Coordonnées

Email : claire.nedellec@inrae.fr Adresse : INRAE - Unité MaIAGE                  Bâtiment 233                  Domaine de Vilvert                  78352 JOUY-EN-JOSAS CEDEX Tel : +33 (0)1 34 65 28 78 Fax : +33 (0)1 34 65 00 00 Administration : +33 (0)1 34 65 28 86

Cursus                                                                                                                  

Claire Nédellec is research director in computer science at INRAE since  INRAE depuis 2001. She leads the Bibliome team.

She has been research assistant at LRI, Université Paris-Sud (now part of Paris-Saclay University) from 1994 to 2001 after she obtained her PhD in Inductive Logic Programming and cooperative machine learning. She joined the MaIAGE laboratory in the Jouy-en-Josas INRAE research center in 2001 where she created the Bibiome  group. She obtained her HDR in 2013.

Research topics

Projects

On-going projects

EcoControl : Community Ecology and Digital Tools to Increase the Natural Regulation of Insect Pests in Agriculture PEPR Agroecology and Digital technology (2025-2029)

FAIROmics H2020 -  FAIRification of multiOmics data to link databases and create knowledge graphs for fermented foods (2024-2027)

HoloOligo ANR - Structure diversity, functionality and modulation of milk oligosaccharides in monogastric livestock species: towards optimal development of rabbit and pig holobionts (2022-2025)

TyDI - Terminology Design Interface (2021-2025)

BEYOND  ANR PPR Cultiver et protéger autrement.-  Building epidemiological surveillance and prophylaxis with observations both near and distant (2021-2025).

D2KAB  Data to Knowledge in Agriculture and Biodiversity - ANR (2019-2024).

Recent projects

TIERS-ESV  Information Processing and Health Risk Assessment for Plant Health Epidemiosurveillance  - IB2021 Départements INRAE MathNum et SPE (2021-2023).

OntoBedding  Ontology-based enhancement of word embeddings for adaptation to specific domains  DIM IdF RFSI, sept STIC Université Paris-Saclay (2019).

ENovFood  Linking a phenotypic and a network food microbe data bases: an application for food microbial ecology and food innovation Métaprogramme MEM (2018-2020).

Visa TM  - BSN, CoSO  Towards a text mining service infrastructure  (2017-2018)

OpenMinTeD H2020 Open Mining Infrastructure for Text and Data (2015-2018)

D-ONT, Optimized use of phenotypic databases - Ontologies for information sharing ACI Phase 2016-2018.

Florilege  - A database gathering microbial phenotypes of food interest. Métaprogramme MEM  - Action ciblée  (2016-2018)

OntoBiotope : Metaprogramme INRA MEM (Metagenomics of microbial ecosystem microbiens). (2012-2013).

Quaero : Automatic multimedia content processing Oséo, BPI France. (2008-2013).

FSOV SAM Blé : Marker-based selection of bread wheat Fond de soutien à l'obtention végétale (2010-2013).

Animation

GT D2K - De la Donnée à la Connaissance. Labex DigiCosme

Scientific boards of INRAE MathNum departement and Graduate School ISN (Université Paris-Saclay). University Paris-Saclay Open Science committee. 

Board of the Artificial intelligence DataIA, University Paris-Saclay.

Organisation of international NLP challenges : Genic Interaction Extraction Challenge at LLL'05 (Learning Language in Logic), BioNLP Shared Task (2011, 2013, 2016) then BioNLP Open Shared Task : 2019

Supervision

On-going supervision

Anne-Sophie Foussat. Language model and analysis of uncertain information: temporal monitoring of the reliability of bibliography on insect vectors of plant pathogens. PhD Co-supervision : V. Guigue (AgroParisTech), and N. Sauvion (PHIM, INRAE). Paris-Saclay University. INRAE funding. Since 2024.

Xingyu Zhu. Design of information extraction methods to characterize molecules produced or degraded by microbes - application to fermented plant food ecosystems. Co-supervision : Robert Bossy (MaIAGE), Mark Jelasity (Université de Szeged, Hongrie). University Paris-Saclay. Since 2024. Funding : ITN FAIROmics.

Recent supervision

Publications

Recent publications

Journal

• Claire Nédellec, Sophie Aubin, Clara Sauvion, Liliana Ibanescu, Sonia Bravo, Jacques Le Gouis, Thierry Marcel, Cyril Pommier, Robert Bossy, Michaël Alaux. Mapping bread wheat trait ontologies for semantic interoperability. F1000Research. 30 Sept, 2024. https://doi.org/10.12688/f1000research.154860.1

• Soubeyrand S.,  Estoup A., Cruaud A., Malembic-Maher S., Meynard C., Ravigné V., Barbier M., Barrès B., Berthier K., Boitard S., Dallot S., Gaba S., Grosdidier M., Hannachi M., Jacques M.-A., Leclerc M., Lucas P., Martinetti D., Mougel C., Robert C., Roques A., Rossi J.-P., Suffert F.^, Abad P., Auger-Rozenberg M.-A., Ay J.-S., Bardin M., Bernard H.¹, Bohan D.A., Candresse T., Castagnone-Sereno P., Delmas C.E.L., Ezanno P., Fabre F., Facon B., Gabriel E., Gaudin J., Gauffre B., Gautier M., Guinat C., Lavigne C., Lemaire O., Martinez C., Michel L., Moury B., Nam K., Nédellec C., Ogliastro M., Papaïx J., Parisey N., Poggi S., Radici A., Rasplus J.-Y., Reboud X., Robin C., Roche M., Rusch A., Sauvion N., Verdin E., Walker A.-S., Xuéreb A. Research strategies for developing integrated plant health surveillance to anticipate and mitigate disease and pest emergence in the face of global change. CABI Agriculture and Bioscience, 2024. https://doi.org/10.1186/s43170-024-00273-8

• Nadia Yacoubi Ayadi, Stephan Bernard, Robert Bossy, Marine Courtin, Bill Gates Happi Happi, Pierre Larmande, Franck Michel, Claire Nédellec, Catherine Roussey, Catherine Faron. (2024) A Unified Approach to Publish Semantic Annotations of Agricultural Documents as Knowledge Graphs. Smart Agricultural Technology, 2024.100484, ISSN 2772-3755, https://doi.org/10.1016/j.atech.2024.100484.

