@misc{camirand_lemyre_distributed_2024,
	type = {Présentation en ligne},
	title = {Distributed statistical analysis: a scoping review and examples of operational frameworks adapted to healthcare},
	url = {https://www.youtube.com/watch?v=YfilSNsOKYg},
	abstract = {About this event
In the fourth webinar in HDRN Canada’s Federated Analysis: State of the Science Collective Learning Series, Dr. Nichole Austin and Dr. Félix Camirand Lemyre will demonstrate the statistical analyses that can and cannot be conducted using practical examples. Moderated by Dr. Kim McGrail, the discussion will focus on key aspects around the value and challenges of using distributed data, as well as the areas where more scientific development is needed.},
	author = {Camirand Lemyre, Félix and Ethier, Jean-François and Lévesque, Simon and Domingue, Marie-Pier and Herrmann, Klaus},
	month = apr,
	year = {2024},
	keywords = {FRQS-Présentations orales ou par affiche, Presentation},
}

About this event In the fourth webinar in HDRN Canada’s Federated Analysis: State of the Science Collective Learning Series, Dr. Nichole Austin and Dr. Félix Camirand Lemyre will demonstrate the statistical analyses that can and cannot be conducted using practical examples. Moderated by Dr. Kim McGrail, the discussion will focus on key aspects around the value and challenges of using distributed data, as well as the areas where more scientific development is needed.

@misc{ethier_pour_2024,
	type = {Présentation en ligne},
	title = {Pour passer à l'échelle nationale en recherche avec les données de santé},
	url = {https://www.obvia.ca/evenements/incursion-dans-lecosysteme-de-sante},
	author = {Ethier, Jean-François},
	month = mar,
	year = {2024},
	keywords = {FRQS-Communications à titre de conférencier invité, Presentation},
}

@misc{ethier_au_2024,
	type = {Présentation en ligne},
	title = {Au confluent des méthodes d'accès aux données pour les systèmes de santé apprenants},
	url = {https://www.obvia.ca/evenements/incursion-dans-lecosysteme-de-sante},
	author = {Ethier, Jean-François},
	month = mar,
	year = {2024},
	keywords = {FRQS-Communications à titre de conférencier invité, Presentation},
}

@article{tarbouriech_slot_2024,
	title = {From slot mereology to a mereology of slots},
	volume = {Preprint},
	issn = {1875-8533},
	doi = {10.3233/AO-230051},
	abstract = {In 2013, Bennett proposed a mereological theory in which the parthood relation is defined on the basis of two primitive relations: a is a part of b iff a fills a slot owned by b . However, this theory has issues counting how many parts an entity has. We explore the various counting problems and propose a new theory to solve them. Keeping the core idea of Bennett’s slots, this theory introduces mereological relations between slots. This theory enables us to solve all known counting problems and to go beyond the limits of Bennett’s theory by theorising expected features of mereological theories: supplementation principles and mereological sum and fusion. The theory is illustrated on ontological issues on the nature of structural universals and informational entities.},
	number = {Preprint},
	journal = {Applied Ontology},
	author = {Tarbouriech, Cédric and Vieu, Laure and Barton, Adrien and Ethier, Jean-François},
	month = apr,
	year = {2024},
	note = {Publisher: IOS Press},
	keywords = {FRQS-Documents revus et publiés, Journal Article, Mereology, informational entity, mereological fusion, mereological sum, slot mereology, structural universal, supplementation},
	pages = {1--50},
}

In 2013, Bennett proposed a mereological theory in which the parthood relation is defined on the basis of two primitive relations: a is a part of b iff a fills a slot owned by b . However, this theory has issues counting how many parts an entity has. We explore the various counting problems and propose a new theory to solve them. Keeping the core idea of Bennett’s slots, this theory introduces mereological relations between slots. This theory enables us to solve all known counting problems and to go beyond the limits of Bennett’s theory by theorising expected features of mereological theories: supplementation principles and mereological sum and fusion. The theory is illustrated on ontological issues on the nature of structural universals and informational entities.

@phdthesis{souid_proposition_2024,
	address = {Sherbrooke, Canada},
	type = {Mémoire de maitrise},
	title = {Proposition de modélisation de la défense en profondeur des actifs informationnels appuyée par une ontologie},
	url = {https://savoirs.usherbrooke.ca/handle/11143/21482},
	abstract = {Les systèmes d'information ont joué un rôle primordial dans la transformation numérique des organisations. Celles-ci, pour assurer la continuité et l'intégrité de leurs activités, ont rapidement ressenti le besoin de mettre en place des mécanismes pour renforcer la protection de leurs actifs. Dans ce contexte la notion de «défense en profondeur» se démarque, visant une protection multicouche des actifs. Afin de formaliser cette approche, nous introduisons l'ontologie de défense en profondeur des actifs informationnels (ODPA: Ontology for Deep Protection of Information Assets). Son objectif est d'obtenir une représentation homogène, robuste et exploitable de l'ensemble des éléments de sécurité. La mise en place d'une telle ontologie soulève plusieurs défis. Tout d'abord, quels sont les méthodes et modèles les plus adaptés pour représenter efficacement la multitude d'actifs et les diverses couches de défense? Ensuite, comment garantir que cette ontologie, une fois élaborée, offre une couverture exhaustive et pertinente des menaces potentielles tout en étant suffisamment agile pour s'adapter à l'évolution des risques? Les outils actuels de gestion de la sécurité de l'information se basent souvent sur des approches fragmentées, parfois redondantes et ne répondant pas toujours aux besoins spécifiques des organisations. Ces outils manquent souvent de formalisation et s'appuient sur des pratiques empiriques plutôt que sur des méthodologies formelles. Dans ce contexte, nous présentons ODPA, un cadre de référence visant à offrir une représentation systématique et exhaustive des actifs à sécuriser et des mécanismes de défense associés. L'ontologie ODPA est conçue pour décrire en détail les éléments constitutifs relatifs à la sécurité, ainsi que les contraintes d'intégrité associées. Grâce à des algorithmes de construction spécifiques, cette ontologie vise à offrir une vision cohérente, structurée et évolutive de la défense en profondeur. L'objectif est de faciliter la mise en œuvre de stratégies de défense adaptées aux besoins des organisations. De plus, compte tenu de l'importance croissante de la protection des données de santé, l'ontologie ODPA pourrait éventuellement être appliquée dans ce contexte spécifique. Elle pourrait ainsi contribuer à renforcer la sécurité des informations de santé et à garantir la confidentialité des données des patients},
	school = {Université de Sherbrooke},
	author = {Souid, Ameni},
	year = {2024},
	keywords = {Thesis},
}

Les systèmes d'information ont joué un rôle primordial dans la transformation numérique des organisations. Celles-ci, pour assurer la continuité et l'intégrité de leurs activités, ont rapidement ressenti le besoin de mettre en place des mécanismes pour renforcer la protection de leurs actifs. Dans ce contexte la notion de «défense en profondeur» se démarque, visant une protection multicouche des actifs. Afin de formaliser cette approche, nous introduisons l'ontologie de défense en profondeur des actifs informationnels (ODPA: Ontology for Deep Protection of Information Assets). Son objectif est d'obtenir une représentation homogène, robuste et exploitable de l'ensemble des éléments de sécurité. La mise en place d'une telle ontologie soulève plusieurs défis. Tout d'abord, quels sont les méthodes et modèles les plus adaptés pour représenter efficacement la multitude d'actifs et les diverses couches de défense? Ensuite, comment garantir que cette ontologie, une fois élaborée, offre une couverture exhaustive et pertinente des menaces potentielles tout en étant suffisamment agile pour s'adapter à l'évolution des risques? Les outils actuels de gestion de la sécurité de l'information se basent souvent sur des approches fragmentées, parfois redondantes et ne répondant pas toujours aux besoins spécifiques des organisations. Ces outils manquent souvent de formalisation et s'appuient sur des pratiques empiriques plutôt que sur des méthodologies formelles. Dans ce contexte, nous présentons ODPA, un cadre de référence visant à offrir une représentation systématique et exhaustive des actifs à sécuriser et des mécanismes de défense associés. L'ontologie ODPA est conçue pour décrire en détail les éléments constitutifs relatifs à la sécurité, ainsi que les contraintes d'intégrité associées. Grâce à des algorithmes de construction spécifiques, cette ontologie vise à offrir une vision cohérente, structurée et évolutive de la défense en profondeur. L'objectif est de faciliter la mise en œuvre de stratégies de défense adaptées aux besoins des organisations. De plus, compte tenu de l'importance croissante de la protection des données de santé, l'ontologie ODPA pourrait éventuellement être appliquée dans ce contexte spécifique. Elle pourrait ainsi contribuer à renforcer la sécurité des informations de santé et à garantir la confidentialité des données des patients

@misc{levesque_inference_2023,
	address = {Ottawa, Canada},
	type = {Présentation orale},
	title = {Inférence distribuée pour les modèles linéaires généralisés},
	url = {https://ssc.ca/en/meeting/annual/program},
	author = {Lévesque, Simon and Camirand Lemyre, Félix and Ethier, Jean-François},
	month = may,
	year = {2023},
	keywords = {FRQS-Présentations orales ou par affiche, Presentation},
}

