Améliorer l’échange de l’information médicale grâce aux ontologies appliquées
Dans le cadre du Open Biological and Biomedical Ontology (OBO) Foundry, le GRIIS joint ses efforts à ceux d’une communauté internationale développant des ontologies compatibles les unes avec les autres.
Une ontologie est une représentation rigoureuse d’un domaine de la réalité (p. ex. le champ médical). Elle utilise un langage compréhensible par l’ordinateur. Cela permet à l’ordinateur d’effectuer du raisonnement de manière automatisée. Au moyen de l’informatique, nous pouvons tester automatiquement la cohérence logique d’une ontologie ou déduire de nouvelles connaissances.
Nous développons des ontologies dans le champ biomédical, par exemple une ontologie des ordonnances de médicaments et une ontologie des maladies cardiovasculaires. Ces ontologies sont par la suite appliquées en informatique de la santé.
Les ontologies mettent en relation des données de santé qui sont diverses et hétérogènes (p. ex. des données d’une clinique et celles d’un hôpital). Grâce aux ontologies, les systèmes informatiques sont capables de communiquer entre eux, bien qu’ils soient construits différemment.
Publications scientifiques connexes
Consultez nos cinq publications les plus récentes en lien avec les ontologies.
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Tarbouriech C, Vieu L, Barton A, Ethier J-F (2024) From slot mereology to a mereology of slots. Applied Ontology 1–50. https://doi.org/10.3233/AO-230051 Cite
Barton A, Fabry P, Ethier J-F (2024) Meaning Holism and Indeterminacy of Reference in Ontologies [FOIS 2024 DISTINGUISHED PAPER AWARD]. In: Proceedings of the 14th International Conference on Formal Ontology Information Systems (FOIS 2024). Enschede, Pays-Bas Cite Download
Fabry P, Barton A, Ethier J-F (2023) Version control for interdependent ontologies: Challenges and first propositions. In: Proceedings of the International Conference on Biomedical Ontologies 2023 together with the Workshop on Ontologies for Infectious and Immune-Mediated Disease Data Science (OIIDDS 2023) and the FAIR Ontology Harmonization and TRUST Data Interoperability Workshop (FOHTI 2023). Brasilila, Brésil, pp 154–165 Cite
Khnaisser C, Lavoie L, Fraikin B, Barton A, Dussault S, Burgun A, Ethier J-F (2022) Using an ontology to derive a sharable and interoperable relational data model for heterogeneous healthcare data and various applications. Methods Inf Med 61:e73–e88. https://doi.org/10.1055/a-1877-9498 Cite Download
Goyer F, Fabry P, Barton A, Ethier J-F (2022) An ontology for healthcare systems. In: Proceedings of the 13th International Conference on Biomedical Ontology (ICBO 2022). Ann Arbor, États-Unis Cite
Ontologies
Prescription of Drugs Ontology (PDRO)
L’ontologie PDRO analyse les types d’instructions contenues dans les ordonnances de médicaments.
L’ontologie PDRO est le sujet d’un article scientifique publié dans la revue Applied Ontology.
Cardiovascular Disease Ontology (CVDO)
L’ontologie CVDO différencie les maladies cardiovasculaires, les troubles sous-jacents et les processus pathologiques qui y sont associés.
Elle se base sur le modèle des maladies que propose l’Ontology for General Medical Science (OGMS).
Clinical Laboratory Test Document Ontology (LABO)
L’ontologie LABO représente les documents qui prescrivent des tests de laboratoire et qui fournissent les résultats de ces tests.
Elle est coordonnée avec des ontologies de l’OBO Foundry comme l’Information Artifact Ontology (IAO) et l’Ontology for Biomedical Investigations (OBI).
Des ontologies libres pour les systèmes de santé apprenants
L’équipe ontologique du GRIIS a publié une dizaine d’ontologies en code source libre. Ces modèles de connaissances alimentent le développement informatique en soutien aux soins et aux systèmes de santé.
