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French FastContext: a Publicly Accessible System for Detecting Negation, Temporality and Experiencer in French Clinical Notes
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In: ISSN: 1532-0464 ; EISSN: 1532-0480 ; Journal of Biomedical Informatics ; https://hal.mines-ales.fr/hal-03184001 ; Journal of Biomedical Informatics, Elsevier, 2021, 117, pp.103733. ⟨10.1016/j.jbi.2021.103733⟩ (2021)
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Semantic Description of Plant Phenological Development Stages, starting with Grapevine
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In: ISSN: 1865-0929 ; Communications in Computer and Information Science ; Communications in Computer and Information Science (CCIS) ; 14th international conference on Metadata and Semantics Research Conference (MTSR) ; https://hal.archives-ouvertes.fr/hal-02996846 ; 14th international conference on Metadata and Semantics Research Conference (MTSR), Dec 2020, Madrid, Spain. pp.257-268, ⟨10.1007/978-3-030-71903-6_25⟩ ; http://www.mtsr-conf.org/home (2020)
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Analysis of Term Reuse, Term Overlap and Extracted Mappings across AgroPortal Semantic Resources
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In: EKAW 2020 - 22nd International Conference on Knowledge Engineering and Knowledge Management ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-02945172 ; EKAW 2020 - 22nd International Conference on Knowledge Engineering and Knowledge Management, Sep 2020, Bozen-Bolzano, Italy. pp.71-87, ⟨10.1007/978-3-030-61244-3_5⟩ ; https://ekaw2020.inf.unibz.it/ (2020)
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Abstract:
International audience ; Ontologies in agronomy facilitate data integration, information exchange, search and query of agronomic data, and other knowledge-intensive tasks. We have developed AgroPortal, an open community-based repository of agronomy and related domains semantic resources. From a corpus of ontologies, terminologies, and thesauri taken from Agro-Portal, we have generated, extracted and analyzed more than 400,000 mappings between concepts based on: (i) reuse of the same URI between concepts in different resources-term reuse; (ii) lexical similarity of concept names and synonyms-term overlap; and (iii) declared map-pings properties between concepts-extracted mappings. We developed an interactive visualization of each mapping construct separately and combined which helps users identify most prominent ontologies, relevant thematic clusters, areas of a domain that are not well covered, and pertinent ontologies as background knowledge. By comparing the size of the semantic resources to the number of their mappings, we found that most of them have under 5% of their terms mapped. Our results show the need of an ontology alignment framework in AgroPortal where map-pings between semantic resources will be assembled, compared, analysed and automatically updated when semantic resources evolve.
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Keyword:
[INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI]; Extracted mappings; Mapping analysis; Ontology alignment; Term overlap; Term reuse; Visualization
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URL: https://hal-lirmm.ccsd.cnrs.fr/lirmm-02945172/document
https://hal-lirmm.ccsd.cnrs.fr/lirmm-02945172/file/EKAW_2020.pdf
https://doi.org/10.1007/978-3-030-61244-3_5
https://hal-lirmm.ccsd.cnrs.fr/lirmm-02945172
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| 4 |
Semantic Indexing of French Biomedical Data Resources
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In: Project Repository Journal ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-02360615 ; Project Repository Journal, 3, pp.16-19, 2019 ; https://www.europeandissemination.eu/the-project-repository-journal (2019)
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| 5 |
A novel framework for biomedical entity sense induction
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In: ISSN: 1532-0464 ; EISSN: 1532-0480 ; Journal of Biomedical Informatics ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-01851988 ; Journal of Biomedical Informatics, Elsevier, 2018, 84, pp.31-41. ⟨10.1016/j.jbi.2018.06.007⟩ (2018)
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| 6 |
ViewpointS: capturing formal data and informal contributions into an adaptive knowledge graph
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In: ISSN: 1741-1009 ; EISSN: 1741-1017 ; International Journal of Knowledge and Learning ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-01605411 ; International Journal of Knowledge and Learning, Inderscience, 2018, 12 (2), ⟨10.1504/IJKL.2017.10012219⟩ (2018)
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| 7 |
SIFR Annotator: Ontology-Based Semantic Annotation of French Biomedical Text and Clinical Notes
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In: ISSN: 1471-2105 ; BMC Bioinformatics ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-01934127 ; BMC Bioinformatics, BioMed Central, 2018, 19 (1), pp.405-431. ⟨10.1186/s12859-018-2429-2⟩ (2018)
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| 8 |
Challenges for ontology repositories and applications to biomedicine & agronomy
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In: 4th Annual International Symposium on Information Management and Big Data ; SIMBig: Symposium on Information Management and Big Data ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-01679500 ; SIMBig: Symposium on Information Management and Big Data, Sep 2017, Lima, Peru. pp.25-37 ; http://simbig.org/SIMBig2017/ (2017)
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| 9 |
Enrichment of French Biomedical Ontologies with UMLS Concepts and Semantic Types for Biomedical Named Entity Recognition Though Ontological Semantic Annotation