@misc{ethier_collaboration_2023,
	address = {Montréal, Canada},
	type = {Présentation orale},
	title = {La collaboration au cœur des systèmes de santé apprenants},
	url = {https://pharm.umontreal.ca/grandesconferences-ia-au-service-de-la-pharmacotherapie/},
	author = {Ethier, Jean-François},
	month = may,
	year = {2023},
	keywords = {FRQS-Présentations orales ou par affiche, Presentation},
}

@misc{barton_ontologies_2023,
	address = {Buffalo, États-Unis},
	type = {Présentation orale},
	title = {Ontologies for a {Learning} {Health} {System}: {Application} to {PARS3} and theoretical challenges},
	url = {https://ncorwiki.buffalo.edu/index.php/Basic_Formal_Ontology_Summit_Meeting},
	author = {Barton, Adrien and Fabry, Paul and Ethier, Jean-François},
	month = may,
	year = {2023},
	keywords = {FRQS-Présentations orales ou par affiche, Presentation},
}

@misc{ethier_learning_2023,
	address = {Ottawa, Canada},
	type = {Présentation orale},
	title = {Learning health systems coming of age: {How} to deploy them in clinic so they truly become more than the sum of their parts},
	url = {https://sites.telfer.uottawa.ca/thtex/upcoming-in-person-event-building-the-foundations-for-connected-agile-and-patient-centered-care-april-13th-2023/},
	author = {Ethier, Jean-François},
	year = {2023},
	keywords = {FRQS-Présentations orales ou par affiche, Presentation},
}

@misc{ethier_intelligence_2023,
	address = {Québec, Canada},
	type = {Présentation orale},
	title = {Intelligence artificielle : êtes-vous prêt à accompagner vos étudiants et vos patients?},
	url = {https://www.apecfmus.com/formation-annuelle1.html},
	author = {Ethier, Jean-François},
	year = {2023},
	keywords = {FRQS-Communications à titre de conférencier invité, Presentation},
}

@phdthesis{baillargeon_categorie_2023,
	address = {Sherbrooke, Canada},
	type = {Mémoire de maitrise},
	title = {La catégorie dérivée d'une catégorie exacte},
	url = {https://savoirs.usherbrooke.ca/handle/11143/20048},
	abstract = {Une catégorie exacte est une paire (A, E) où A est une catégorie additive et E est une structure exacte. Une structure exacte est une classe de suites exactes qui satisfait à certains axiomes. L’objectif de ce mémoire est d’étudier la catégorie dérivée d’une catégorie exacte. Dans ce travail, nous allons voir les définitions des catégories exactes et des catégories triangulées. Puis, nous allons voir la définition de la catégorie d’homotopie d’une catégorie exacte et que celle-ci est équivalente à la catégorie dérivée sous certaines conditions. Ensuite, nous allons voir comment calculer la catégorie dérivée d’une algèbre aimable et nous allons calculer la catégorie d’homotopie pour deux catégories exactes qui correspondent à des algèbres aimables. Finalement, nous allons définir les mutations « silting » dans la catégorie d’homotopie d’une catégorie exacte.},
	language = {Français},
	school = {Université de Sherbrooke},
	author = {Baillargeon, Rose-Line},
	year = {2023},
	note = {http://hdl.handle.net/11143/20048},
	keywords = {Thesis},
}

Une catégorie exacte est une paire (A, E) où A est une catégorie additive et E est une structure exacte. Une structure exacte est une classe de suites exactes qui satisfait à certains axiomes. L’objectif de ce mémoire est d’étudier la catégorie dérivée d’une catégorie exacte. Dans ce travail, nous allons voir les définitions des catégories exactes et des catégories triangulées. Puis, nous allons voir la définition de la catégorie d’homotopie d’une catégorie exacte et que celle-ci est équivalente à la catégorie dérivée sous certaines conditions. Ensuite, nous allons voir comment calculer la catégorie dérivée d’une algèbre aimable et nous allons calculer la catégorie d’homotopie pour deux catégories exactes qui correspondent à des algèbres aimables. Finalement, nous allons définir les mutations « silting » dans la catégorie d’homotopie d’une catégorie exacte.

@article{khnaisser_combining_2023,
	title = {Combining ontology and temporal databases for data reuse: the example of hospital organizational structures},
	journal = {International Journal of Medical Informatics},
	author = {Khnaisser, Christina and Looten, Vincent and Ethier, Jean-François and Lavoie, Luc and Burgun, Anita},
	year = {2023},
	keywords = {Journal Article, pars3},
	pages = {*** accepted with minor changes},
}

@article{bilodeau_utilisations_2023,
	title = {Utilisations secondaires des données de santé : impacts de la transparence [soumis]},
	abstract = {La notion de transparence ressort régulièrement des discussions autour des utilisations secondaires des données de santé. Peu d’études se penchent toutefois sur les impacts de la présence ou de l’absence de transparence sur les membres du public. Cette revue de littérature répond à cette lacune de la littérature scientifique. Elle résulte d’une analyse secondaire de 124 textes issus d’une recension de la portée sur la transparence. La méthodologie respecte les directives PRISMAS-ScR. Les résultats contribuent principalement à identifier les impacts négatifs ou positifs de la communication transparente ou de son manque, puis à les associer à certaines composantes communicationnelles relatives aux utilisations secondaires de données de santé. Ils permettent également d’identifier les composantes associées à une communication jugée transparente ou opaque par les parties prenantes. La transparence, et plus particulièrement la continuité de la communication, est fortement associée à une augmentation de la confiance et de l’acceptabilité sociale, alors qu’en général les membres du public perçoivent négativement un manque de transparence. Cette revue de littérature approfondit les connaissances sur les risques d’impacts négatifs d’une communication transparente.},
	journal = {Revue Canadienne de Bioéthique},
	author = {Bilodeau, Emmanuel and Cumyn, Annabelle and Ménard, Jean-Frédéric and Dault, Roxanne and Barton, Adrien and Ethier, Jean-François},
	month = sep,
	year = {2023},
	keywords = {Emmanuel, Journal Article},
}

La notion de transparence ressort régulièrement des discussions autour des utilisations secondaires des données de santé. Peu d’études se penchent toutefois sur les impacts de la présence ou de l’absence de transparence sur les membres du public. Cette revue de littérature répond à cette lacune de la littérature scientifique. Elle résulte d’une analyse secondaire de 124 textes issus d’une recension de la portée sur la transparence. La méthodologie respecte les directives PRISMAS-ScR. Les résultats contribuent principalement à identifier les impacts négatifs ou positifs de la communication transparente ou de son manque, puis à les associer à certaines composantes communicationnelles relatives aux utilisations secondaires de données de santé. Ils permettent également d’identifier les composantes associées à une communication jugée transparente ou opaque par les parties prenantes. La transparence, et plus particulièrement la continuité de la communication, est fortement associée à une augmentation de la confiance et de l’acceptabilité sociale, alors qu’en général les membres du public perçoivent négativement un manque de transparence. Cette revue de littérature approfondit les connaissances sur les risques d’impacts négatifs d’une communication transparente.

@article{cumyn_portrait_2023,
	title = {Portrait de l’évolution de la responsabilité sociale d’une faculté de médecine canadienne basé sur le modèle de {Boelen}. [soumis]},
	journal = {CMEJ},
	author = {Cumyn, Annabelle and Larouche, C and Dubé, Tim and Millette, C-A and Gagné, E-R},
	year = {2023},
	keywords = {Journal Article},
}

@article{dube_pathways_2023,
	title = {Pathways, journeys and experiences: {Integrating} curricular activities related to social accountability within an undergraduate medical curriculum},
	doi = {10.1111/medu.15260},
	journal = {Medical Education},
	author = {Dubé, Tim and Cumyn, Annabelle and Fourati, Mariem and Chamberland, Martine and Hatcher, Sharon and Landry, Michel},
	month = oct,
	year = {2023},
	keywords = {Journal Article},
	pages = {1--10},
}

@misc{levesque_claret_2022,
	type = {Présentation en ligne},
	title = {{CLARET} {Transparence} - vers un portail citoyen de transparence sur l'accès et l'utilisation secondaire des données de santé},
	url = {https://reseau1quebec.ca/13029-2/},
	author = {Lévesque, Frédérique and Cumyn, Annabelle and Ménard, Jean-Frédéric and Dault, Roxanne and Barton, Adrien and Ethier, Jean-François},
	month = jun,
	year = {2022},
	keywords = {FRQS-Présentations orales ou par affiche, Presentation},
}

@misc{cumyn_enjeux_2022,
	address = {Val d'Or, Canada},
	type = {Présentation en ligne},
	title = {Enjeux autour de l'utilisation secondaire des données de santé et pistes de solution},
	url = {https://www.uqat.ca/ethiqueautochtone/},
	author = {Cumyn, Annabelle and Ethier, Jean-François},
	month = nov,
	year = {2022},
	keywords = {FRQS-Présentations orales ou par affiche, Presentation},
}

