Nédellec Claire

Address

Email : claire.nedellec@jouy.inra.fr Adresse : INRA - Unité MaIAGE                  Bâtiment 233                  Domaine de Vilvert                  78352 JOUY-EN-JOSAS CEDEX Tél : +33 (0)1 34 65 28 78 Fax : +33 (0)1 34 65 00 00 Secrétariat : +33 (0)1 34 65 28 86

Cursus                                                                                                                  

Claire Nédellec has a permanent research position at l'INRA since 2001. She is research director and leader of Bibliome team.

She has been researcher at LRI, Université Paris-Sud from 1994 to 2001 after a PhD in Inductive Logic Programming applied to cooperative machine learning. She was co-chair of ECML (European Conference on Machine Learning) in 1998. She has defended her HDR and became Principal Investigator in October 2013.

Research interests

Projects

On-going projects

Infrastructure H2020 Text-mining OpenMinTeD (2015-2018)

D-ONT, Exploitation optimisée des bases de données phénotypiques - Des ontologies pour le partage d’information, ACI Phase 2016-2018.

Florilege  - Métaprogramme MEM  - Action ciblée  (2016-2018)

FoodMicrobiome Transfert  - CNIEL-Inra  (2015-2019)  

Visa TM  - BSN  Vers une infrastructure de services avancés pour le text-mining (2017-2018)  

Recent projects

IMSV, Institut de modélisation des systèmes vivants, Lidex de l'Université Paris-Saclay (2014-2016)

SeeDev, Regulations in the developement of Arabidopsis thaliana seed (Challenge Lidex CDS) (2015)

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

Triphase: Semantic information system for publications in animal physiology and agricultural systems. PHASE department (2013-2014).

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

FSOV SAM Blé: Selection of wheat by genetic markers Fond de soutien à l'obtention végétale (2010-2013).

Animation

Workgroup Labex DigiCosme D2K (from Data to Knowledge)

INRA CATI ICAT (Knowledge Engineering and Text Analysis)

BioNLP-Shared Task (2011, 2013, 2016)

Supervision

Current supervision

Jean-Baptiste Bohuon, R&D, OpenMinTeD project.

Estelle Chaix, post-doc, OpenMinTeD project.

 Arnaud Ferré, PhD preparation, IDEX IDI, co-supervision with Pierre Zweigenbaum (LIMSI).

Recent supervision

 Frédéric Papazian. Engineer in Computer Science February 2008 - September 2012. Projects Quaero, FSOV and TriPhase.

 Wiktoria Golik Engineer in knowledge Engineering and Computational Linguistics August 2009 - May 2013. Projects Quaero and TriPhase.

 Pierre Warnier PhD in Computer Sciences Dec 2010 - 2013. Projet Quaero : Distributional semantics, co-supervision with Eric Gaussier and Gilles Bisson, LIG.

 Zorana Ratkovic PhD in computational linguistics, co-supervision with Thierry Poibeau, LaTTiCE October 2010 - December 2015. 

 Dialekti Valsamou, PhD preparation, IDEX IDI, co-supervision with Pierre Zweigenbaum (LIMSI).

Publications

Recent publications

Journal

• Agnès Girard et le réseau des documentalistes du Département Phase, Inra Rennes et Claire Nédellec et l’équipe de recherche Bibliome. Triphase : co-construction d’une ressource termino-ontologique. Arabesque, Revue trimestrielle de l'agence bibliographique de l'Enseignement Supérieur, August 2016.

• Robert Bossy, Wiktoria Golik, Zorana Ratkovic, Dialekti Valsamou, Philippe Bessières, Claire Nédellec. An Overview of the  Gene Regulation Network and the Bacteria Biotope Tasks in BioNLP’13. BMC Bioinformatics, Vol 16 Suppl 10, 2015

• Golik W., Bossy R., Ratkovic Z., Nédellec C. " Improving term extraction with linguistic analysis in the biomedical domain" Special Issue of the journal Research in Computing Science, vol 70 ISSN 1870-4069, 2014.

• Robert Bossy, Julien Jourde, Alain-Pierre Manine, Philippe Veber, Erick Alphonse, Maarten van de Guchte, Philippe Bessières, Claire Nédellec. BioNLP Shared Task - The Bacteria Track. BMC Bioinformatics, (Suppl 11):S3, June 2012.

