Maître de conférences, HDR


Depuis septembre 2007   Maître de conférences en Informatique à l’Université de Bordeaux
Février 06 – août 07          ATER en Informatique à l’Université de Rennes 2 – temps complet
Septembre 03 – mai 04    ATV en Informatique à l’Université de Rennes 2


2019 HDR de l’Université de Bordeaux
Titre : Enjeux liés aux ressources termino-ontologiques en santé
Laboratoire : ERIAS, centre de recherche Bordeaux Population Health, Inserm U1219

2006 Doctorat de l’Université de Rennes 1
Titre : Conception d’un modèle Web sémantique appliqué à la génomique fonctionnelle
Laboratoire : E.A 3888 « Modélisation Conceptuelle des Connaissances Biomédicales »

2002 DESS Traitement de l’Information Médicale et Hospitalière (TIMH), Université de Rennes I
2001 Maîtrise d’informatique, IFSIC, Université de Rennes I
1999 Licence d’informatique, IFSIC, Université de Rennes I
1998 DEUG Mathématiques et Informatique Appliquées aux Sciences (MIAS), Université de Rennes I


  • Maître de conférences en Informatique à l’Isped, Université de Bordeaux
  • Co-responsable de la commission pédagogique Gestion de l’offre de formation de l’ISPED
  • Responsable du Master 2 SITIS (Systèmes d’Information et Technologies Informatiques pour la Santé) de l’ISPED
  • Membre élue du conseil du Collège Sciences de la Santé, Université de Bordeaux
  • Membre associée du LaBRI
  • Membre des associations scientifiques AIM et AFIA

Publications (depuis 2009)

Revues internationales

Ayllón-Benítez A, Bourqui B, Thébault P*, Mougin F*. GSAn: an alternative to enrichment analysis for annotating gene sets. Nucleic Acids Research Genomics and Bioinformatics. 2020

Ayllón-Benítez A, Mougin F*, Allali J, Thiebaut R, Thébault P*. A new method for evaluating the impacts of semantic similarity measures on the annotation of gene sets. PLoS ONE. 2018;13(11): e0208037

Diallo G, Mougin F. Preface of the Special Issue of the Sixth French-Speaking Conference on Ontologies. J Biomed Semantics. 2018;7:189

Mougin F, Auber A, Bourqui R, Diallo G, Dutour I, Jouhet V, Thiessard F, Thiebaut R, Thébault P. Visualizing omics and clinical data: which challenges for dealing with their variety? Methods. 2018 Jan 1;132:3-18

Nikiema JN, Jouhet V*, Mougin F*. Integrating cancer diagnosis terminologies based on logical definitions of SNOMED CT concepts. J Biomed Inform. 2017;74:46-58

Jouhet V, Mougin F, Bréchat B, Thiessard F. Building a model for disease classification integration in oncology: an approach based on the National Cancer Institute thesaurus. J Biomed Semantics. 2017 Feb 7;8(1):6

Hamon T, Grabar N, Mougin F. Querying Biomedical Linked Data with Natural Language Questions. Semantic Web. 2017 Jan 27;8(4):581-599

Dramé K, Mougin F, Diallo G. Large scale biomedical texts classification: a kNN and an ESA-based approaches. J Biomed Semantics. 2016 Jun 16;7:40

Mougin F, Grabar N. Auditing the multiply-related concepts within the UMLS. J Am Med Inform Assoc 2014;21:185-193

Drame K, Diallo G, Delva F, Dartigues JF, Mouillet E, Salamon R, Mougin F. Reuse of termino-ontological resources and text corpora for building a multilingual domain ontology : an application to Alzheimer’s disease. J Biomed Inform. 2014 Apr;48:171-182

Avillach P, Dufour JC, Diallo G, Salvo F, Joubert M, Thiessard F, Mougin F, Triro G, Fourrier-Reglat A, Pariente A, Fieschi M. Design and Validation of an Automated Method to Detect Known Adverse Drug Reactions in MEDLINE : a Contribution from the EU-ADR project. J Am Med Inform Assoc. 2013 May 1;20(3):446-452

Avillach P, Coloma PM, Gini R, Schuemie M, Mougin F, Dufour JC, Mazzaglia G, Giaquinto C, Fornari C, Herings R, Molokhia M, Pedersen L, Fourrier-Réglat A, Fieschi M, Sturkenboom M, van der Lei J, Pariente A, Trirp G; on behalf of the EU-ADR consortium. Harmonization process for the identication of medical events in eight European healthcare databases : the experience from the EU-ADR project. J Am Med Inform Assoc. 2013 Jan 1;20(1):184-192