@article{khnaisser_using_2022,
	title = {Using an ontology to derive a sharable and interoperable relational data model for heterogeneous healthcare data and various applications},
	volume = {61},
	copyright = {Georg Thieme Verlag KG Rüdigerstraße 14, 70469 Stuttgart, Germany},
	issn = {0026-1270},
	url = {http://www.thieme-connect.de/DOI/DOI?10.1055/a-1877-9498},
	doi = {10.1055/a-1877-9498},
	abstract = {Background. A large volume of heavily fragmented data is generated daily in different healthcare contexts and is stored using various structures with different semantics. This fragmentation and heterogeneity make secondary use of data a challenge. Data integration approaches that derive a common data model from sources or requirements have some advantages. However, these approaches are often built for a specific application where the research questions are known. Thus, the semantic and structural reconciliation is often not reusable nor reproducible. A recent integration approach using knowledge models has been developed with ontologies that provide a strong semantic foundation. Nonetheless, deriving a data model that captures the richness of the ontology to store data with its full semantic remains a challenging task. Objectives. This paper addresses the question: How to design a sharable and interoperable data model for storing heterogeneous healthcare data and its semantic to support various applications? Method. This paper describes a method using an ontological knowledge model to automatically generate a data model for a domain of interest. The model can then be implemented in a relational database which efficiently enables the collection, storage, and retrieval of data while keeping semantic ontological annotations so that the same data can be extracted for various applications for further processing. Results. This paper (1) presents a comparison of existing methods for generating a relational data model from an ontology using 23 criteria, (2) describes standard conversion rules, and (3) presents , a prototype developed to demonstrate the conversion rules. Conclusion. This work is a first step towards automating and refining the generation of sharable and interoperable relational data models using ontologies with a freely available tool. The remaining challenges to cover all the ontology richness in the relational model are pointed out.},
	language = {EN},
	number = {S 02},
	urldate = {2022-07-05},
	journal = {Methods of Information in Medicine},
	author = {Khnaisser, Christina and Lavoie, Luc and Fraikin, Benoît and Barton, Adrien and Dussault, Samuel and Burgun, Anita and Ethier, Jean-François},
	month = dec,
	year = {2022},
	note = {Number: AAM
Publisher: Georg Thieme Verlag KG},
	keywords = {FRQS-Documents revus et publiés, Journal Article, pars3},
	pages = {e73--e88},
}

Background. A large volume of heavily fragmented data is generated daily in different healthcare contexts and is stored using various structures with different semantics. This fragmentation and heterogeneity make secondary use of data a challenge. Data integration approaches that derive a common data model from sources or requirements have some advantages. However, these approaches are often built for a specific application where the research questions are known. Thus, the semantic and structural reconciliation is often not reusable nor reproducible. A recent integration approach using knowledge models has been developed with ontologies that provide a strong semantic foundation. Nonetheless, deriving a data model that captures the richness of the ontology to store data with its full semantic remains a challenging task. Objectives. This paper addresses the question: How to design a sharable and interoperable data model for storing heterogeneous healthcare data and its semantic to support various applications? Method. This paper describes a method using an ontological knowledge model to automatically generate a data model for a domain of interest. The model can then be implemented in a relational database which efficiently enables the collection, storage, and retrieval of data while keeping semantic ontological annotations so that the same data can be extracted for various applications for further processing. Results. This paper (1) presents a comparison of existing methods for generating a relational data model from an ontology using 23 criteria, (2) describes standard conversion rules, and (3) presents , a prototype developed to demonstrate the conversion rules. Conclusion. This work is a first step towards automating and refining the generation of sharable and interoperable relational data models using ontologies with a freely available tool. The remaining challenges to cover all the ontology richness in the relational model are pointed out.

@article{cumyn_canadian_2022,
	title = {Canadian general internal medicine residents’ perception of a pedagogical tool of online cases in obstetric medicine},
	volume = {15},
	url = {https://doi.org/10.1177/1753495X211045614},
	doi = {10.1177/1753495X211045614},
	abstract = {BackgroundSufficient exposure to rarer medical problems around pregnancy is a challenge during short rotations in obstetric medicine (OM). A Canadian research group created online clinical cases, the CanCOM cases, to overcome this.MethodsWe conducted an exploratory study to document the use and perceived utility of the CanCOM cases. 77 residents doing an OM rotation participated in our study. We used a survey to document their perception of CanCOM cases (12 items, 7-point scale), clinical exposure to several conditions (pre and post rotation; 41 items, 7-point scale) and use of the educational tool (1 item, 4-option scale).ResultsCanCOM cases was perceived as an accessible and useful tool. Participants completed a median of 6/20 cases (range 1–20), and highly recommended the cases (6.48 ± 0.73 SD on a 7-point Likert scale).ConclusionDespite some technical limitations, CanCOM cases was shown to contribute to clinical exposure to rare but essential medical conditions.},
	number = {4},
	journal = {Obstetric Medicine},
	author = {Cumyn, Annabelle and Sauvé, Nadine and St-Onge, Christina},
	year = {2022},
	note = {\_eprint: https://doi.org/10.1177/1753495X211045614},
	keywords = {Journal Article},
	pages = {243--247},
}

BackgroundSufficient exposure to rarer medical problems around pregnancy is a challenge during short rotations in obstetric medicine (OM). A Canadian research group created online clinical cases, the CanCOM cases, to overcome this.MethodsWe conducted an exploratory study to document the use and perceived utility of the CanCOM cases. 77 residents doing an OM rotation participated in our study. We used a survey to document their perception of CanCOM cases (12 items, 7-point scale), clinical exposure to several conditions (pre and post rotation; 41 items, 7-point scale) and use of the educational tool (1 item, 4-option scale).ResultsCanCOM cases was perceived as an accessible and useful tool. Participants completed a median of 6/20 cases (range 1–20), and highly recommended the cases (6.48 ± 0.73 SD on a 7-point Likert scale).ConclusionDespite some technical limitations, CanCOM cases was shown to contribute to clinical exposure to rare but essential medical conditions.

@inproceedings{toyoshima_representing_2022,
	address = {Bolzano, Italie},
	title = {Representing {Gender} in {Ontologies}: {A} {Dispositional} {Perspective}},
	volume = {3073},
	url = {http://ceur-ws.org/Vol-3073/paper1.pdf},
	abstract = {Like biological sex, gender is a crucial determinant of health. Its representation nonetheless remains underdeveloped in many electronic medical records and health information standards. This paper explores an ontological characterization of gender in compliance with the OBO principles for ontology development and the BFO upper ontology. In particular, we deploy J. McKitrick’s dispositional account of gender (identity). Our main proposal is that gender can be analyzed as a behavioral and “extrinsic” disposition, as distinct from the BFO category of disposition. We also briefly discuss the implications of our dispositional approach to gender for so-called “gender roles” and gender-related information entities in existing ontologies.},
	language = {en},
	booktitle = {Proceedings of the 12th {International} {Conference} on {Biomedical} {Ontology} ({ICBO} 2021)},
	publisher = {CEUR Workshop Proceedings},
	author = {Toyoshima, Fumiaki and Barton, Adrien and Fabry, Paul and Ethier, Jean-François},
	month = jan,
	year = {2022},
	keywords = {Conference Paper, FRQS-Résumés et notes publiés},
	pages = {1--12},
}

Like biological sex, gender is a crucial determinant of health. Its representation nonetheless remains underdeveloped in many electronic medical records and health information standards. This paper explores an ontological characterization of gender in compliance with the OBO principles for ontology development and the BFO upper ontology. In particular, we deploy J. McKitrick’s dispositional account of gender (identity). Our main proposal is that gender can be analyzed as a behavioral and “extrinsic” disposition, as distinct from the BFO category of disposition. We also briefly discuss the implications of our dispositional approach to gender for so-called “gender roles” and gender-related information entities in existing ontologies.

@misc{cumyn_defis_2022,
	type = {Présentation en ligne},
	title = {Défis éthiques pour l'accès aux données au {Québec}},
	url = {https://frq.gouv.qc.ca/evenement/ameliorer-la-sante-des-populations-a-laide-des-banques-dechantillons-et-de-donnees-au-quebec/},
	author = {Cumyn, Annabelle},
	month = nov,
	year = {2022},
	keywords = {Presentation},
}

@misc{cumyn_cadre_2022,
	address = {Montréal, Canada},
	type = {Présentation orale},
	title = {Cadre de gouvernance, principes directeurs et perspectives citoyennes},
	url = {https://observatoire-ia.ulaval.ca/colloque-donnees-sante/},
	author = {Cumyn, Annabelle},
	month = nov,
	year = {2022},
	keywords = {Presentation},
}

@misc{menard_modeconsentement_2022,
	type = {Présentation en ligne},
	title = {Modèles de consentement dans le {PL19} : l’exemple de la recherche utilisant des renseignements de santé et de services sociaux},
	url = {https://observatoire-ia.ulaval.ca/colloque-reforme-acces-renseignements-sante-au-quebec/},
	author = {Ménard, Jean-Frédéric},
	month = jan,
	year = {2022},
	keywords = {Presentation},
}

@misc{fabry_ontology_2022,
	address = {Ann Arbor, États-Unis},
	type = {Présentation orale},
	title = {An ontology for healthcare systems},
	url = {https://icbo-conference.github.io/icbo2022/icbo-schedule/},
	author = {Fabry, Paul},
	month = sep,
	year = {2022},
	keywords = {Presentation},
}

@inproceedings{goyer_ontology_2022,
	address = {Ann Arbor, États-Unis},
	title = {An ontology for healthcare systems},
	abstract = {Modern patient care is becoming increasingly complex and is now most commonly delivered through healthcare systems. Understanding the structure surrounding care is an important tool in optimizing it. This article proposes a unified ontological analysis of healthcare systems following the OBO Foundry Methodology, by exploring the relationships between the caring of individuals, the health workers and healthcare providing organisations. This ontological model strives to enable interoperability in the context of Learning Health Systems.},
	booktitle = {Proceedings of the 13th {International} {Conference} on {Biomedical} {Ontology} ({ICBO} 2022)},
	author = {Goyer, François and Fabry, Paul and Barton, Adrien and Ethier, Jean-François},
	month = sep,
	year = {2022},
	keywords = {Conference Paper},
}

Modern patient care is becoming increasingly complex and is now most commonly delivered through healthcare systems. Understanding the structure surrounding care is an important tool in optimizing it. This article proposes a unified ontological analysis of healthcare systems following the OBO Foundry Methodology, by exploring the relationships between the caring of individuals, the health workers and healthcare providing organisations. This ontological model strives to enable interoperability in the context of Learning Health Systems.

