Professor

Appointments

September 2021-      Full professor of Computer science, University of Bordeaux
2007-2021                 Associate professor of Computer science, University of Bordeaux
2006-2007               Assistant professor of Computer science, University of Rennes 2
2003-2004               Teaching assistant of Computer science, University of Rennes 2

Main degrees

2019 HDR in Computer science, University of Bordeaux
Title: Issues related to termino-ontological resources in health
Team: ERIAS, Bordeaux Population Health research center, Inserm U1219

2006 PhD in Computer science, University of Rennes 1
Title: Conception of a semantic Web model applied to functional genomics
Team: University team 3888 « Conceptual Modeling of Biomedical Knowledge »

2002 DESS (fifth-year university degree) in Medical Informatics, University of Rennes 1, France

2001 Maîtrise (fourth-year university degree) in Computer engineering, University of Rennes 1, France

Activities

  • Full professor of Computer science, Isped, University of Bordeaux
    • Teaching about 180 hours in class each year (Isped – Medical school – School of cognitive engineering), main topics:
      • Database management
      • Terminologies and ontologies in the biomedical domain
      • Design and analysis of case-control studies
  • Co-responsible of the pedagogical commission Management of the training offer of ISPED
  • Graduate Program Director, MSc Public Health, SITIS (Information Systems and Computer Technologies for Health) concentration, since 2015
  • Elected member of the board of the College of Health Sciences, University of Bordeaux
  • Associate member of LaBRI
  • Member of the French scientific associations of medical informatics (AIM) and of artificial intelligence (AFIA)
  • Associate editor of the IMIA Yearbook of Medical Informatics 

 

Publications (since 2009)

International journals

Nikiema JN, Griffier R, Jouhet V*, Mougin F*. Aligning an interface terminology to the Logical Observation Identifiers Names and Codes (LOINC). J Am Med Inform Assoc Open. 2021;4(2):ooab035

Soualmia LF, Hollis KF, Mougin F, Séroussi B. Health Data, Information, and Knowledge Sharing for Addressing the COVID-19. Yearb Med Inform. 2021 Aug;30(1):4-7

Altman MC, Rinchai D, Baldwin N, Toufiq M, Whalen E, Garand M, Syed Ahamed Kabeer B, Alfaki M, Presnell SR, Khaenam P, Ayllón-Benítez A, Mougin F, Thébault P, Chiche L, Jourde-Chiche N, Phillips JT, Klintmalm G, O’Garra A, Berry M, Bloom C, Wilkinson RJ, Graham CM, Lipman M, Lertmemongkolchai G, Bedognetti D, Thiebaut R, Kheradmand F, Mejias A, Ramilo O, Palucka K, Pascual V, Banchereau J, Chaussabel D. Development of a fixed module repertoire for the analysis and interpretation of blood transcriptome data. Nat Commun. 2021 Jul 19;12(1):4385

Ayllón-Benítez A, Bourqui B, Thébault P*, Mougin F*. GSAn: an alternative to enrichment analysis for annotating gene sets. NAR Genom Bioinform. 2020 Mar 14;2(2): lqaa017

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

International conferences (published proceedings)

Drancé M, Boudin M, Mougin F, Diallo G. Neuro-symbolic XAI for compu-tational drug repurposing. Proceedings of the 13th International Joint Conference on Knowledge Discovery, Knowledge Engineering and Knowledge Management – KEOD. 2021, p. 220-225.

Lalanne F, Bedouch P, Simonnet C, Depras V, Bordea G, Bourqui R, Hamon T, Thiessard F, Mougin F. Visualizing food-drug interactionsin the Thériaque database. Stud Health Technol Inform. 2021 May 27;281:253-257

Bordea G, Nikiema JN, Griffier R, Mougin F. FIDEO: Food Inter-actions with Drugs Evidence Ontology. In Proceedings of the 11th International Conference on Biomedical Ontologies. T. 2807. CEUR Workshop Proceedings, 2020, p. L. 1-10.

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. 2020:933-942.

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;264:1445-1446

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

National journal

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

National conferences (published proceedings)

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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