Claire Nédellec
Publications
Publications
SCoNE: a Self-Correcting and Noise-Augmented Method for Biological and Chemical Named Entity RecognitionThe 19th Conference of the European Chapter of the Association for Computational Linguistics, Mar 2026, Rabat, Morocco |
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SCoNE: a Self-Correcting and Noise-Augmented Method for Complex Biological and Chemical Named Entity RecognitionEuropean Chapter of the Association for Computational Linguistics (EACL), Mar 2026, Rabat (MOROCCO), Morocco |
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Transfert de modèles de langue pour la classification rhétorique des citations à travers les disciplines20e Conférence en Recherche d’Information et Applications (CORIA), 2025, Marseille, France. pp.233-248 |
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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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Semantically-Informed Domain Adaptation for Named Entity RecognitionISMIS 2024 - 27. International symposium on methodologies for intelligent systems, Jun 2024, Poitiers, France. pp.55-64, ⟨10.1007/978-3-031-62700-2_6⟩ |
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Exploitation de plongements de graphes pour l'extraction de relations biomédicalesCORIA-TALN 2023 30e Conférence sur le Traitement Automatique des Langues Naturelles (TALN), Jun 2023, Paris, France. pp.298-310 |
What is the added value of one health for plant health?12. International Congress of Plant Pathology (ICPP 2023), SFP; ISPP, Aug 2023, Lyon, France. pp.1 |
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Could KeyWord Masking Strategy Improve Language Model?28. International Conference on Natural Language & Information Systems. NLDB23, Métais, E., Meziane, F., Sugumaran, V., Manning, W., Reiff-Marganiec, S., Jun 2023, Derby, United Kingdom. pp.271-284, ⟨10.1007/978-3-031-35320-8_19⟩ |
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Taec : Un corpus annoté pour l'extraction de traits et phénotypes dans la littérature sur la sélection du bléAtelier INtégration de sources/masses de données hétérogènes et Ontologies, dans le domaine des sciences du VIVant et de l’Environnement, (IN-OVIVE), associé à la Plateforme Intelligence Artificielle (PFIA 2023),, Jul 2023, Strasbourg, France |
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Does constituency analysis enhance domain-specific pre-trained BERT models for relation extraction?BioCreative VII Challenge Evaluation Workshop, Nov 2021, on-line, Spain |
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Global alignment for relation extraction in MicrobiologyJunior Conference on Data Science and Engineering, Feb 2021, Orsay, France |
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Handling Entity Normalization with no Annotated Corpus: Weakly Supervised Methods Based on Distributional Representation and Ontological Information12th Conference on Language Resources and Evaluation, May 2020, Marseille, France. pp.1959-1966 |
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Bacteria Biotope at BioNLP Open Shared Tasks 20195th Workshop on BioNLP Open Shared Tasks BioNLP-OST@EMNLP-IJCNLP 2019, Association for Computational Linguistics, Jin-Dong Kim; Claire Nédellec; Robert Bossy; Louise Deléger, Nov 2019, Hong-Kong, Hong Kong SAR China. ⟨10.18653/v1/D19-5719⟩ |
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Relier automatiquement des entités textuelles à des concepts d'une ontologie par apprentissage avec (presque) aucune donnéeAtelier IN-OVIVE 7ème édition, des 30èmes Journées francophones d'Ingénierie des Connaissances, Jul 2019, Toulouse, France |
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Projet VisaTM : l'interconnexion OpenMinTeD – AgroPortal – ISTEX, un exemple de service de Text et Data Mining pour les scientifiques françaisIC 2018 - 29es Journées francophones d'Ingénierie des Connaissances, PFIA, Jul 2018, Nancy, France. pp.247-249 |
Ouverture des données, ouverture des logiciels, ouverture des servicesJNSO - Journées Nationales de la Science Ouverte, Dec 2018, Paris, France |
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L'ontologie OntoBiotope pour l'étude de la biodiversité microbienneEGC'2018: 18èmes Conférence Internationale sur l'Extraction et la Gestion des Connaissances, Jan 2018, Paris, France |
Reconstruction and visualisation of gene regulatory networks from different provenances : application at Arabidopsis thalianaBLAH4, Jan 2018, Tokyo, Japan. 2 p |
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Ontologie ATOL : amélioration de l'outil par l'intégration des caractères de santéJournées d'Animation Scientifique du département Phase (JAS Phase 2018), Apr 2018, Rennes, France |
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Projet VisaTM : l’interconnexion OpenMinTeD – AgroPortal – ISTEX, un exemple de service de Text et Data Mining pour les scientifiques françaisIC 2018 - 29es journées francophones d'Ingénierie des Connaissances, PFIA, Jul 2018, Nancy, France |