@inproceedings{khnaisser_querying_2022,
	title = {Querying {Temporal} {Anomalies} in {Healthcare} {Information} {Systems} and {Beyond} [{BEST} {PAPER} {AWARD}]},
	isbn = {978-3-031-15740-0},
	abstract = {Finding anomalies in temporal relational databases is a difficult and challenging task, in particular if data is integrated from different sources. The problem is especially pressing in healthcare information systems, where temporal anomalies can pinpoint critical events such as erroneous drug administration or prescription. In this paper, we define three different temporal anomalies, which we call temporal redundancy, contradiction, and incompleteness. We define two different operators for each of these anomalies: the retrieval operator to retrieve all tuples of a relation that cause anomalous behaviour, and the labelling operator to annotate a temporal relation with additional information that marks normal and anomalous tuples. Finally, we present and evaluate different implementation techniques for the two operators for relational database systems.},
	booktitle = {Advances in {Databases} and {Information} {Systems}},
	publisher = {Springer International Publishing},
	author = {Khnaisser, Christina and Hamrouni, Hind and Blumenthal, David B. and Dignös, Anton and Gamper, Johann},
	editor = {Chiusano, Silvia and Cerquitelli, Tania and Wrembel, Robert},
	year = {2022},
	keywords = {Conference Paper, MEIE},
	pages = {209--222},
}

Finding anomalies in temporal relational databases is a difficult and challenging task, in particular if data is integrated from different sources. The problem is especially pressing in healthcare information systems, where temporal anomalies can pinpoint critical events such as erroneous drug administration or prescription. In this paper, we define three different temporal anomalies, which we call temporal redundancy, contradiction, and incompleteness. We define two different operators for each of these anomalies: the retrieval operator to retrieve all tuples of a relation that cause anomalous behaviour, and the labelling operator to annotate a temporal relation with additional information that marks normal and anomalous tuples. Finally, we present and evaluate different implementation techniques for the two operators for relational database systems.

@misc{cumyn_projet_2021,
	type = {Présentation orale},
	title = {Projet {CLARET} : {Données} de santé et méta-consentement},
	author = {Cumyn, Annabelle and Barton, Adrien and Ethier, Jean-François},
	month = jul,
	year = {2021},
	keywords = {CLARET\_PRESENTATION\_PHASE1, FRQS-Communications à titre de conférencier invité, Presentation},
}

@misc{cumyn_projet_2021-1,
	address = {Sherbrooke, Canada},
	type = {Présentation orale},
	title = {Projet {CLARET} : {Données} de santé et méta-consentement},
	author = {Cumyn, Annabelle and Barton, Adrien and Ethier, Jean-François},
	year = {2021},
	keywords = {CLARET\_PRESENTATION\_PHASE1, FRQS-Communications à titre de conférencier invité, Presentation},
}

@misc{khnaisser_partage_2021,
	address = {Sherbrooke, Canada},
	type = {Présentation orale},
	title = {Partage des données de santé au {Québec} avec {PARS3} : les systèmes de santé apprenants au service des citoyens},
	author = {Khnaisser, Christina and Lavoie, Luc and Ethier, Jean-François},
	year = {2021},
	keywords = {FRQS-Présentations orales ou par affiche, Presentation},
}

@misc{goyer_pratique_2021,
	address = {Sherbrooke, Canada},
	type = {Présentation orale},
	title = {La pratique réflexive pour faire une différence dans la vie de nos patients},
	author = {Goyer, François and Ethier, Jean-François},
	year = {2021},
	keywords = {FRQS-Présentations orales ou par affiche, Presentation},
}

@misc{cumyn_acceptabilite_2021,
	type = {Présentation en ligne},
	title = {Acceptabilité sociale - conditions et solutions},
	author = {Cumyn, Annabelle and Ethier, Jean-François},
	month = nov,
	year = {2021},
	keywords = {CLARET\_PRESENTATION\_PHASE1, FRQS-Présentations orales ou par affiche, Presentation},
}

@article{ethier_prescription_2021,
	title = {The prescription of drug ontology 2.0 ({PDRO}): {More} than the sum of its parts},
	volume = {18},
	url = {https://www.mdpi.com/1660-4601/18/22/12025},
	doi = {10.3390/ijerph182212025},
	abstract = {While drugs and related products have profoundly changed the lives of people around the world, ongoing challenges remain, including inappropriate use of a drug product. Inappropriate uses can be explained in part by ambiguous or incomplete information, for example, missing rea-sons for treatments, ambiguous information on how to take a medication, or lack of information on medication-related events outside the health care system. In order to fully assess the situation, data from multiple systems (electronic medical records, pharmacy and radiology information systems, laboratory management systems, etc.) from multiple organizations (outpatient clinics, hospitals, long-term care facilities, laboratories, pharmacies, registries, governments) on a large geographical scale is needed. Formal knowledge models like ontologies can help address such an information integration challenge. Existing approaches like the Observational Medical Outcomes Partnership are discussed and contrasted with the use of ontologies and systems using them for data integration. The PRescription Drug Ontology 2.0 (PDRO 2.0) is then presented and entities that are paramount in addressing this problematic are described. Finally, the benefits of using PDRO are discussed through a series of exemplar situation. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.},
	number = {22},
	journal = {International Journal of Environmental Research and Public Health},
	author = {Ethier, Jean-François and Goyer, François and Fabry, Paul and Barton, Adrien},
	year = {2021},
	note = {Number: 22},
	keywords = {Data annotation, Drug ontology, Drug prescription, FRQS-Documents revus et publiés, Journal Article, Medication management, Ontology development, Optimization of prescription},
}

While drugs and related products have profoundly changed the lives of people around the world, ongoing challenges remain, including inappropriate use of a drug product. Inappropriate uses can be explained in part by ambiguous or incomplete information, for example, missing rea-sons for treatments, ambiguous information on how to take a medication, or lack of information on medication-related events outside the health care system. In order to fully assess the situation, data from multiple systems (electronic medical records, pharmacy and radiology information systems, laboratory management systems, etc.) from multiple organizations (outpatient clinics, hospitals, long-term care facilities, laboratories, pharmacies, registries, governments) on a large geographical scale is needed. Formal knowledge models like ontologies can help address such an information integration challenge. Existing approaches like the Observational Medical Outcomes Partnership are discussed and contrasted with the use of ontologies and systems using them for data integration. The PRescription Drug Ontology 2.0 (PDRO 2.0) is then presented and entities that are paramount in addressing this problematic are described. Finally, the benefits of using PDRO are discussed through a series of exemplar situation. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.

@inproceedings{fabry_ontological_2021,
	address = {Bolzano, Italie},
	title = {An {Ontological} {Analysis} of {Health} {Procedure} {Information}},
	volume = {3073},
	url = {http://ceur-ws.org/Vol-3073/paper4.pdf},
	abstract = {Health care processes can be formally analyzed as involving two kinds of planned processes that are mereologically related: health procedures and health activities. They can involve a number of informational entities that derive from orders meant to fulfill requests such as prescriptions. This article provides definitions and axioms for such entities, following the OBO Foundry methodology. This representation could serve as a foundation for an ontological model that aims to enable interoperability between various clinical data sources in the context of a Learning Health System. © 2021 Copyright for this paper by its authors.},
	booktitle = {Proceedings of the 12th {International} {Conference} on {Biological} {Ontology} ({ICBO} 2021)},
	publisher = {CEUR Workshop Proceedings},
	author = {Fabry, Paul and Goyer, François and Barton, Adrien and Ethier, Jean-François},
	year = {2021},
	keywords = {Conference Paper, FRQS-Résumés et notes publiés, Health care process, Health procedure, Information content entity, Prescription},
	pages = {36--47},
}

Health care processes can be formally analyzed as involving two kinds of planned processes that are mereologically related: health procedures and health activities. They can involve a number of informational entities that derive from orders meant to fulfill requests such as prescriptions. This article provides definitions and axioms for such entities, following the OBO Foundry methodology. This representation could serve as a foundation for an ontological model that aims to enable interoperability between various clinical data sources in the context of a Learning Health System. © 2021 Copyright for this paper by its authors.

