA: Applications Pratiques de l'Intelligence Artificielle, Institut National de Recherche en Informatique et en Automatique (INRIA). FRA., Jul 2015, Rennes, France. pp.117-124 |
Ontology-based services and knowledge management in the Agronomic DomainRDA: Research Data Alliance, Sep 2015, Paris, France |
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Exposing French agronomic resources as Linked Open DataSWAT4LS: Semantic Web Applications and Tools for Life Sciences, Dec 2015, Cambridge, United Kingdom |
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Towards a multi-scale and formalized representation of protein sequence-structure-function relationships : the nsLTP family as a case of studyJOBIM2010, Sep 2010, Montpellier, France |
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Towards a multi-scale and formalized representation of protein sequence-structure-function relationships : the nsLTP family as a case of studySéminaire Génomique Végétale, Mar 2010, Pont-Royal en Provence, France |
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Towards a multi-scale and formalized representation of protein sequence-structure-function relationships : the nsLTP family as a case of study18. Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Jul 2010, Boston, United States |
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A personalized integrated system for functional genomic analysis17. Conference Plant & Animal Genomes, Jan 2009, San Diego, United States |
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Integration of Data Sources for Plant GenomicsICEIS'06: 8th International Conference on Enterprise Information Systems, May 2006, Paphos, Cyprus. pp.314-318 |
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BReIF: une e-infrastructure pour accélérer l'utilisation de ressources biologiques diversifiéesTrans Numériques 2026, Feb 2026, Rennes, France. |
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Protein Function Prediction: Graph Neural Networks as Multimodal Aggregators of Sequences, Networks, and OntologiesJOBIM 2025 - 25es Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2025, Bordeaux, France. |
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Leveraging ontology structure for machine learning in knowledge graphsJOBIM 2024 - 24es Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2024, Toulouse, France |
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Graph Neural Networks For Biological Knowledge DiscoveryJOBIM 2024 - 24es Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2024, Toulouse, France. |
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Integration of variation data through SPARQL Micro-ServicesSemantic Web for Health Care and Life Science (SWA4HCLS), Feb 2024, Leiden (DE), Netherlands |
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The AgroLD project : A Knowledge Graph Database for plant functional genomicsFête de la Science - 30 ans du LIRMM, Oct 2022, Montpellier, France. |
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AgroLD: A Knowledge Graph Database for plant functional genomicsJOBIM 2021, Jul 2021, Paris, France. 2018, ⟨10.1101/325423⟩ |
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D2KAB project taking off: Data to Knowledge in Agronomy and Biodiversity14th Research Data Alliance Plenary Conference (RDA P14), Best poster award, Oct 2019, Helsinki, Finland. , 2019, ⟨10.5281/zenodo.3520300⟩ |
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Integration and Visualization of Epigenome and Mobilome Data in CropsJOBIM: Journées Ouvertes Biologie Informatique Mathématiques, Jun 2016, Lyon, France. , 2016 |
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Construction d’un gold standard pour les données agronomiquesIC 2016 - 27es Journées francophones d'Ingénierie des Connaissances, Jun 2016, Montpellier, France. , 2016 |
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AgroPortal: an open repository of ontologies and vocabularies for agriculture and nutrition dataBen Schaap. GODAN Summit, Sep 2016, New York, NY, United States. , 2016 |
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AgroLD indexing tools with ontological annotationsSWAT4LS: 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 |
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AgroPortal : A Proposition for Ontology-Based Services in the Agronomic DomainXXIV International Plant & Animal Genome Conference (PAG 2016), Poster session, Jan 2016, San Diego, United States. , P0343, 2016, Systems Biology and Ontologies, Poster session |
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Development of a generic indexing tool to optimize the use of biological dataJOBIM: Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. , Post-096 (#21), 2015 |
South Green bioinformatics platform: Update 20153. Plant Genomics Congress, May 2015, London, United Kingdom. Global Engage, 2015, Plant Genomics Congress |
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Data integration in the agronomic domain : national and international data discovery systemJOBIM: Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. , Post-105 (#59), 2015 |
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Semantic Annotation Workflow using Bio-OntologiesWorkshop on Crop Ontology and Phenotyping Data Interoperability, Mar 2014, Montpellier, France. , 1 p., 2014 |
Facilitating efficient knowledge management and discovery in the Agronomic Sciences4. Research Data Alliance Plenary Meeting (RDA P4), Sep 2014, Amsterdam, Netherlands. , 2014 |
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Managing High-Density Genotyping Data with GigwaPlant Bioinformatics, 2443, Springer US, pp.415-427, 2022, Methods in Molecular Biology, ⟨10.1007/978-1-0716-2067-0_21⟩ |
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AgroLD: A Knowledge Graph Database for Plant Functional GenomicsPlant Bioinformatics, 2443, Springer US, pp.527-540, 2022, Methods in Molecular Biology, ⟨10.1007/978-1-0716-2067-0_28⟩ |
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Fine-tuning Large Language Models (LLMs) for Entity Alignment in Knowledge Graphs (KG)2024 |
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GRU-SCANET: Unleashing the Power of GRU-based Sinusoidal CApture Network for Precision-driven Named Entity Recognition2024 |
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DMP projet ANR DIG-AIIRD. Institut de Recherche pour le Développement. 2023 |
Intégration de Sources de Données pour la Génomique Végétale2005 |
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Mutualiser et partager, un défi pour la génomique fonctionnelle végétaleBio-informatique [q-bio.QM]. Universite Montpellier 2, 2007. Français. ⟨NNT : ⟩ |
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Intégration de données multi-échelles et extraction de connaissances en agronomie : exemples et perspectivesBio-informatique [q-bio.QM]. Montpellier II, 2019 |
Benchmarcking Application main portal2016 |