Colloque international

• Arnaud Ferré, Louise Deléger, Pierre Zweigenbaum, Claire Nédellec. Combining rule-based and embedding-based approaches to normalize textual entities with an ontology, The 11th edition of Language Resources and Evaluation Conference (LREC-2018), European Language Resources Association (ELRA) publisher, Miyazaki, mai 2018.

Nédellec C., Bossy R., Chaix E., Deléger L. Text-mining and ontologies: new approaches to knowledge discovery of microbial diversity. In Proceedings of the 4th International Microbial Diversity Conference. pp. 221-227, ed. Marco Gobetti. Pub. Simtra. ISBN 978-88-943010-0-7, Bari, October 2017.

Estelle Chaix, Sophie Aubin, Louise Deléger, and Claire Nédellec. Text-mining needs of the food microbiology research community, In Ovive workshop joint to European Federation for Information Technology in Agriculture, Food and the Environment (EFITA) conference. Montpellier, 12 pages, juillet 2017.

• Arnaud Ferré, Pierre Zweigenbaum, Claire Nédellec, Representation of complex terms in a vector space structured by an ontology for a normalization task. In Proceedings of the BioNLP 2017 Workshop, Association for Computational Linguistics, Vancouver, 8 pages, Canada 2017.

Nédellec C., Bossy R., Chaix E., Deléger L. Text-mining and ontologies: new approaches to knowledge discovery of microbial diversity. In Proceedings of the 4th International Microbial Diversity Conference. pp. 221-227, ed. Marco Gobetti. Pub. Simtra. ISBN 978-88-943010-0-7, Bari, October 2017.

• Estelle Chaix, Bertrand Dubreucq, Abdelhak Fatihi, Dialekti Valsamou, Robert Bossy, Mouhamadou Ba, Louise Deléger, Pierre Zweigenbaum, Philippe Bessières, Loïc Lepiniec, Claire Nédellec. Overview of the Regulatory Network of Plant Seed Development (SeeDev) Task at the BioNLP Shared Task.  In Proceedings of the BioNLP Shared Task 2016 Workshop, Association for Computational Linguistics, Berlin, Germany 2016.

• Louise Deléger, Robert Bossy, Estelle Chaix, Mouhamadou Ba, Arnaud Ferré, Philippe Bessières, Claire Nédellec, Overview of the Bacteria Biotope Task at BioNLP Shared Task,  In Proceedings of the BioNLP Shared Task 2016 Workshop, Association for Computational Linguistics, Berlin, Germany 2016.

•  Estelle Chaix, Bertrand Dubreucq, Dialekti Valsamou, Abdelhak Fatihi , Robert Bossy, Louise Deléger, Pierre Zweigenbaum, Philippe Bessières, Loïc Lepiniec, Claire Nédellec. Knowledge model of regulatory networks involved in Arabidopsis seed development for information extraction and integration from text. Abstract and poster, BioCreative Workshop 2015, Sevilla, Spain.

• Bertrand Dubreucq, Dialekti Valsamou, Abdelhak Fatihi, Estelle Chaix, Robert Bossy, Philippe Bessières, Louise Deleger, Pierre Zweigenbaum, Claire Nédellec and Loïc Lepiniec.Information extraction from articles for the elaboration of the regulatory networks involved in Arabidopsis seed development. Poster of the  26th International Conference on Arabidopsis Research, Paris, 5-9 July 2015.

• Claire Nédellec, Robert Bossy, Dialekti Valsamou, Marion Ranoux, Wiktoria Golik, Pierre Sourdille. Information Extraction from Bibliography for Marker Assisted Selection in Wheat. In proceedings of Metadata and Semantics for Agriculture, Food & Environment (AgroSEM'14), special track of the 8th Metadata and Semantics Research Conference (MTSR’14), Springer Communications in Computer and Information Science, Series Volume 478, Karlsruhe, pp 301-313, Germany, 2014. DOI: 10.1007/978-3-319-13674-5_28

• P.-Y. Le Bail, J. Bugeon, O. Dameron, A. Fatet, W. Golik, J.-F. Hocquette, C. Hurtaud, I. Hue, C. Jondreville, L. Joret, M.-C. Meunier-Salaün, J. Vernet, C. Nédellec, M. Reichstadt, P. Chemineau. Un langage de référence pour le phénotypage des animaux d’élevage : l’ontologie ATOL, INRA Prod. Anim., 2014, 27 (3), 195-208.