@misc{cumyn_projet_2021-2,
	address = {Sherbrooke, Canada},
	type = {Présentation orale},
	title = {Projet {CLARET}  : {Données} de santé et méta-consentement},
	author = {Cumyn, Annabelle and Barton, Adrien and Ethier, Jean-François},
	year = {2021},
	keywords = {CLARET\_PRESENTATION\_PHASE1, FRQS-Communications à titre de conférencier invité, Presentation},
}

@misc{barton_ontologies_2021,
	address = {Sherbrooke, Canada},
	type = {Présentation orale},
	title = {Ontologies biomédicales},
	author = {Barton, Adrien and Ethier, Jean-François},
	year = {2021},
	keywords = {FRQS-Communications à titre de conférencier invité, Presentation},
}

@misc{aimez_contribution_2021,
	address = {Sherbrooke, Canada},
	title = {Contribution des différents acteurs politiques et de la recherche pour renforcer la collaboration franco-québécoise},
	author = {Aimez, V. and de Lastours, V. and Ethier, Jean-François and Sandrin, A.},
	year = {2021},
	keywords = {FRQS-Communications à titre de conférencier invité, Presentation},
}

@inproceedings{barton_expressions_2021,
	address = {Bolzano, Italie},
	title = {Expressions, {Utterances} and {Directive} {Slots}},
	volume = {2969},
	url = {http://ceur-ws.org/Vol-2969/paper46-FOUST.pdf},
	abstract = {The same linguistic entity can play a directive or a descriptive role, e.g. "cook dinner" can be moved from a column "to do" in a Kanban board to a column "done". We propose to account for such directive roles by enriching a previous framework of slot mereology for informational entities with the notion of directive slot. We differentiate expressions from the utterances they constitute in order to accommodate for the insight from the literature in pragmatics that most (if not all) expressions can constitute directive utterances in the appropriate context. We propose axioms involving constitution, slot-having and slot-filling on utterances, and articulate this theory with former work on directing actions.},
	language = {English},
	booktitle = {Proceedings of the {Joint} {Ontology} {Workshops} 2021 ({JOWO} 2021)},
	publisher = {CEUR Workshop Proceedings},
	author = {Barton, Adrien and Vieu, Laure and Ethier, Jean-François},
	month = sep,
	year = {2021},
	keywords = {Conference Paper, FRQS-Résumés et notes publiés},
}

The same linguistic entity can play a directive or a descriptive role, e.g. "cook dinner" can be moved from a column "to do" in a Kanban board to a column "done". We propose to account for such directive roles by enriching a previous framework of slot mereology for informational entities with the notion of directive slot. We differentiate expressions from the utterances they constitute in order to accommodate for the insight from the literature in pragmatics that most (if not all) expressions can constitute directive utterances in the appropriate context. We propose axioms involving constitution, slot-having and slot-filling on utterances, and articulate this theory with former work on directing actions.

@inproceedings{tarbouriech_flight_2021,
	title = {Flight {Procedures} {Description} {Using} {Semantic} {Roles}},
	volume = {2969},
	url = {http://ceur-ws.org/Vol-2969/paper25-FOMI.pdf},
	booktitle = {Proceedings of the {Joint} {Ontology} {Workshops} 2021 ({JOWO} 2021)},
	publisher = {CEUR Workshop Proceedings},
	author = {Tarbouriech, Cédric and Bernard, Denys and Vieu, Laure and Barton, Adrien and Ethier, Jean-François},
	year = {2021},
	keywords = {Conference Paper, FRQS-Résumés et notes publiés},
}

@misc{ethier_systemes_2021,
	address = {Toulouse, France},
	title = {Les systèmes de santé apprenants : mettre le patient au cœur de sa santé},
	author = {Ethier, Jean-François},
	year = {2021},
	keywords = {FRQS-Communications à titre de conférencier invité, Presentation},
}

@misc{souid_formalisation_2021,
	address = {Sherbrooke, Canada},
	type = {Présentation en ligne},
	title = {Formalisation du cycle de vie et des propriétés de sécurité associées aux informations classifiées dans une stratégie de défense en profondeur},
	url = {https://www.acfas.ca/evenements/congres/programme/88/600/614/c},
	abstract = {La majorité des cyberattaques qui impliquent des organisations de santé ont pour conséquence le vol de données. Lors de l’enquête, les officiers ont de la difficulté à identifier les objets volés et à définir les stratégies de défense. Ces difficultés sont dues par la complexité des systèmes et au manque d’outil pour assurer la traçabilité.

Afin d’appréhender ces difficultés, la stratégie de défense en profondeur est adoptée pour atténuer les menaces. Toutefois, les modèles existants ne couvrent pas l’ensemble du cycle de vie des données et les caractéristiques de sécurité associées.

La couverture de ces caractéristiques passe par une formalisation des processus qui manipulent des données classifiées. Ceci permet un suivi temporel des propriétés de sécurité et offre une vision complète du cycle de vie des ressources granulaires. La caractérisation se traduit par une modélisation de flux de données affiliés à des critères de sécurité selon un contexte défini. L’implémentation sous la forme d’un automate sert à valider le respect des exigences. L’évaluation de la sécurité des ressources est réalisée en introduisant des métriques en fonction de la classification des données, le contexte et les moyens de défense.

Ce modèle sert à améliorer le suivi des moyens mis en œuvre dans une stratégie de défense en profondeur et d’unifier les méthodes d’analyse de vulnérabilité avec les changements d’états des données classifiées dans des fenêtres temporelles.},
	author = {Souid, Ameni and Ecarot, Thibaud},
	year = {2021},
	keywords = {Presentation},
}

La majorité des cyberattaques qui impliquent des organisations de santé ont pour conséquence le vol de données. Lors de l’enquête, les officiers ont de la difficulté à identifier les objets volés et à définir les stratégies de défense. Ces difficultés sont dues par la complexité des systèmes et au manque d’outil pour assurer la traçabilité. Afin d’appréhender ces difficultés, la stratégie de défense en profondeur est adoptée pour atténuer les menaces. Toutefois, les modèles existants ne couvrent pas l’ensemble du cycle de vie des données et les caractéristiques de sécurité associées. La couverture de ces caractéristiques passe par une formalisation des processus qui manipulent des données classifiées. Ceci permet un suivi temporel des propriétés de sécurité et offre une vision complète du cycle de vie des ressources granulaires. La caractérisation se traduit par une modélisation de flux de données affiliés à des critères de sécurité selon un contexte défini. L’implémentation sous la forme d’un automate sert à valider le respect des exigences. L’évaluation de la sécurité des ressources est réalisée en introduisant des métriques en fonction de la classification des données, le contexte et les moyens de défense. Ce modèle sert à améliorer le suivi des moyens mis en œuvre dans une stratégie de défense en profondeur et d’unifier les méthodes d’analyse de vulnérabilité avec les changements d’états des données classifiées dans des fenêtres temporelles.

@article{lachance_high-dose_2021,
	title = {High-dose vitamin-{C} induced prolonged factitious hyperglycemia in a peritoneal dialysis patient: a case report},
	volume = {15},
	issn = {1752-1947},
	url = {https://doi.org/10.1186/s13256-021-02869-4},
	doi = {10.1186/s13256-021-02869-4},
	abstract = {High-dose vitamin C is increasingly used for sepsis and more recently for coronavirus disease 2019 (COVID-19) infections. Proponents argue that the low cost and near perfect safety profile of vitamin C support its early adoption. Yet, adverse events might be underreported and underappreciated.},
	number = {1},
	journal = {Journal of Medical Case Reports},
	author = {Lachance, Olivier and Goyer, François and Adhikari, Neill K. J. and Masse, Marie-Hélène and Bilodeau, Jean-François and Lamontagne, François and Leclair, Marc-André},
	month = may,
	year = {2021},
	keywords = {Journal Article},
	pages = {297},
}

High-dose vitamin C is increasingly used for sepsis and more recently for coronavirus disease 2019 (COVID-19) infections. Proponents argue that the low cost and near perfect safety profile of vitamin C support its early adoption. Yet, adverse events might be underreported and underappreciated.

@misc{cumyn_integration_2021,
	address = {Sherbrooke, Canada},
	type = {Table ronde},
	title = {Intégration recherche et soins : méta-consentement},
	url = {https://ivado.ca/evenements/journees-quebecoises-de-valorisation-des-donnees/},
	author = {Cumyn, Annabelle},
	month = oct,
	year = {2021},
	keywords = {CLARET\_PRESENTATION\_PHASE1, Presentation},
}

@misc{cumyn_acces_2021,
	type = {Présentation orale},
	title = {Accès aux données : des pistes de solutions de citoyens et chercheurs},
	author = {Cumyn, Annabelle and Wilhelmy, Catherine},
	month = oct,
	year = {2021},
	keywords = {CLARET\_PRESENTATION\_PHASE1, Presentation},
}

@misc{cumyn_projet_2021-3,
	type = {Présentation orale},
	title = {Projet {CLARET} : {Données} de santé et méta-consentement},
	author = {Cumyn, Annabelle and Barton, Adrien and Ethier, Jean-François},
	month = jul,
	year = {2021},
	keywords = {CLARET\_PRESENTATION\_PHASE1, FRQS-Communications à titre de conférencier invité, Presentation},
}

@misc{cumyn_projet_2021-4,
	type = {Presentation orale},
	title = {Projet {CLARET} : {Données} de santé et méta-consentement},
	author = {Cumyn, Annabelle},
	month = may,
	year = {2021},
	keywords = {CLARET\_PRESENTATION\_PHASE1, Presentation},
}