Mougin F, Bodenreider O, Burgun A. Analyzing polysemous concepts from a clinical perspective: application to auditing concept categorization in the UMLS. J Biomed Inform. 2009 Jun;42(3):440-451

*equal contribution

Actes de conférences internationales (avec comité de lecture)

Bordea G, Faralli G, Mougin F, Buitelaar P, Diallo G. Evaluation Dataset and Methodology for Extracting Application-Specific Taxonomies from the Wikipedia Knowledge Graph. Proceedings of The 12th Language Resources and Evaluation Conference. European Language Resources Association. 2020: 2341-2347. ISBN: 979-10-95546-34-4

Nikiema JN, Mougin F*, Jouhet V*. Building a Graph Representation of LOINC to Facilitate its Alignment to French terminologies. AMIA Annu Symp Proc. 2020: to appear

Bordea G, Randriatsitohaina T, Mougin F, Grabar N, Hamon T. Query selection methods for automated corpora construction with a use case in food-drug interactions. ACL BioNLP workshop, 2019

Cossin S, Lebrun L, Lobre G, Loustau R, Jouhet V, Griffier R, Mougin F, Diallo G, Thiessard F. Romedi: An Open Data Source About French Drugs on the Semantic Web. Stud Health Technol Inform. 2019 Aug 21;264:79-82

Cossin S, Lebrun L, Aymeric N, Mougin F, Lambert M, Diallo G, Thiessard F, Jouhet V. SmartCRF: A Prototype to Visualize, Search and Annotate an Electronic Health Record from an i2b2 Clinical Data Warehouse. Stud Health Technol In-form. 2019 Aug 21;264:1445-6

Bordea G, Thiessard F, Hamon T, Mougin F. Automatic query selection for acquisition and discovery of food-drug interactions, 9th International Conference of the CLEF Association, CLEF 2018, Avignon, France, September 10-14, 2018, Proceedings. LNCS 11018:115-120.

Cossin S, Jouhet V, Mougin F, Diallo G, Thiessard F. IAM at CLEF eHealth 2018: Concept Annotation and Coding in French Death Certificates. CLEF eHealth Evaluation Lab (Working Notes) 2018

Hamon T, Tabanou V, Mougin F, Grabar N, Thiessard T. POMELO: Medline corpus with manually annotated food-drug interactions, Proceedings of the Biomedical NLP Workshop associated with Recent Advances in Natural Language Processing – RANLP 2017:73-80

Ayllón-Benítez A, Thébault P, Fernández-Breis J.T., Quesada-Martínez M, Mougin F, Bourqui R. Deciphering gene sets annotations with Ontology based visualization, 21st International Conference on Information Visualization, 2017:170-175

Hamon T, Mougin F, Grabar N. Generating and Executing Complex Natural Language Queries across Linked Data, Stud Health Technol Inform. 2015;216:815-820

Mougin F. Identifying redundant and missing relations in the Gene Ontology, Stud Health Technol Inform. 2015;210:195-199

Bigeard E, Jouhet V, Mougin F, Thiessard F, Grabar N. Automatic extraction of numerical values from unstructured data in EHRs, Stud Health Technol Inform. 2015;210:50-54

Drame K, Mougin F, Diallo G. A k-nearest neighbor based method for improving large scale biomedical document indexing. Proceedings of the 6th International Symposium on Semantic Mining in Biomedicine (SMBM). In Bodenreider O, Oliveira J, Rinaldi F. Aveiro, 2014:19-26

Hamon T, Grabar N, Mougin F. Natural Language Question Analysis for Querying Biomedical Linked Data. Proceedings of the 1st Natural Language Interfaces for Web of Data workshop (NLIWoD), ISWC 2014

Drame K, Mougin F, Diallo G. Query Expansion using External Resources for Improving Information Retrieval in the Biomedical Domain. CLEF (Working Notes) 2014 :189-194

Hamon T, Grabar N, Mougin F, Thiessard F. Description of the POMELO System for the Task 2 of QALD-2014. CLEF (Working Notes) 2014:1212-1223

Mougin F, Grabar N. Using a cross-language approach to acquire new mappings between two biomedical terminologies. In Peek N, Marin R, and Peleg M (editors). Artificial Intelligence in Medicine. Berlin Heidelberg : Springer ; 2013. LNAI 7885:221-226

Mougin F, Burgun A, Bodenreider O. Comparing drug-class membership in ATC and NDF-RT. Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium, ISBN:978-1-4503-0781-9, 2012 :437-443

Drame K, Diallo G, Mougin F. Towards a bilingual Alzheimer’s disease terminology acquisition using a parallel corpus. Stud Health Technol Inform. 2012 ;180 :179-183