• Claire Nédellec, Clara Sauvion, Robert Bossy, Mariya Borovikova, Louise Deléger. (2024) TaeC: a Manually annotated text dataset for trait and phenotype extraction and entity linking in wheat breeding literature. Plos One. June 2024. 10.1371/journal.pone.0305475.Mathilde Rumeau, François Fenaille, Agnès Girard, Valentin Loux, Mouhamadou Ba, Claire Nédellec, Louise Deléger, Robert Bossy, Sophie Aubin, Christelle Knudsen, Sylvie Combes. (2024) MilkOligoThesaurus, A mammalian milk oligosaccharide thesaurus for automatic annotation and text data mining of scientific articles: a dataset of synonyms from the scientific literature. Data in Brief. 2024, 110404, ISSN 2352-3409, https://doi.org/10.1016/j.dib.2024.110404.

• Cindy E. Morris, Andrea Radici, Christine N. Meynard, Nicolas Sauvion, Claire Nédellec, et al.. More than food: Why restoring the cycle of organic matter in sustainable plant production is essential for the One Health nexus. CAB Reviews Perspectives in Agriculture Veterinary Science Nutrition and Natural Resources, 2024, 19, pp.1. ⟨10.1079/cabireviews.2024.0008⟩. ⟨hal-04524528⟩

• Dérozier S, Bossy R, Deléger L, Ba M, Chaix E, Harlé O, Loux V., Falentin H., Nédellec C. (2023) Omnicrobe, an open-access database of microbial habitats and phenotypes using a comprehensive text mining and data fusion approach. PLoS ONE 18(1): e0272473. https://doi.org/10.1371/journal.pone.0272473. 

• Anfu Tang, Louise Deléger, Robert Bossy, Pierre Zweigenbaum, Claire Nédellec. (2022) Do syntactic trees enhance domain-specific BERT models for relation extraction? Database, Volume 2022. https://doi.org/10.1093/database/baac070.

• Morris, C.E., Géniaux, G., Nédellec, C., Sauvion, N. & Soubeyrand, S. (2021) One Health concepts and challenges for surveillance, forecasting, and mitigation of plant disease beyond the traditional scope of crop production. Plant Pathology, 00, 1– 12. https://doi.org/10.1111/ppa.13446

• Ferré, A., Deléger, L., Bossy, R., Zweigenbaum, P., Nédellec, C., (2020). C-Norm: a neural approach to few-shot entity normalization. BMC Bioinformatics 21, 579 https://doi.org/10.1186/s12859-020-03886-8

• Claire Nédellec, Liliana Ibanescu, Robert Bossy, Pierre Sourdille (2020)^. WTO, an ontology for wheat traits and phenotypes in scientific publications. 18(2) Genomics & Informatics. juin 2020. doi: 10.5808/GI.2020.18.2.e14

• Ferré, A., Deléger, L., Bossy, R., Zweigenbaum, P., Nédellec, C.,. C-Norm: a neural approach to few-shot entity normalization. BMC Bioinformatics 21, 579 (2020). https://doi.org/10.1186/s12859-020-03886-8

Conference

• Tang. A. Bossy R., Nédellec C., Deléger L. Exploiting Graph Embeddings from Knowledge Bases for Neural Biomedical Relation Extraction. In proceedings of the 29th Annual International Conference on Natural Language & Information Systems (NLDB 2024), Torino, Italy, June 2024. 

• Mariya Borovikova, Arnaud Ferré, Robert Bossy, Mathieu Roche and Claire Nédellec. Semantically-Informed Domain Adaptation for Named Entity Recognition. ISMIS-2024 (International Symposium on Methodologies for Intelligent Systems), Poitiers, 2024.

• Mariya Borovikova, Arnaud Ferré, Robert Bossy, Mathieu Roche, Claire Nédellec. Could keyword masking strategy improve language model? In: Proceedings of the 28th International Conference on Natural Language & Information Systems (NLDB 2023), Métais, E., Meziane, F., Sugumaran, V., Manning, W., Reiff-Marganiec, S. (eds). Lecture Notes in Computer Science, vol 13913. Springer, Cham. University of Derby, United Kingdom, 21-23 June 2023. https://doi.org/10.1007/978-3-031-35320-8_19

• Arnaud Ferré, Robert Bossy, Mouhamadou Ba, Louise Deléger, Thomas Lavergne, Pierre Zweigenbaum, Claire Nédellec. Handling Entity Normalization with no Annotated Corpus: Weakly Supervised Methods Based on Distributional Representation and Ontological Information, Proceedings of the 12th international conference on Language Resources and Evaluation (LREC-2020), pages 1959–1966. European Language Resources Association (ELRA) publisher, mai 2020. https://www.aclweb.org/anthology/2020.lrec-1.241/

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