@article{barton_gift_2021,
	title = {Gift, {Reciprocity} and {Learning} {Health} {Systems}},
	volume = {21},
	issn = {1536-0075},
	url = {https://doi.org/10.1080/15265161.2021.1891341},
	doi = {10.1080/15265161.2021.1891341},
	language = {eng},
	number = {4},
	journal = {The American Journal of Bioethics},
	author = {Barton, Adrien and Cumyn, Annabelle and Dault, Roxanne and Ethier, Jean-François},
	month = apr,
	year = {2021},
	keywords = {Altruism, CLARET\_ARTICLE\_PHASE1, Cognition, FRQS-Commentaires, perspectives, éditoriaux, Humans, Journal Article, Learning Health System, Motivation, Precision Medicine},
	pages = {91--93},
}

@article{cumyn_meta-consent_2021,
	title = {Meta-consent for the secondary use of health data within a learning health system: a qualitative study of the public's perspective},
	volume = {22},
	issn = {1472-6939},
	shorttitle = {Meta-consent for the secondary use of health data within a learning health system},
	url = {https://doi.org/10.1186/s12910-021-00647-x},
	doi = {10.1186/s12910-021-00647-x},
	abstract = {BACKGROUND: The advent of learning healthcare systems (LHSs) raises an important implementation challenge concerning how to request and manage consent to support secondary use of data in learning cycles, particularly research activities. Current consent models in Quebec were not established with the context of LHSs in mind and do not support the agility and transparency required to obtain consent from all involved, especially the citizens. Therefore, a new approach to consent is needed. Previous work identified the meta-consent model as a promising alternative to fulfill the requirements of LHSs, particularly large-scale deployments. We elicited the public's attitude toward the meta-consent model to evaluate if the model could be understood by the citizens and would be deemed acceptable to prepare for its possible implementation in Quebec.
METHODS: Eight focus groups, with a total of 63 members of the general public from various backgrounds were conducted in Quebec, Canada, in 2019. Explicit attention was given to literacy levels, language spoken at home and rural vs urban settings. We assessed attitudes, concerns and facilitators regarding key components of the meta-consent model: predefined categories to personalized consent requests, a dynamic web-based infrastructure to record meta-consent, and default settings. To analyse the discussions, a thematic content analysis was performed using a qualitative software.
RESULTS: Our findings showed that participants were supportive of this new approach of consent as it promotes transparency and offers autonomy for the management of their health data. Key facilitators were identified to be considered in the implementation of a meta-consent model in the Quebec LHSs: information and transparency, awareness campaigns, development of educational tools, collaboration of front-line healthcare professionals, default settings deemed acceptable by the society as well as close partnerships with recognized and trusted institutions.
CONCLUSIONS: This qualitative study reveals the openness of a sample of the Quebec population regarding the meta-consent model for secondary use of health data for research. This first exploratory study conducted with the public is an important step in guiding decision-makers in the next phases of implementing the various strategies to support access and use of health data in Quebec.},
	language = {eng},
	number = {1},
	journal = {BMC medical ethics},
	author = {Cumyn, Annabelle and Barton, Adrien and Dault, Roxanne and Safa, Nissrine and Cloutier, Anne-Marie and Ethier, Jean-François},
	month = jun,
	year = {2021},
	keywords = {CLARET\_ARTICLE\_PHASE1, Canada, FRQS-Documents revus et publiés, Focus groups, Health data, Humans, Informed Consent, Journal Article, Learning Health System, Learning healthcare system, Meta-consent, Public opinion, Qualitative Research, Quebec},
	pages = {81},
}

BACKGROUND: The advent of learning healthcare systems (LHSs) raises an important implementation challenge concerning how to request and manage consent to support secondary use of data in learning cycles, particularly research activities. Current consent models in Quebec were not established with the context of LHSs in mind and do not support the agility and transparency required to obtain consent from all involved, especially the citizens. Therefore, a new approach to consent is needed. Previous work identified the meta-consent model as a promising alternative to fulfill the requirements of LHSs, particularly large-scale deployments. We elicited the public's attitude toward the meta-consent model to evaluate if the model could be understood by the citizens and would be deemed acceptable to prepare for its possible implementation in Quebec. METHODS: Eight focus groups, with a total of 63 members of the general public from various backgrounds were conducted in Quebec, Canada, in 2019. Explicit attention was given to literacy levels, language spoken at home and rural vs urban settings. We assessed attitudes, concerns and facilitators regarding key components of the meta-consent model: predefined categories to personalized consent requests, a dynamic web-based infrastructure to record meta-consent, and default settings. To analyse the discussions, a thematic content analysis was performed using a qualitative software. RESULTS: Our findings showed that participants were supportive of this new approach of consent as it promotes transparency and offers autonomy for the management of their health data. Key facilitators were identified to be considered in the implementation of a meta-consent model in the Quebec LHSs: information and transparency, awareness campaigns, development of educational tools, collaboration of front-line healthcare professionals, default settings deemed acceptable by the society as well as close partnerships with recognized and trusted institutions. CONCLUSIONS: This qualitative study reveals the openness of a sample of the Quebec population regarding the meta-consent model for secondary use of health data for research. This first exploratory study conducted with the public is an important step in guiding decision-makers in the next phases of implementing the various strategies to support access and use of health data in Quebec.

@article{cumyn_citizens_2021,
	title = {Citizens, {Research} {Ethics} {Committee} {Members} and {Researchers}' {Attitude} {Toward} {Information} and {Consent} for the {Secondary} {Use} of {Health} {Data}: {Implications} for {Research} {Within} {Learning} {Health} {Systems}},
	volume = {16},
	issn = {1556-2654},
	shorttitle = {Citizens, {Research} {Ethics} {Committee} {Members} and {Researchers}' {Attitude} {Toward} {Information} and {Consent} for the {Secondary} {Use} of {Health} {Data}},
	url = {http://dx.doi.org/10.1177/1556264621992214},
	doi = {10.1177/1556264621992214},
	abstract = {A survey was conducted to assess citizens, research ethics committee members, and researchers' attitude toward information and consent for the secondary use of health data for research within learning health systems (LHSs). Results show that the reuse of health data for research to advance knowledge and improve care is valued by all parties; consent regarding health data reuse for research has fundamental importance particularly to citizens; and all respondents deemed important the existence of a secure website to support the information and consent processes. This survey was part of a larger project that aims at exploring public perspectives on alternate approaches to the current consent models for health data reuse to take into consideration the unique features of LHSs. The revised model will need to ensure that citizens are given the opportunity to be better informed about upcoming research and have their say, when possible, in the use of their data.},
	language = {eng},
	number = {3},
	journal = {Journal of empirical research on human research ethics},
	author = {Cumyn, Annabelle and Dault, Roxanne and Barton, Adrien and Cloutier, Anne-Marie and Ethier, Jean-François},
	month = jul,
	year = {2021},
	keywords = {Attitude, CLARET\_ARTICLE\_PHASE1, Ethics Committees, Research, FRQS-Documents revus et publiés, Humans, Informed Consent, Journal Article, Learning Health System, Research Personnel, health data, informed consent, learning health systems, research ethics, secondary use, survey},
	pages = {165--178},
}

A survey was conducted to assess citizens, research ethics committee members, and researchers' attitude toward information and consent for the secondary use of health data for research within learning health systems (LHSs). Results show that the reuse of health data for research to advance knowledge and improve care is valued by all parties; consent regarding health data reuse for research has fundamental importance particularly to citizens; and all respondents deemed important the existence of a secure website to support the information and consent processes. This survey was part of a larger project that aims at exploring public perspectives on alternate approaches to the current consent models for health data reuse to take into consideration the unique features of LHSs. The revised model will need to ensure that citizens are given the opportunity to be better informed about upcoming research and have their say, when possible, in the use of their data.

@article{wouterlood_pregnancyassociated_2021,
	title = {Pregnancy‐associated pelvic vein thrombosis: {Insights} from a multicenter case series},
	volume = {19},
	issn = {1538-7836},
	url = {https://www.sciencedirect.com/science/article/pii/S1538783622018384},
	doi = {https://doi.org/10.1111/jth.15333},
	abstract = {Background Pelvic vein thrombosis (PVT) is a rare complication of pregnancy that can lead to life‐threatening complications, such as pulmonary embolism (PE). Objective To describe characteristics of PVT and its treatment in pregnancy in the province of Quebec, Canada. Patients/Methods We developed a province‐wide case series of PVT in pregnancy including four tertiary care centers and the Registry of Rare Diseases of the Groupe d’Étude en Médecine Obstétricale du Québec. Using diagnostic codes, we included cases with confirmed PVT on imaging during pregnancy or within 6 weeks postpartum from July 2003 to June 2018. Results A total of 47 cases were identified. PVT diagnosis was generally made in the early postpartum period (median of 9 [interquartile range (IQR) 4.5–12] days postpartum). Most PVT (94\%) included in this series were symptomatic. Women presented primarily with abdominal pain (77\%) and fever (55\%), often prolonged despite antibiotics (mean 4.45 ± 2.39 days, with 39\% having fever for more than 5 days). The most common risk factor was surgery (57\%) and peripartum infections (54\%). Thirty‐eight (83\%) women received antibiotics and 41 (89\%) were anticoagulated. Three cases of PE (7\%) occurred concomitantly, 11\% of women required intensive care, and 19\% had inferior vena cava (IVC) clot extension. The episode resulted in prolonged hospitalization (median 6 [IQR 3–10.75] days), with 48\% being hospitalized more than 7 days. Conclusion Symptomatic PVT has significant clinical implications with prolonged fever and risks of extension in the IVC and PE, leading to prolonged hospitalization including in the intensive care unit. Therapeutic anticoagulation and antibiotics, when infection is documented, should be considered for management.},
	number = {8},
	journal = {Journal of Thrombosis and Haemostasis},
	author = {Wouterlood, Marijke Allain and Malhamé, Isabelle and Lévesque, Kateri and Dayan, Natalie and Mahone, Michèle and Côté, Anne-Marie and Cumyn, Annabelle and Malick, Mandy and Sauvé, Nadine},
	year = {2021},
	keywords = {Journal Article, postpartum period, pregnancy, pulmonary embolism, thrombophlebitis, thrombosis},
	pages = {1926--1931},
}