Thiessard F, Mougin F, Diallo G, Jouhet V, Cossin S, Garcelon N, Campillo B, Jouini W, Grosjean J, Massari P, Grion N, Dupuch M, Tayalati F, Dugas E, Balvet A, Grabar N, Pereira S, Frandji B, Darmoni S, Cuggia M. RAVEL : Retrieval And Visualization in ELectronic health records. Stud Health Technol Inform. 2012;180 :194-198

Mougin F, Dupuch M, Grabar N. Improving the mapping between MedDRA and SNOMED CT. In Peleg M, Lavrac N, and Combi C (editors). Articial Intelligence in Medicine. Berlin Heidelberg: Springer ; 2011. LNAI 6747:220-224

Grabar N, Dupuch M, Mougin F. Dommages collatéraux de la fusion de terminologies. Proceedings of the 9th International Conference on Terminology and Articial Intelligence, 2011:10-16

Mougin F, Bodenreider O, Burgun A. Looking for Anemia (and Other Disorders) in SNOMED CT: Comparison of Three Approaches and practical Implications. AMIA Annu Symp Proc. 2010:527-231

Bodenreider O, Mougin F, Burgun A. Automatic determination of anticoagulation status with NDF-RT. Proceedings of the 13th ISMB’2010 SIG meeting Bio-ontologies 2010:140-143

Avillach P, Joubert M, Thiessard F, Trirp G, Dufour JC, Pariente A, Mougin F, Polimeni G, Catania MA, Giaquinto C, Mazzaglia G, Fornari C, Herings R, Gini R, Hippisley-Cox J, Molokhia M, Pedersen L, Fourrier-Réglat A, Sturkenboom M, Fieschi M. Design and evaluation of a semantic approach for the homogeneous identication of events in eight patient databases : a contribution to the European EU-ADR project. Stud Health Technol Inform. 2010;160:1085-1089

Mougin F, Burgun A, Bodenreider O. Identifying anatomical concepts associated with ICD10 diseases, proceedings of the 8th International Conference on Terminology and Articial Intelligence, 2009, CEUR Workshop proceedings, Vol . 578, ISSN: 1613-0073

Burgun A, Mougin F, Bodenreider O. Two approaches to integrating phenotype and clinical information, AMIA Annu Symp Proc 2009:75-79

Avillach P, Mougin F, Joubert M, Thiessard F, Pariente A, Dufour JC, Trirp G, Polimeni G, Catania MA, Giaquinto C, Mazzaglia G, Baio G, Herings R, Gini R, Hippisley-Cox J, Molokhia M, Pedersen L, Fourrier-Réglat A, Sturkenboom M, Fieschi M. A semantic approach for the homogeneous identication of events in eight patient databases : a contribution to the European eu-ADR project, Stud Health Technol Inform. 2009;150:190-194

Revue nationale

Avillach P, Mougin F, Joubert M, Thiessard F, Pariente A, Dufour JC, Fieschi M. Approche sémantique pour l’identication homogène d’eets indésirables et de médicaments dans huit bases de données de patients : une contribution au projet européen ALERT, JFIM, Springer Verlag, Informatique et Santé 17. 2009:251-261

Conférences nationales (avec comité de lecture)

Ayllón-Benítez A, Mougin F, Thébault P. Une nouvelle méthode pour évaluer l’impact des mesures de similarité sémantique sur l’annotation d’un groupe de gènes”. Actes des Journées Ouvertes Biologie Informatique Mathématiques (JOBIM). 2019, 118-119

Nikiema JN, Mougin F, Jouhet V. Processus de prétraitement des libellés d’une terminologie d’interface, Actes du symposium sur l’Ingénierie de l’Information Médicale, SIIM 2017, Toulouse, France, 95-103

Nikiema JN, Mougin F, Jouhet V. Utilisation de la SNOMED CT comme support à l’alignement de terminologies diagnostiques en cancérologie, Actes des 6èmes Journées Francophones sur les Ontologies, JFO 2016, ISBN 978-2-9558601-0-6, France, 142-148

Bréchat B, Mougin F, Thiessard F, Jouhet V. Mapping de terminologies diagnostiques en cancérologie par l’intermédiaire du NCI Metathesaurus, Actes des Journées Francophones d’Informatique Médicale, JFIM 2014, Maroc, 34-43

Drame K, Diallo G, Mougin F. Construction d’une ontologie bilingue de la maladie d’Alzheimer à partir de textes médicaux. Atelier IC pour l’Interopérabilité Sémantique dans les applications en e-Santé ; 26 Juin 2012, Paris, France

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