Combining rule-based and embedding-based approaches to normalize textual entities with an ontologyInternational Conference on Language Resources and Evaluation, May 2018, Miyazaki, Japan |
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Recovering the complexity in scientific knowledge: towards automatically reconstructing the maize floral transition gene regulatory networkInternational Conférence on Ecological Science, Oct 2018, Paris, France |
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A text mining approach to enhance knowledge of food microorganismsNext Generation Challenges in Food Microbiology, FoodMicro, Aug 2018, Athens, Greece |
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Fouille de texte, un écosystème en évolutionJNSO - Journées Nationales de la Science Ouverte, Dec 2018, Paris, France |
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Data Exchange Solution between PubAnnotation and AlvisAEBLAH4, Jan 2018, Tokyo, Japan. pp.1 |
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Representation of complex terms in a vector space structured by an ontology for a normalization taskBioNLP 2017 Workshop, Association for Computational Linguistics, Aug 2017, Vancouver, Canada. ⟨10.18653/v1/W17-2312⟩ |
Florilège: a database gathering microbial phenotypes of food interest2017 Scientific MEM days: Journées scientifiques MEM (Métaomiques et écosystèmes microbiens), Jan 2017, Paris, France |
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Customized automatic corpus annotations using AlvisNLP/MLBLAH3, Jan 2017, Tokyo, Japan. 11 diapos |
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Text-mining and ontologies: new approaches to knowledge discovery of microbial diversity4th International Conference on Microbial Diversity 2017, Oct 2017, Bari, Italy |
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Text-mining needs of the food microbiology research community2017 EFITA WCCA Congress, Jul 2017, Montpellier, France |
Integration of Alvis within the OpenMinTeD platform as Galaxy utilitiesGalaxy Community Conference, Jun 2017, Montpellier, France. pp.1, ⟨10.5281/zenodo.200370⟩ |
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Text mining tools for extracting information about microbial biodiversity in foodMicrobial Spoilers in Food 2017, Association pour le Développement de la Recherche Appliquée aux Industries Agricoles et Alimentaires (ADRIA). FRA., Jun 2017, Quimper, France. pp.95 |
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OntoBiotope, text mining and ontologies for a standard description of microorganism habitats18th GSC meeting, Genome Standards Consortium, Jun 2016, Heraklion, Greece. pp.24 slides |
Overview of the bacteria biotope task at BioNLP shared taskBioNLP Shared Task, Aug 2016, Berlin, Germany. pp.101 |
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Shared Task SeeDev : Extraction de régulations impliquées dans le développement de la graine d’Arabidopsis thaliana à partir de publications scientifiquesLes journées Bioinformatique de l'Inra, Mar 2016, Montpellier, France. pp.1 |
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OntoBiotope: une ontologie pour croiser les habitats microbiens avec les analyses de génomes.Les journées Bioinformatique de l'Inra, Mar 2016, Montpellier, France. pp.1 |
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Overview of the regulatory network of plant seed development (SeeDev) task at the BioNLP shared task 2016BioNLP Shared Task, Aug 2016, Berlin, Germany. pp.113 |
Le TDM par l'exemple : des microbes dans mon fromage !La loi numérique, et après ? Colloque de Meudon, Nov 2016, Meudon, France |
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L'informatique à l'INRASPECIF Campus, Journée Enseignement et recherche en informatique "hors les murs", Nov 2016, Paris, France. pp.32 slides |
TriPhase : co-construction IST - recherche MIAEvolutions de la recherche et impacts pour l'IST, May 2015, Magny-Le-Hongre, France |
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Knowledge model of regulatory networks involved in Arabidopsis seed development for information extraction and integration from textBioCreative 5, Sep 2015, Madrid, Spain |
Information extraction from articles for the elaboration of the regulatory networks involved in Arabidopsis seed development26th International Conference on Arabidopsis Research, Jul 2015, Paris, France |
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Validation de marqueurs liés à des gènes d’intérêt en vue de l’établissement d’une base de données pour la sélection assistée chez le blé tendreSynthèse des Programmes de Recherche FSOV. Actes de la 4ème Rencontre Scientifique, FSOV., Jan 2015, Paris, France. 5 p |