Background Pelvic vein thrombosis (PVT) is a rare complication of pregnancy that can lead to life‐threatening complications, such as pulmonary embolism (PE). Objective To describe characteristics of PVT and its treatment in pregnancy in the province of Quebec, Canada. Patients/Methods We developed a province‐wide case series of PVT in pregnancy including four tertiary care centers and the Registry of Rare Diseases of the Groupe d’Étude en Médecine Obstétricale du Québec. Using diagnostic codes, we included cases with confirmed PVT on imaging during pregnancy or within 6 weeks postpartum from July 2003 to June 2018. Results A total of 47 cases were identified. PVT diagnosis was generally made in the early postpartum period (median of 9 [interquartile range (IQR) 4.5–12] days postpartum). Most PVT (94%) included in this series were symptomatic. Women presented primarily with abdominal pain (77%) and fever (55%), often prolonged despite antibiotics (mean 4.45 ± 2.39 days, with 39% having fever for more than 5 days). The most common risk factor was surgery (57%) and peripartum infections (54%). Thirty‐eight (83%) women received antibiotics and 41 (89%) were anticoagulated. Three cases of PE (7%) occurred concomitantly, 11% of women required intensive care, and 19% had inferior vena cava (IVC) clot extension. The episode resulted in prolonged hospitalization (median 6 [IQR 3–10.75] days), with 48% being hospitalized more than 7 days. Conclusion Symptomatic PVT has significant clinical implications with prolonged fever and risks of extension in the IVC and PE, leading to prolonged hospitalization including in the intensive care unit. Therapeutic anticoagulation and antibiotics, when infection is documented, should be considered for management.

@article{trahan_physician_2021,
	title = {Physician {Perspectives} on {Including} {Pregnant} {Women} in {Covid}-19 {Clinical} {Trials}: {Time} for a {Paradigm} {Change}},
	volume = {43},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/eahr.500107},
	doi = {https://doi.org/10.1002/eahr.500107},
	abstract = {Abstract Excluding pregnant people from Covid-19 clinical trials may lead to unintended harmful consequences. For this study, an online questionnaire was sent to physicians belonging to Canadian professional medical associations in order to evaluate their perspectives on the participation of pregnant women in Covid-19 clinical trials. The majority of respondents expressed support for including pregnant women in Covid-19 trials (119/165; 72\%), especially those investigating therapies with a prior safety record in pregnancy (139/164; 85\%). The main perceived barriers to inclusion identified were unwillingness of pregnant patients to participate and of treating teams to offer participation, the burden of regulatory approval, and a general “culture of exclusion” of pregnant women from trials. We describe why some physicians may be reluctant to include pregnant individuals in trials, and we identify barriers to the appropriate participation of pregnant people in clinical research.},
	number = {6},
	journal = {Ethics \& Human Research},
	author = {Trahan, Marie-Julie and Cumyn, Annabelle and Cheng, Matthew P. and McDonald, Emily G. and Lapinsky, Stephen E. and Daneman, Nick and Abenhaim, Haim A. and Malhamé, Isabelle},
	year = {2021},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/eahr.500107},
	keywords = {Covid-19 clinical trials, Journal Article, human subjects research, inclusion of pregnant women in trials, maternal-fetal ethics, pregnant research participants, research with pregnant women},
	pages = {19--27},
}

Abstract Excluding pregnant people from Covid-19 clinical trials may lead to unintended harmful consequences. For this study, an online questionnaire was sent to physicians belonging to Canadian professional medical associations in order to evaluate their perspectives on the participation of pregnant women in Covid-19 clinical trials. The majority of respondents expressed support for including pregnant women in Covid-19 trials (119/165; 72%), especially those investigating therapies with a prior safety record in pregnancy (139/164; 85%). The main perceived barriers to inclusion identified were unwillingness of pregnant patients to participate and of treating teams to offer participation, the burden of regulatory approval, and a general “culture of exclusion” of pregnant women from trials. We describe why some physicians may be reluctant to include pregnant individuals in trials, and we identify barriers to the appropriate participation of pregnant people in clinical research.

@article{toyoshima_roles_2021,
	title = {Roles and their three facets: {A} foundational perspective},
	volume = {16},
	issn = {1570-5838},
	shorttitle = {Roles and their three facets},
	url = {https://content.iospress.com/articles/applied-ontology/ao210244},
	doi = {10.3233/AO-210244},
	abstract = {Roles remain nebulous entities, notwithstanding their extensive interdisciplinary research. This paper argues through a meta-ontological conceptual tool of grounding that there are three key facets of roles: a role position, a role specification, and a role potential. A foundational perspective on roles can be specified by “role choices” as to which facet of roles is primary. Role choices are illustrated with theories of roles that are built in compliance with four well-known upper ontologies: GFO, DOLCE, BFO, and UFO. The relationship between such three facets of roles and the GFO-based three kinds of roles (relational, processual, and social) is closely examined. These three facets are also comparatively studied from linguistic (e.g. ‘have a role’ versus ‘play a role’) and methodological (realism versus conceptualism regarding ontology design) perspectives. Furthermore, the family resemblance view of roles as “epistemic trackers” is proposed: the general notion of role is merely (partially) unified by its three facets and helps to keep track of some entity with respect to its role-related aspects. Finally, defining characteristics of roles in conceptual modeling are considered in terms of the three-facet theory. This work provides the grist for future practical development of an ontological module for generic role representation.},
	language = {en},
	number = {2},
	urldate = {2022-07-19},
	journal = {Applied Ontology},
	author = {Toyoshima, Fumiaki},
	month = jan,
	year = {2021},
	note = {Number: 2
Publisher: IOS Press},
	keywords = {Journal Article},
	pages = {161--192},
}

Roles remain nebulous entities, notwithstanding their extensive interdisciplinary research. This paper argues through a meta-ontological conceptual tool of grounding that there are three key facets of roles: a role position, a role specification, and a role potential. A foundational perspective on roles can be specified by “role choices” as to which facet of roles is primary. Role choices are illustrated with theories of roles that are built in compliance with four well-known upper ontologies: GFO, DOLCE, BFO, and UFO. The relationship between such three facets of roles and the GFO-based three kinds of roles (relational, processual, and social) is closely examined. These three facets are also comparatively studied from linguistic (e.g. ‘have a role’ versus ‘play a role’) and methodological (realism versus conceptualism regarding ontology design) perspectives. Furthermore, the family resemblance view of roles as “epistemic trackers” is proposed: the general notion of role is merely (partially) unified by its three facets and helps to keep track of some entity with respect to its role-related aspects. Finally, defining characteristics of roles in conceptual modeling are considered in terms of the three-facet theory. This work provides the grist for future practical development of an ontological module for generic role representation.

@misc{menard_peut-prendre_2021,
	address = {Sherbrooke, Canada},
	type = {Présentation orale},
	title = {Peut-on prendre n'importe quel moyen pour y arriver? {Intérêt} supérieur, influence et manipulation.},
	abstract = {Réunion scientifique, organisée par le Groupe de recherche interdisciplinaire en informatique de la santé (GRIIS), Université de Sherbrooke},
	author = {Ménard, Jean-Frédéric},
	month = jun,
	year = {2021},
	keywords = {Presentation},
}

Réunion scientifique, organisée par le Groupe de recherche interdisciplinaire en informatique de la santé (GRIIS), Université de Sherbrooke

@misc{cumyn_systemes_2021,
	address = {France},
	type = {Présentation orale},
	title = {Les systèmes de santé apprenants et {PARS3} : mettre le patient au cœur de sa santé},
	author = {Cumyn, Annabelle and Ethier, Jean-François},
	year = {2021},
	keywords = {FRQS-Communications à titre de conférencier invité, Presentation},
}

@inproceedings{toyoshima_towards_2021,
	address = {Bolzano, Italie},
	title = {Towards a {Unified} {Dispositional} {Framework} for {Realizable} {Entities}},
	url = {https://ebooks.iospress.nl/doi/10.3233/FAIA210371},
	doi = {10.3233/FAIA210371},
	abstract = {Realizable entities are properties that can be realized in processes of specific correlated types in which the bearer participates. It will be valuable to create a systematic classification of realizable entities because they are useful for various modeling purposes in ontologies. In this paper we outline a unifying framework for realizable entities (including dispositions and roles) in the upper ontology Basic Formal Ontology (BFO) that is theoretically underpinned by J. McKitrick’s pragmatic approach to dispositions. In particular, we develop a formal ontological account of “extrinsic dispositions” and illustrate its potential applications with clarification of functions and roles in BFO.},
	language = {en},
	urldate = {2022-07-19},
	booktitle = {Proceedings of the 12th {International} {Conference} on {Formal} {Ontology} in {Information} {Systems} ({FOIS} 2021)},
	publisher = {IOS Press},
	author = {Toyoshima, Fumiaki and Barton, Adrien and Jansen, Ludger and Ethier, Jean-François},
	year = {2021},
	note = {Publisher: IOS Press},
	keywords = {Conference Paper, FRQS-Résumés et notes publiés},
	pages = {64--78},
}

Realizable entities are properties that can be realized in processes of specific correlated types in which the bearer participates. It will be valuable to create a systematic classification of realizable entities because they are useful for various modeling purposes in ontologies. In this paper we outline a unifying framework for realizable entities (including dispositions and roles) in the upper ontology Basic Formal Ontology (BFO) that is theoretically underpinned by J. McKitrick’s pragmatic approach to dispositions. In particular, we develop a formal ontological account of “extrinsic dispositions” and illustrate its potential applications with clarification of functions and roles in BFO.