Partenaires
Partenaires principaux
Avec le soutien de
Direction des ontologies appliquées
Jean-François Ethier
Cofondateur et codirecteur scientifique du GRIIS
Professeur titulaire en médecine à l’Université de Sherbrooke
Titulaire de la Chaire en informatique de la santé de l’Université de Sherbrooke
Médecin titulaire au CHUS
Chercheur au Centre de recherche sur le vieillissement
Adrien Barton
Chargé de recherche CNRS à l’Institut de recherche en informatique de Toulouse
Professeur associé au Département de médecine de l’Université de Sherbrooke
Publications scientifiques connexes
Consultez toutes nos publications en lien avec les ontologies.
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Tarbouriech C, Vieu L, Barton A, Ethier J-F (2024) From slot mereology to a mereology of slots. Applied Ontology 1–50. https://doi.org/10.3233/AO-230051 Cite
Barton A, Fabry P, Ethier J-F (2024) Meaning Holism and Indeterminacy of Reference in Ontologies [FOIS 2024 DISTINGUISHED PAPER AWARD]. In: Proceedings of the 14th International Conference on Formal Ontology Information Systems (FOIS 2024). Enschede, Pays-Bas Cite Download
Fabry P, Barton A, Ethier J-F (2023) Version control for interdependent ontologies: Challenges and first propositions. In: Proceedings of the International Conference on Biomedical Ontologies 2023 together with the Workshop on Ontologies for Infectious and Immune-Mediated Disease Data Science (OIIDDS 2023) and the FAIR Ontology Harmonization and TRUST Data Interoperability Workshop (FOHTI 2023). Brasilila, Brésil, pp 154–165 Cite
Khnaisser C, Lavoie L, Fraikin B, Barton A, Dussault S, Burgun A, Ethier J-F (2022) Using an ontology to derive a sharable and interoperable relational data model for heterogeneous healthcare data and various applications. Methods Inf Med 61:e73–e88. https://doi.org/10.1055/a-1877-9498 Cite Download
Goyer F, Fabry P, Barton A, Ethier J-F (2022) An ontology for healthcare systems. In: Proceedings of the 13th International Conference on Biomedical Ontology (ICBO 2022). Ann Arbor, États-Unis Cite
Toyoshima F, Barton A, Fabry P, Ethier J-F (2022) Representing Gender in Ontologies: A Dispositional Perspective. In: Proceedings of the 12th International Conference on Biomedical Ontology (ICBO 2021). CEUR Workshop Proceedings, Bolzano, Italie, pp 1–12 Cite Download
Toyoshima F, Barton A, Ethier J-F (2022) Affordances and their ontological core. Applied Ontology 17:285–320. Cite
Barton A, Tarbouriech C, Vieu L, Ethier J-F (2022) A Mereological System for Informational Templates. In: CEUR Workshop Proceedings Cite
Fabry P, Goyer F, Barton A, Ethier J-F (2022) An informational perspective on the ontology of services. In: CEUR Workshop Proceedings Cite
Ethier J-F, Goyer F, Fabry P, Barton A (2021) The prescription of drug ontology 2.0 (PDRO): More than the sum of its parts. International Journal of Environmental Research and Public Health 18. https://doi.org/10.3390/ijerph182212025 Cite
Toyoshima F, Barton A, Jansen L, Ethier J-F (2021) Towards a Unified Dispositional Framework for Realizable Entities. In: Proceedings of the 12th International Conference on Formal Ontology in Information Systems (FOIS 2021). IOS Press, Bolzano, Italie, pp 64–78 Cite Download
Toyoshima F, Barton A, Ethier J-F (2020) Functional Parthood: A Dispositional Perspective. In: Proceedings of the 6th Joint Ontology Workshops (JOWO 2020). CEUR Workshop Proceedings, Bolzano, Italie (évènement virtuel), p 8 Cite Download
