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Semantic Indexing of French Biomedical Data Resources - mobility

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Publications

Two years later: the landscape of vocabularies and ontologies in the AgroPortal

Author(s): Jonquet, Clement; Toulet, Anne; Emonet, Vincent
Published in: 5th International Workshop on sources and data integration in agriculture, food and environment using ontologies (IN-OVIVE @ EFITA 2017), 2017

ICD-10 coding of death certificates with the NCBO and SIFR Annotators at CLEF eHealth 2017

Author(s): Tchechmedjiev, Andon; Abdaoui, Amine; Emonet, Vincent; Jonquet, Clement
Published in: Working Notes of CLEF eHealth Evaluation Lab, 2017

AgroPortal: an ontology repository for agronomy

Author(s): Jonquet, Clement
Published in: European conference dedicated to the future use of ICT in the agri-food sector, bioresource and biomass sector, EFITA'17, demonstration session, 2017

Enrichment of French Biomedical Ontologies with UMLS Concepts and Semantic Types for Biomedical Named Entity Recognition Though Ontological Semantic Annotation

Author(s): Tchechmedjiev, Andon; Jonquet, Clement
Published in: Language, Ontology, Terminology and Knowledge Structures Workshop (LOKTS 2017), 2017

French ConText: Détecter la négation, la temporalité et le sujet dans les textes cliniques Français

Author(s): Abdaoui, Amine; Tchechmedjiev, Andon; Digan, William; Bringay, Sandra; Jonquet, Clement
Published in: 4ème Symposium sur l'Ingénierie de l'Information Médicale, SIIM'17, 2017

Challenges for ontology repositories and applications to biomedicine & agronomy

Author(s): Jonquet , Clement
Published in: SIMBig: Symposium on Information Management and Big Data, Issue 1, 2017

MuEVo, a breast cancer Consumer Health Vocabulary built out of web forums

Author(s): Jonquet, Clement; Tapi-Nzali, Mike-Donald; Bringay, Sandra; TAPI NZALI, Mike Donald; Eholié, Solène
Published in: A. Paschke; A. Burger; A. Splendiani; M.S. Marshall; P. Romano. SWAT4LS: Semantic Web Applications and Tools for Life Sciences, 2016, Amsterdam, Netherlands. 9th International Semantic Web Applications and Tools for Life Sciences, 2016, Issue 1, 2016, Page(s) 10

Maitriser une technologie de gestion des ontologies et vocabulaires en France : défis et enjeux

Author(s): Jonquet , Clement
Published in: SemWebPro Conference, Issue 1, 2018, Page(s) 2

Projet VisaTM : l'interconnexion OpenMinTeD – AgroPortal – ISTEX, un exemple de service de Text et Data Mining pour les scientifiques français

Author(s): Kettani , Fabienne; Schneider , Stéphane; Aubin , Sophie; Bossy , Robert; François , Claire; Jonquet , Clement; Tchechmedjiev , Andon; Toulet , Anne; Nédellec , Claire
Published in: 29es Journées Francophones d'Ingénierie des Connaissances, Session poster, Issue 1, 2018, Page(s) 247-249

YAM-BIO – Results for OAEI 2017

Author(s): Amina Annane, Zohra Bellahsene, Faiçal Azouaou, Clement Jonquet
Published in: System paper Ontology Alignment Evaluation Initiative 2017 Campaign, 2017, Page(s) 5

Assessing the Practice of Ontology Metadata: A Survey Result

Author(s): Anne Toulet; Biswanath Dutta; Clement Jonquet
Published in: Issue 1, 2018
DOI: 10.5281/zenodo.3484530

NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation

Author(s): Marcos Martínez-Romero, Clement Jonquet, Martin J. O’Connor, John Graybeal, Alejandro Pazos, Mark A. Musen
Published in: Journal of Biomedical Semantics, Issue 8/1, 2017, Page(s) Journal of Biomedical Semantics, ISSN 2041-1480
DOI: 10.1186/s13326-017-0128-y