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Information extraction challenge Gene Regulation Network in Arabidopsis thaliana (GRNA)Paris-Saclay Center for Data Science: Open Software Initiative (OSI), Oct 2015, Orsay, France. pp.14 slides, ⟨10.13140/RG.2.1.4286.6326⟩ |
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Content Mining in Life SciencesScience Europe TDM workshop, Oct 2015, Bruxelles, Belgium |
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From Text to Knowledge and back - issues and challenges in Life SciencesBiomedical Linked Annotation Hackathon, Nov 2015, Mishima, Japan. 36 diapos |
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Information extraction from bibliography for Marker Assisted Selection in wheatMTSR 2014 : 8th Metadata and Semantics, Nov 2014, Karlsruhe, Germany. pp.301-313, ⟨10.1007/978-3-319-13674-5_28⟩ |
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Extraction d'information pour la sélection du blé par marqueur génétiqueAtelier IN-OVIVE 2ème édition des 25èmes Journées francophones d'Ingénierie des Connaissances, May 2014, Clermont-Ferrand, France |
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ATOL and EOL ontologies, steps towards embryonic phenotypes shared worldwide?4. Mammalian Embryo Genomics Meeting, Université Laval. CAN., Oct 2013, Hilton Quebec City, Canada. 102 p., ⟨10.1016/j.anireprosci.2014.06.013⟩ |
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Les ontologies ATOL et EOL, des outils en appui aux nouveaux challenges en production porcine46. Journées de la Recherche Porcine, Feb 2014, Paris, France. pp.281-285 |
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AlvisAE, un éditeur d'annotation sémantique structurée guidée par une ontologie évolutiveworkshop IC 2013 In_Ovive, Intégration de sources/masses de données hétérogènes et Ontologies, dans le domaine des sciences du VIVant et de l’Environnement, Plateforme AFIA, J Dibie-Barthélémy, Jul 2013, Lille, France |
Etat d'avancement d'ATOL et notion de robustesseTransversalité du groupe "Domestication" INRA-IFREMER, Jun 2013, Paris, France |
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Improving term extraction with linguistic analysis in the biomedical domain14th International Conference on Intelligent Text Processing and Computational Linguistics, Mar 2013, Samos, Greece |
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Des technologies sémantiques pour l'information scientifique et techniqueFrédoc 2013, Oct 2013, Aussois, France |
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AlvisAE: a collaborative Web text annotation editor for knowledge acquisitionLAW VI '12 - Sixth Linguistic Annotation Workshop, Jul 2012, Jeju, South Korea. pp.184 |
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ATOL: The Multi-species Livestock Trait Ontology6. Research Conference, MTSR, Nov 2012, Cadiz, Spain. pp.289-300, ⟨10.1007/978-3-642-35233-1_28⟩ |
Atol: Animal Trait Ontology for Livestock. Atol: Où en sommes-nous ?4. Journées d'Animation Scientifique du département Phase (JAS Phase 2012), Institut National de Recherche Agronomique (INRA). UAR Département Physiologie Animale et Systèmes d'Elevage (0558)., Jan 2012, Rennes, France. 30 diapositives |
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BioNLP 2011 Task Bacteria Biotope - The Alvis systemThe 49th Annual Meeting of the Association for Computational Linguistics:Human Language Technologies, Jun 2011, Portland, Oregon, United States. pp.206 |
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BioNLP shared tasks 2011 - Bacteria BiotopeThe 49th Annual Meeting of the Association for Computational Linguistics:Human Language Technologies, Jun 2011, Portland, Oregon, United States. pp.56-64 |
Text AnalysisAnimal Journal Management Board, May 2011, Edimbourg, United Kingdom |
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Sentence filtering for BioNLP: Searching for renaming actsThe 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies, Jun 2011, Portland, Oregon, United States |
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Corpus-based extension of termino-ontology by linguistic analysis: a use case in biomedical event extraction9. International conference onterminology andartificial intelligence, Nov 2011, Paris, France |
Ontologies et recherche d’informations dans le domaine scientifiqueComunication technique de plein champ : recherche et innovation, Mar 2011, Université Paris Diderot, Paris, France |
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Named and specific entity detection in varied data: the Quaero named entity baseline evaluation7. Conference on international language resources and evaluation, May 2010, Valletta, Malta |
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Building large lexicalized ontologies from text: a use case in automatic indexing of biotechnology patentsEKAW 2010 - Knowledge Engineering and Knowledge Management by the Masses, Cimiano, Philipp, Pinto, H. Sofia, Oct 2010, Lisbonne, Portugal. ⟨10.1007/978-3-642-16438-5_41⟩ |
