Improving the exchange of medical information through applied ontologies
As part of the Open Biological and Biomedical Ontology (OBO) Foundry, the GRIIS is joining forces with an international community that develops compatible ontologies.
An ontology is a rigorous representation of a domain of reality (e.g. the medical field). It uses language that computers understand. This allows computers to reason in an automated way. By means of computer science, we can automatically test the logical coherence of an ontology or infer new knowledge.
At the GRIIS, we develop ontologies in the biomedical field, such as an ontology of drug prescriptions or an ontology of cardiovascular diseases. These ontologies are subsequently applied in health informatics.
Ontologies can assist the linkage of health data that is diverse and heterogeneous (e.g. clinic and hospital data). With ontologies, computer systems can communicate with each other, even though they may be constructed differently.
Related scientific publications
Consult five of our most recent publications on ontologies.
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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
Ontologies
Prescription of Drugs Ontology (PDRO)
PDRO is a realist ontology that aims to represent the domain of drug prescriptions. PDRO’s central focus is the structure of a drug prescription.
The PDRO ontology is the topic of a scientific article published in the journal Applied Ontology.
Cardiovascular Disease Ontology (CVDO)
The CVDO ontology differentiates between cardiovascular diseases, underlying disorders and associated pathological processes.
It is based on the disease model proposed by the Ontology for General Medical Science (OGMS).
Clinical Laboratory Test Document Ontology (LABO)
The LABO ontology represents documents that prescribe laboratory tests and that provide their results.
It is coordinated with OBO Foundry ontologies like the Information Artifact Ontology (IAO) and the Ontology for Biomedical Investigations (OBI).
Open source ontologies for learning health systems
The GRIIS ontology team has published a dozen open source ontologies. These knowledge models are used in software development to support health care and health systems.
Partners
Key partners
With the support of
Applied ontologies directors
Adrien Barton
CNRS research fellow at the Institut de recherche en informatique in Toulouse
Associate professor at the Département de médecine of the Université de Sherbrooke
Jean-François Ethier
Co-founder and scientific co-director of the GRIIS
Full Professor of medicine at Université de Sherbrooke
Research Chair in Health Informatics, Université de Sherbrooke
Licensed physician at the CHUS
Related scientific publications
See all our publications related to ontologies.
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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
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
Goodbrand JA, Hughes LD, Cochrane L, Donnan PT, McGilchrist MM, Frost H, McMurdo MET, Witham MD (2017) Association between bisphosphonate therapy and outcomes from rehabilitation in older people. Arch Gerontol Geriatr 70:195–200. https://doi.org/10.1016/j.archger.2017.01.017 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
Ethier J-F, Curcin V, Barton A, McGilchrist MM, Bastiaens H, Andreasson A, Rossiter J, Zhao L, Arvanitis TN, Taweel A, Delaney BC, Burgun A (2015) Clinical data integration model: Core interoperability ontology for research using primary care data. Methods Inf Med 54:16–23. https://doi.org/10.3414/ME13-02-0024 Cite Download
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