AgroPortal: A vocabulary and ontology repository for agronomy

Author(s): Clément Jonquet, Anne Toulet, Elizabeth Arnaud, Sophie Aubin, Esther Dzalé Yeumo, Vincent Emonet, John Graybeal, Marie-Angélique Laporte, Mark A. Musen, Valeria Pesce, Pierre Larmande
Published in: Computers and Electronics in Agriculture, Issue 144, 2018, Page(s) 126-143, ISSN 0168-1699
DOI: 10.1016/j.compag.2017.10.012

Building an effective and efficient background knowledge resource to enhance ontology matching

Author(s): Amina Annane, Zohra Bellahsene, Faiçal Azouaou, Clement Jonquet
Published in: Journal of Web Semantics, Issue 51, 2018, Page(s) 51-68, ISSN 1570-8268
DOI: 10.1016/j.websem.2018.04.001

Enhanced functionalities for annotating and indexing clinical text with the NCBO Annotator+

Author(s): Andon Tchechmedjiev, Amine Abdaoui, Vincent Emonet, Soumia Melzi, Jitendra Jonnagaddala, Clement Jonquet
Published in: Bioinformatics, Issue 34/11, 2018, Page(s) 1962-1965, ISSN 1367-4803
DOI: 10.1093/bioinformatics/bty009

Developing data interoperability using standards: A wheat community use case

Author(s): Esther Dzale Yeumo, Michael Alaux, Elizabeth Arnaud, Sophie Aubin, Ute Baumann, Patrice Buche, Laurel Cooper, Hanna Ćwiek-Kupczyńska, Robert P. Davey, Richard Allan Fulss, Clement Jonquet, Marie-Angélique Laporte, Pierre Larmande, Cyril Pommier, Vassilis Protonotarios, Carmen Reverte, Rosemary Shrestha, Imma Subirats, Aravind Venkatesan, Alex Whan, Hadi Quesneville
Published in: F1000Research, Issue 6, 2017, Page(s) 1843, ISSN 2046-1402
DOI: 10.12688/f1000research.12234.1

Harnessing the Power of Unified Metadata in an Ontology Repository: The Case of AgroPortal

Author(s): Clement Jonquet, Anne Toulet, Biswanath Dutta, Vincent Emonet
Published in: Journal on Data Semantics, 2018, Page(s) 1-31, ISSN 1861-2032
DOI: 10.1007/s13740-018-0091-5

PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison

Author(s): Pierre Monnin, Joël Legrand, Graziella Husson, Patrice Ringot, Andon Tchechmedjiev, Clément Jonquet, Amedeo Napoli, Adrien Coulet
Published in: BMC Bioinformatics, Issue 20/S4, 2019, ISSN 1471-2105
DOI: 10.1186/s12859-019-2693-9

SIFR annotator: ontology-based semantic annotation of French biomedical text and clinical notes

Author(s): Andon Tchechmedjiev, Amine Abdaoui, Vincent Emonet, Stella Zevio, Clement Jonquet
Published in: BMC Bioinformatics, Issue 19/1, 2018, ISSN 1471-2105
DOI: 10.1186/s12859-018-2429-2

New Generation Metadata Vocabulary for Ontology Description and Publication

Author(s): Biswanath Dutta, Anne Toulet, Vincent Emonet, Clement Jonquet
Published in: Metadata and Semantic Research, Issue 755, 2017, Page(s) 173-185
DOI: 10.1007/978-3-319-70863-8_17

Proceedings of the 2nd International Workshop on Semantics for Biodiversity, S4BioDiv'17

Author(s): Algergawy, Alsayed; Karam, Naouel; Klan, Friederike; Jonquet, Clement
Published in: 2nd International Workshop on Semantics for Biodiversity (S4BioDiv 2017), 2017

Semantic Indexing of French Biomedical Data Resources

Author(s): Clement Jonquet
Published in: Project Repository Journal, Issue 3, 2019, Page(s) 16-19, ISSN 2632-4067

Ontology Repository and Ontology-Based Services – Challenges, contributions and applications to biomedicine & agronomy

Author(s): Clement Jonquet
Published in: University of Montpellier HDR manuscript, 2019