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TyDI : un outil d’assistance à la construction de terminologie structurée8. International conference on terminology and artificial intelligence: TIA 2009, Nov 2009, Toulouse, France |
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BioAlvis II, NLP-based semantic mining of literature on molecular biology of bacteriaBioCreative II.5 workshop 2009: special session on digital annotations, Oct 2009, Madrid, Spain |
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Close integration of ML and NLP tools in BioAlvis semantic search in bacteriologySemantic web applications and tools for life sciences, SWAT4LS 2008, Nov 2008, Edinburgh, United Kingdom |
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Semantic annotation in the Alvis projectInternational Workshop on Intelligent Information Access, Jul 2006, Helsinki, Finland |
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Getting the unknown from the known in bacteria, and the role of text miningData and Text Mining in Integrative Biology Workshop, associ ECML/PKDD, Sep 2006, Berlin, Germany |
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Annotation guidelines for machine learning-based named entity recognition in microbiologyProceeding of Data and Text Mining for Integrative Biology Workshop 17. European Conference on Machine Learning 10. European Conference on Principles and Practice of Knowledge Discovery in Databases, Sep 2006, Berlin, Germany |
Adapting a general parser to a sublanguageInternational Conference: RANLP - 2005 (Recent Advances in Natural Language Processing), Sep 2005, Borovets, Bulgaria |
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Learning language in logic - genic interaction extraction challenge4. Learning language in logic workshop (LLL05), Aug 2005, Born, Germany |
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Adapting a general parser to a sublanguage2005, pp.89-93 |
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Machine learning for information extraction in genomics: state of the art and perspectives1. International workshop on text mining and its application, Apr 2003, Patras, Greece |
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Extraction d'information appliquée au domaine biomédical : apprentissage et traitement automatique de la langueConférence internationale de fouille de texte, CIFT-04, Jun 2004, La Rochelle, France |
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Event-based Information Extraction for the biomedical domain: the Caderige projectProceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and Its Applications (COLING'04), 2004, Geneva, Switzerland. pp.43-49 |
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Machine learning applied to information extraction in specific domains: an example: gene interaction extraction from bibliography in genomics2nd Workshop on Semantic Web Mining joint with ECML/PKDD'2002 13th European Conference on Machine Learning (ECML'02)., Berendt B. et al., Aug 2002, Helsinki, Finland |
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Sentence filtering for information extraction in genomics, a classification problemPrinciples of Data Mining and Knowledge Discovery. PKDD 2001, Sep 2001, Freiburg, Germany. ⟨10.1007/3-540-44794-6_27⟩ |
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A practitioner’s framework for reorienting plant health surveillance toward agroecological outcomes2026 |
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Taec: a Manually annotated text dataset for trait and phenotype extraction and entity linking in wheat breeding literature2024 |
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Omnicrobe, an open-access database of microbial habitats and phenotypes using a comprehensive text mining and data fusion approach2022 |
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Deliverable D5.1: Report on method and language for the production of the augmented document representations2006 |
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MilkOligoCorpus annotation guidelinesINRAE. 2024 |
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Guidelines for the Annotation of the Taec Corpus - Phenotype and Trait information in WheatINRAE MaIAGE. 2023 |
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Recommandations sur l'analyse automatique de documents : acquisition, gestion, exploration[Rapport de recherche] Comité pour la science ouverte. 2019, 12 p |
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HoloOLIGO corpus, a manually annotated text dataset supporting schema-based relational information extraction for mammalian milk oligosaccharide diversity pattern comprehensionJournées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jun 2024, Toulouse, France |
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Omnicrobe : une base de données d’habitats et de phénotypes microbiens23ème édition du colloque du Club des Bactéries Lactiques, Jun 2022, Rennes, France. , 2022 |