Barton A, Toyoshima F, Vieu L, Fabry P, Ethier J-F (2020) The Mereological Structure of Informational Entities. In: Brodaric B, Neuhaus F (eds) Proceedings of the 11th International Conference (FOIS 2020). IOS Press Cite Download
Toyoshima F (2020) Foundations for Ontology of Persistence: Beyond Talk of Temporal Parts. In: Brodaric B, Neuhaus F (eds) Frontiers in Artificial Intelligence and Applications. IOS Press, pp 17–31 Cite
Toyoshima F, Barton A, Grenier O (2020) Foundations for an Ontology of Belief, Desire and Intention. In: Brodaric B, Neuhaus F (eds) Frontiers in Artificial Intelligence and Applications. IOS Press, pp 140–154 Cite
Fabry P, Barton A, Ethier J-F (2020) QUESTO – An ontology for questionnaires. In: ICBO|ODLS 2020 International Conference on Biomedical Ontologies 2020. CEUR-WS.org, Bolzano, Italie, p B.1-12 Cite Download
Barton A, Toyoshima F, Ethier J-F (2020) Clinical Documents and Their Parts. In: Hastings J, Loebe F (eds) ICBO|ODLS 2020 International Conference on Biomedical Ontologies 2020. CEUR-WS.org, Bolzano, Italie (évènement virtuel), p A.1-11 Cite Download
Fabry P, Barton A, Ethier J-F (2020) An Ontological Representation of Sex and Gender Information. In: Hastings J, Loebe F (eds) ICBO|ODLS 2020 International Conference on Biomedical Ontologies 2020. CEUR-WS.org, Bolzano, Italy, p O.1-5 Cite Download
Barton A, Toyoshima F, Ethier J-F (2020) Approaching Roles with Affordances. In: Proceedings of the Joint Ontology Workshops. CEUR Workshop Proceedings, Virtuel et Bolzano, Italie, pp 1–14 Cite Download
Barton A (2020) L'ontologie appliquée : un dialogue entre métaphysique analytique et traitement de l'information. In: Lacroix A (ed) La philosophie pratique : un passage obligé pour penser la société. Presses de l'Université Laval, pp 87–108 Cite
Toyoshima F, Barton A (2019) Linking image schemas with affordances: An ontological approach. In: Seppälä S, Porello D (eds) Proceedings of the 5th Joint Ontology Workshops (JOWO 2019). CEUR Workshop Proceedings, Graz, Autriche, pp 1–9 Cite
Barton A, Seppälä S, Porello D (2019) Proceedings of the Joint Ontology Workshops 2019 - Episode V: The Styrian Autumn of Ontology. In: JOWO 2019 The Joint Ontology Workshops. CEUR Workshop Proceedings, Graz, Autriche Cite
Barton A, Fabry P, Ethier J-F (2019) A classification of instructions in drug prescriptions and pharmacist documents. In: Proceedings of the 10th International Conference on Biomedical Ontology (ICBO 2019). CEUR Workshop Proceedings, Buffalo, États-Unis, pp 1–7 Cite
Khnaisser C, Lavoie L, Fraikin B, Barton A, Burgun A, Ethier J-F (2019) Generating a relational database for heterogeneous data using an ontology Cite Download
Barton A, Vieu L, Ethier J-F (2019) Directing actions. In: Proceedings of the Joint Ontology Workshops 2019 (JOWO 2019). Graz, Autriche, pp 1–10 Cite
Barton A, Fabry P, Lavoie L, Ethier J-F (2019) LABO: An ontology for laboratory test prescription and reporting. In: Proceedings of the Joint Ontology Workshops 2019 (JOWO 2019). Graz, Autriche, pp 1–9 Cite
Masolo C, Barton A (2019) The identity of property particulars. In: Proceedings of the Joint Ontology Workshops 2019 (JOWO 2019). Graz, Autriche, pp 1–10 Cite
Barton A, Grenier O, Ethier J-F (2018) The identity and mereology of pathological dispositions. In: Jaiswal P, Cooper L, Haendel MA, Mungall CJ (eds) Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018). CEUR Workshop Proceedings, Corvallis, Oregon, États-Unis, pp 1–6 Cite