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In: Workshop on Language, Ontology, Terminology and Knowledge Structures ; LOTKS: Language, Ontology, Terminology and Knowledge Structures ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-01605517 ; LOTKS: Language, Ontology, Terminology and Knowledge Structures, Sep 2017, Montpellier, France ; https://langandonto.github.io/LangOnto-TermiKS-2017/index.html (2017)
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| 10 |
MuEVo, un vocabulaire multi-expertise (patient/médecin) dédié au cancer du sein
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In: 27èmes Journées francophones d'Ingénierie des Connaissances ; IC: Ingénierie des Connaissances ; https://hal.archives-ouvertes.fr/hal-01379272 ; IC: Ingénierie des Connaissances, Jun 2016, Montpellier, France ; https://ic2016.sciencesconf.org (2016)
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| 11 |
Biomedical term extraction: overview and a new methodology
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In: ISSN: 1386-4564 ; EISSN: 1573-7659 ; Information Retrieval Journal ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-01274539 ; Information Retrieval Journal, Springer, 2016, Medical Information Retrieval, 19 (1), pp.59-99. ⟨10.1007/s10791-015-9262-2⟩ (2016)
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| 12 |
Réconciliation d'alignements multilingues dans BioPortal
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In: 27es Journées francophones d'Ingénierie des Connaissances ; IC: Ingénierie des Connaissances ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-01395900 ; IC: Ingénierie des Connaissances, Jun 2016, Montpellier, France ; https://ic2016.sciencesconf.org/ (2016)
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| 13 |
Multilingual Mapping Reconciliation between English-French Biomedical Ontologies
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In: 6th International Conference on Web Intelligence, Mining and Semantics ; WIMS: Web Intelligence, Mining and Semantics ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-01395880 ; WIMS: Web Intelligence, Mining and Semantics, Jun 2016, Nîmes, France. ⟨10.1145/2912845.2912847⟩ ; http://wims2016.mines-ales.fr/ (2016)
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| 14 |
Roadmap for a multilingual BioPortal
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In: 4th Workshop on the Multilingual Semantic Web ; MSW: Multilingual Semantic Web ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-01172218 ; MSW: Multilingual Semantic Web, Jun 2015, Portoroz, Slovenia (2015)
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| 15 |
Scoring semantic annotations returned by the NCBO Annotator
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In: 7th International Semantic Web Applications and Tools for Life Sciences ; SWAT4LS: Semantic Web Applications and Tools for Life Sciences ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-01099860 ; SWAT4LS: Semantic Web Applications and Tools for Life Sciences, Dec 2014, Berlin, Germany ; http://ceur-ws.org/Vol-1320/ (2014)
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| 16 |
Yet Another Ranking Function for Automatic Multiword Term Extraction
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In: 9th International Conference on Natural Language Processing (PolTAL) ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-01068556 ; 9th International Conference on Natural Language Processing (PolTAL), Sep 2014, Warsaw, Poland. pp.52-64, ⟨10.1007/978-3-319-10888-9_6⟩ ; http://poltal.ipipan.waw.pl/ (2014)
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| 17 |
Integration of Linguistic and Web Information to Improve Biomedical Terminology Extraction
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In: 18th International Database Engineering & Applications Symposium ; IDEAS: International Database Engineering & Applications Symposium ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-01068547 ; IDEAS: International Database Engineering & Applications Symposium, Jul 2014, Porto, Portugal. pp.265-269, ⟨10.1145/2628194.2628208⟩ ; http://confsys.encs.concordia.ca/IDEAS/ideas14/ideas14.php (2014)
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| 18 |
Biomedical Terminology Extraction: A new combination of Statistical and Web Mining Approaches
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In: 13èmes Journées Internationales d'Analyse statistique des Données Textuelles ; JADT: Journées d'Analyse statistique des Données Textuelles ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-01056598 ; JADT: Journées d'Analyse statistique des Données Textuelles, Jun 2014, Paris, France. pp.421-432 ; http://www.inalco.fr/evenement/jadt-2014-journees-internationales-analyse-statistique-donnees-textuelles (2014)
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| 19 |
Towards a mixed approach to extract biomedical terms from text corpus
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In: ISSN: 1947-9115 ; EISSN: 1947-9123 ; International journal of Knowledge Discovery in Bioinformatics ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-00859846 ; International journal of Knowledge Discovery in Bioinformatics, IGI Global, 2014, 4 (1), pp.1-15. ⟨10.4018/ijkdb.2014010101⟩ ; http://www.igi-global.com/journal/international-journal-knowledge-discovery-bioinformatics/1143 (2014)
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| 20 |
Gestion du multilinguisme dans un portail d’ontologies: étude de cas pour le NCBO BioPortal
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In: Terminology & Ontology: Theories and applications Workshop ; TOTh Workshop ; https://hal-lirmm.ccsd.cnrs.fr/lirmm-01099882 ; TOTh Workshop, Dec 2014, Bruxelles, Belgique ; http://toth.condillac.org/workshop-2014 (2014)
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