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Florilege, a database gathering microbial habitats, phenotypes and usesJOBIM 2020, Jun 2020, Montpellier, France |
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Combining String-based and Embeddings-based Methods for Medical Concept Normalization: LIMSI-CEA-INRA@n2c2 20192019 n2c2/OHNLP Shared-Task and Workshop, Nov 2019, Washington, D.C., United States. 2019 |
Bioinformatics tools as a way to select microbial strains for fermented food products15.Symposium on Bacterial Genetics and Ecology "Ecosystem drivers in a changing planet", May 2019, Lisbonne, Portugal. , 2019 |
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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⟩ |
To better benefit from shared tasks in biomedical text miningGalaxy Community Conference, Jul 2019, Freiburg, Germany. 2019 |
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FLORILEGE: an integrative database using text mining and ontologiesJOBIM 2018, Jul 2018, Marseille, France. , 2018, ABSTRACTS JOBIM 2018 |
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Florilege : a database gathering microbial phenotypes of food interest4. International Conference on Microbial Diversity 2017, Oct 2017, Bari, Italy. , 2017 |
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La suite Alvis, plateforme d’analyse de contenu textuel, et son intégration dans OpenMinTeDJDEV 2017, Jul 2017, Marsaille, France. , pp.1, 2017 |
OntoBiotope, technologies sémantiques pour l’étude des habitats microbiensMéta-omiques des Ecosystèmes Microbiens, Sep 2015, Paris, France |
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ATOL: an ontology for livestock63. Annual Meeting of the European Federation of Animal Science (EAAP), Aug 2012, Bratislava, Slovakia. Academic Publishers, Annual Meeting of the European Association for Animal Production, 18, 476 p., 2012, Annual Meeting of the European Association for Animal Production |
Proceedings of The 5th Workshop on BioNLP Open Shared Tasks5th Workshop on BioNLP Open Shared Tasks BioNLP-OST@EMNLP-IJNCLP 2019, Nov 2019, Hong-Kong, China. , 2019 |
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Workshop on data and text mining for integrative biology17. European conference on machine learning (ECML), Sep 2006, Berlin, Germany. , 98 p., 2006 |
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Proceedings of the learning language in logic ICML joint workshop and the challenge task, extracting relations from biomedical texts4. Learning language in logic workshop (LLL05), Jun 2005, York, United Kingdom. 75 p., 2005 |
Introduction au chapitre V, Web, réseaux sociaux et recherche d’informationLes Big Data à découvert, CNRS Editions Alpha, pp.368, 2017, 978-2-271-11464-8 |
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BioinformatiquePierre Marquis and Odile Papini and Henri Prade. Panorama de l'intelligence artificielle Ses bases méthodologiques, ses développements, 3, Cépaduès, 374 p., 2014, 9782364930438 |
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Information extractionHandbook on ontologies, Springer Science - Business Media Deutschland GmbH, 2009, International Handbooks on Information Systems, 978-3-540-70999-2 |
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Information ExtractionS. Staab, R. Studer. Handbook on Ontologies, Springer Verlag, pp.663-686, 2009, Springer Series on Handbooks in Information Systems |
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Apprentissage automatiqueEncyclopédie de l'informatique et des systèmes d'information, Vuibert, 2006, 978-2-7117-4846-4 |
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Ontologies and information extraction: a necessary symbiosisOntology learning from text: method, evaluation and applications, 123, IOS Press, 2005, Frontiers in Artificial Intelligence and Applications, 1-58603-523-1 |
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Ontology and Information Extraction: a necessary symbiosisPaul Buitelaar, Philipp Cimiano, Bernardo Magnini. Ontology Design and Population, IOS Press, pp.155-170, 2005 |
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Fouille de données et analyse du transcriptomeJean-François Boulicaut, Olivier Gandrillon. Informatique pour l'analyse du transcriptome, Lavoisier, pp.101-141, 2004, Traité IC2, série Informatique et Systèmes d'Information, 978-2-212-12471-2 |
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Fouille de données pour l'analyse du transcriptomeInformatique pour l'analyse du transcriptome, Lavoisier Editions, 2004, 978-2-212-12471-2 |
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Extraction et modélisation de connaissance à partir de texte – Applications à la biologieLinguistique. Université Blaise Pascal (Clermont Ferrand 2), 2013 |
Ontologies and information extraction, 23 p., 2005 |