Barton A, Jansen L, Rosier A, Ethier J-F (2018) What is a risk? A formal representation of risk of stroke for people with atrial fibrillation. In: Proceedings of the 8th International Conference on Biomedical Ontology. Newcastle, Royaume-Uni, pp 1–6 Cite Download
Barton A, Duncan W, Toyoshima F, Ethier J-F (2018) First steps towards an ontology of belief. In: Proceedings of the Joint Ontology Workshops 2018 (JOWO 2018). Cape Town, Afrique du Sud, pp 1–5 Cite Download
Barton A, Jansen L, Ethier J-F (2018) A taxonomy of disposition-parthood. In: Galton A, Neuhaus F (eds) Proceedings of the Joint Ontology Workshops 2017, CEUR Workshop proceedings. CEUR Workshop Proceedings, Bolzano, Italie, pp 1–10 Cite Download
Khnaisser C, Lavoie L, Burgun A, Ethier J-F (2018) Generating relational database using ontology review : Issues, challenges and trends. International Journal of Advanced Computer Science and Applications (IJACSA) 9. Cite Download
Bibault J-E, Zapletal E, Rance B, Giraud P, Burgun A (2018) Labeling for Big Data in radiation oncology: The Radiation Oncology Structures ontology. PLoS One 13:e0191263. https://doi.org/10.1371/journal.pone.0191263 Cite
Ethier J-F, Barton A, Taseen R (2018) An ontological analysis of drug prescriptions. Applied Ontology 13:273–294. https://doi.org/10.3233/AO-180202 Cite Download
Barton A, Khnaisser C, Lavoie L, Ethier J-F (2017) Ambiguities in medical bitemporalized relational databases: A referent tracking view. In: Proceedings of the Joint Ontology Workshops 2017. Boeker, M., Herre, H., Jansen, L., Loebe, F., & Shober, D., Bolzano, Italie, pp 1–5 Cite Download
Barton A (2017) L’ontologie est-elle une science? In: Silberstein M (ed) Qu’est-ce que la science... pour vous?, Editions Matériologiques. Paris, France, pp 21–26 Cite
Barton A, Taseen R, Ethier J-F (2017) PDRO: une ontologie des prescriptions médicales Cite
Barton A, Rosier A (2016) Ontologies appliquées biomédicales et ontologie philosophique : un développement complémentaire. Lato Sensu 3:1–8 Cite
Liang SF, Ethier J-F, Porat T, Tapuria A, Delaney BC, Curcin V (2016) MeTMapS—Medical terminology mapping system. In: 7th Workshop on Ontologies and Data in Life Sciences. Halle, Allemagne Cite Download
Barton A, Ethier J-F (2016) The two ontological faces of velocity. In: Ferrario R, Kuhn W (eds) Formal Ontology in Information Systems. Proceedings of the 9th International Conference (FOIS 2016). IOS Press, Amsterdam, Pays-Bas, pp 123–136 Cite Download Download
Ethier J-F, Taseen R, Lavoie L, Barton A (2016) Improving the semantics of drug prescriptions with a realist ontology. In: Jaiswal P, Hoehndorf R, Arighi C, Meier A (eds) Proceedings of the Joint International Conference on Biological Ontology and BioCreative. Oregon, États-Unis, p IT603:1-6 Cite Download
Barton A, Jansen L (2016) A modelling pattern for multi-track dispositions for life-science ontologies. In: Loebe F, Boeker M, Herre H, Jansen L, Schober D (eds) ODLS 2016 - Ontologies and Data in Life Sciences. p H.1-2 Cite Download
Rosier A, Mabo P, Temal L, Van Hille P, Dameron O, Deleger L, Grouin C, Zweigenbaum P, Jacques J, Chazard E, Laporte L, Henry C, Burgun A (2016) Remote Monitoring of Cardiac Implantable Devices: Ontology Driven Classification of the Alerts. Stud Health Technol Inform 221:59–63 Cite
Barton A, Ethier J-F, Taseen R (2016) Ontologies to support learning health systems Cite