• Hue I , Bugeon J Dameron O, Fatet A, Hurtaud C, Joret L, Meunier-Salaün MC, Nédellec C, Reichstadt M, Vernet J, Le Bail PY.ATOL AND EOL ONTOLOGIES, STEPS TOWARDS EMBRYONIC PHENOTYPES SHARED WORLDWIDE?, 4th Mammalian Embryo Genomics meeting, Québec, October 2013. 

• Wiktoria Golik, Robert Bossy, Zorana Ratkovic, Claire Nédellec. " Improving term extraction with linguistic analysis in the biomedical domain" in Proceedings of the 14th International Conference on Intelligent Text Processing and Computational Linguistics (CICLing'13), 24-30 March, Samos, Greece, 2013.

• Bossy R., Bessières P., Nédellec C. BioNLP Shared Task 2013 – An overview of the Genic Regulation Network Task. In Proceedings of the BioNLP 2013 Workshop, Association for Computational Linguistics, Sofia, Bulgaria, 2013.

• Bossy R., Golik W., Ratkovic Z., Bessières P., Nédellec C. BioNLP shared Task 2013 – An Overview of the  Bacteria Biotope Task. In Proceedings of the BioNLP 2013 Workshop, Association for Computational Linguistics, Sofia, Bulgaria, 2013.

• Nédellec C., Bossy R., Kim J.-D., Kim J.-J., Ohta T., Pyysalo P., Zweigenbaum P.. Overview of BioNLP Shared Task 2013.In Proceedings of the BioNLP 2013 Workshop, Association for Computational Linguistics, Sofia, Bulgaria, 2013.

• Salaun, M.-C., Bugeon, J.,  Dameron, O.,  Fatet, A., Hue, I.,  Hurtaud, C., Nédellec, C., Reichstadt, M., Vernet, J., Reecy, J.,  Park, C., Le Bail, P.-Y. ATOL: an ontology for livestock. In : Book of abstracts of the 63rd Annual Meeting of the European Federation of Animal Science (2012-08-27-2012-08-31), Bratislava (Slovaquie).Wageningen (NLD) : Wageningen Academic Publishers (EAAP Book of Abstracts, 18), 2012. 

• Wiktoria Golik, Olivier Dameron, Jérôme Bugeon, Alice Fatet, Isabelle Hue, Catherine Hurtaud, Matthieu Reichstadt, Marie-Christine Salaün, Jean Vernet, Léa Joret, Frédéric Papazian, Claire Nédellec et Pierre-Yves Le Bail. " ATOL: the multi-species livestock trait ontology" in proceedings of The 6th Metadata and Semantics Research Conference (MTSR 2012), pp 289-300. Springer Verlag Communications in Computer and Information Science Serie. Cadiz, Espagne, 28 to 30 November 2012. 

• Frédéric Papazian, Robert Bossy and Claire Nédellec, "AlvisAE: a collaborative Web text annotation editor for knowledge acquisition", The 6th Linguistic Annotation Workshop (The LAW VI), Jeju, Korea, 2012.

• Zorana Ratkovic   Wiktoria Golik, Pierre Warnier   Philippe Veber   Claire Nédellec, "BioNLP 2011 Task Bacteria Biotope – The Alvis system", ACL BioNLP workshop, Portland, USA, 2011. 

• Robert Bossy, Julien Jourde, Philippe Bessières, Maarten van de Guchte, Claire Nédellec, « BioNLP shared Tasks 2011 - Bacteria Biotope », ACL BioNLP workshop Portland, USA, 2011.

• Pierre Warnier, Claire Nédellec « Sentence Filtering for BioNLP: Searching for Renaming Acts » ACL BioNLP workshop, Portland, USA, 2011.

• Claire Nédellec, Wiktoria Golik, Sophie Aubin, Robert Bossy, "Building Large Lexicalized Ontologies from Text: a Use Case in Indexing Biotechnology Patents", International Conference on Knowledge Engineering and Knowledge Management (EKAW 2010), Lisbon, Portugal, 11th 15th October, 2010.

  Galibert O., Quintard L., Rosset S., Zweigenbaum P., Nédellec C., Aubin S., Gillard L., Raysz J.-P., Pois D., Tannier X., Deléger L., Laurent D., " Named and specific entity detection in varied data: The Quaero Named Entity baseline evaluation", The seventh international conference on Language Resources and Evaluation (LREC-2010), European Language Resources Association (ELRA) publisher, Malta, 19-21 May 2010.

Chapitre de livre

• Nédellec C., Nazarenko A., Bossy R. "Information Extraction", Handbook on Ontology., S. Staab, R. Studer (eds.), Springer Verlag, 2009.

 Liste complète