@inproceedings{toyoshima_semantics_2021,
	address = {Bolzano, Italie},
	title = {Semantics {Matters}: {A} {New} {Light} on {Ontological} {Commitments} of {Logics}},
	volume = {2969},
	url = {http://ceur-ws.org/Vol-2969/paper44-FOUST.pdf},
	abstract = {It is a central foundational theme to specify ontological commitments that are implicitly embedded in formal logic. In this paper, we address a largely unexplored topic of ontological commitments of the semantics of logic. In particular, we focus on the idea of “modal logic without possible worlds” in contradistinction with the widespread usage of the possible-world semantics in formal ontology. More concretely, we present B. Vetter’s potentiality-based theory of possibility and discuss how to develop a modal semantics that would accord with the modal primacy of dispositions in the upper ontology Basic Formal Ontology (BFO).},
	language = {en},
	booktitle = {Proceedings of the 7th {Joint} {Ontology} {Workshops} ({JOWO} 2021)},
	publisher = {CEUR Workshop Proceedings},
	author = {Toyoshima, Fumiaki and Niki, Satoru},
	month = oct,
	year = {2021},
	keywords = {Conference Paper},
	pages = {16},
}

It is a central foundational theme to specify ontological commitments that are implicitly embedded in formal logic. In this paper, we address a largely unexplored topic of ontological commitments of the semantics of logic. In particular, we focus on the idea of “modal logic without possible worlds” in contradistinction with the widespread usage of the possible-world semantics in formal ontology. More concretely, we present B. Vetter’s potentiality-based theory of possibility and discuss how to develop a modal semantics that would accord with the modal primacy of dispositions in the upper ontology Basic Formal Ontology (BFO).

@misc{dussault_integration_2021,
	address = {Sherbrooke, Canada},
	type = {Présentation par affiche},
	title = {Intégration de données biomédicales : pourquoi toujours recommencer le même travail?},
	url = {https://www.acfas.ca/evenements/congres/programme/88/600/614/c},
	abstract = {L’informatisation massive des données médicales ouvre de nouvelles possibilités d’amélioration des soins et de recherche biomédicale. Par exemple, la conception d’études prospectives et rétrospectives de grande échelle et le développement d’outils sophistiqués d’aide à la décision pour les professionnelles et professionnels de la santé. Cependant, l’implantation d’une telle plateforme se heurte à de multiples problématiques, comme l’hétérogénéité naturelle des données médicales. Les données sont difficilement interopérables puisqu’elles sont générées par des processus uniques à chaque établissement, sont consignées pour des besoins distincts, sont stockées à l’aide de technologies tout aussi hétérogènes et sont régies par des structures organisationnelles indépendantes. Ce faisant, chaque nouveau projet nécessite de découvrir et de maîtriser les sources de données pertinentes au projet afin d’en faire l’intégration dans un environnement homogène.  

Cette présentation a pour but de montrer l’intérêt de notre méthode d’intégration de données par rapport aux méthodes actuelles. En particulier, nous expliquerons comment l’intégration de données basées sur la représentation ontologique des connaissances permet d’arrêter de refaire le même travail à chaque nouveau projet. Permettant, ainsi, d’économiser énormément de temps dans l’initiation de projets s’appuyant sur des données biomédicales issues de la pratique et de la recherche.},
	language = {fr},
	author = {Dussault, Samuel},
	month = may,
	year = {2021},
	note = {Presenters: \_:n93},
	keywords = {Presentation},
}

L’informatisation massive des données médicales ouvre de nouvelles possibilités d’amélioration des soins et de recherche biomédicale. Par exemple, la conception d’études prospectives et rétrospectives de grande échelle et le développement d’outils sophistiqués d’aide à la décision pour les professionnelles et professionnels de la santé. Cependant, l’implantation d’une telle plateforme se heurte à de multiples problématiques, comme l’hétérogénéité naturelle des données médicales. Les données sont difficilement interopérables puisqu’elles sont générées par des processus uniques à chaque établissement, sont consignées pour des besoins distincts, sont stockées à l’aide de technologies tout aussi hétérogènes et sont régies par des structures organisationnelles indépendantes. Ce faisant, chaque nouveau projet nécessite de découvrir et de maîtriser les sources de données pertinentes au projet afin d’en faire l’intégration dans un environnement homogène. Cette présentation a pour but de montrer l’intérêt de notre méthode d’intégration de données par rapport aux méthodes actuelles. En particulier, nous expliquerons comment l’intégration de données basées sur la représentation ontologique des connaissances permet d’arrêter de refaire le même travail à chaque nouveau projet. Permettant, ainsi, d’économiser énormément de temps dans l’initiation de projets s’appuyant sur des données biomédicales issues de la pratique et de la recherche.

@misc{ethier_partage_2020,
	address = {Sherbrooke, Canada},
	title = {Partage des données de santé au {Québec} : {Permettons} de changer le devenir des patients avec {PARS3}},
	author = {Ethier, Jean-François},
	year = {2020},
	keywords = {FRQS-Présentations orales ou par affiche, Presentation},
}

@misc{dault_point_2020,
	address = {Webinaires Réseau-1 Québec 2019-2020},
	title = {Point de vue des citoyens sur le consentement à l’utilisation des données de santé en recherche – {Projet} {CLARET}},
	url = {https://www.youtube.com/watch?v=iyL-VB9aCUE&t=10s},
	author = {Dault, Roxanne and Cumyn, Annabelle},
	month = jan,
	year = {2020},
	keywords = {CLARET\_PRESENTATION\_PHASE1, Presentation},
}

@article{parfenova_impact_2020,
	title = {Impact of an {Educational} {Pamphlet} on {Knowledge} about {Health} {Risks} after {Hypertensive} {Disorders} of {Pregnancy}:  {A} {Randomized} {Trial}},
	volume = {43},
	url = {https://doi.org/10.1016/j.jogc.2020.07.008},
	abstract = {Objective
To evaluate patients’ knowledge, risk perception, and anxiety about future health risks after an episode of hypertensive disorder of pregnancy (HDP), as well as their satisfaction with an educational pamphlet.

Methods
From January 2016 to June 2017, participants were randomly assigned to one of 2 groups and asked to complete questionnaire \#1 (demographics, knowledge, risk perception, anxiety, and satisfaction) after receiving medical counselling at the HDP postpartum clinic. Participants in the intervention group then received the educational pamphlet. One month later, both groups completed the questionnaire again (questionnaire \#2). The primary outcome of this study was improvement in the global knowledge score at 1 month, reflecting improved understanding of the health risks of HDP. Secondary outcomes included retention of information, risk perception, satisfaction, and anxiety level.

Results
Of 137 eligible women, 57 were randomly assigned to the intervention group and 56, to the control group. Participants in both groups had similar baseline characteristics. Thirteen percent of participants did not complete questionnaire \#2. The knowledge score was higher in the intervention group than the control group at 1 month, (88.2\%; 95\% confidence interval [CI] 26.37–28.32 and 71.3\%; 95\% CI 20.78–23.45, respectively [ P {\textless}0.0001]). No difference was seen in anxiety level between the groups (4.0 ± 1.00 vs. 3.8 ± 0.92; P = 0.6746). The intervention group was highly satisfied with the medical counselling they received (5.5 ± 0.84 out 6) and with the pamphlet (5.6 ± 0.66 out 6).

Conclusion
The educational pamphlet increased women's knowledge about future health risks of HDP without increasing anxiety and it may be helpful in promoting lifestyle changes necessary to modify these risks.},
	number = {2},
	journal = {Journal of Obstetrics and Gynaecology Canada},
	author = {Parfenova, Maria and Côté, Anne-Marie and Cumyn, Annabelle and Pesant, Marie-Hélène and Champagne, Myriam and Roy-Lacroix, Marie-Ève and Malick, Mandy and Sauvé, Nadine},
	year = {2020},
	keywords = {Journal Article},
	pages = {182--190},
}

Objective To evaluate patients’ knowledge, risk perception, and anxiety about future health risks after an episode of hypertensive disorder of pregnancy (HDP), as well as their satisfaction with an educational pamphlet. Methods From January 2016 to June 2017, participants were randomly assigned to one of 2 groups and asked to complete questionnaire #1 (demographics, knowledge, risk perception, anxiety, and satisfaction) after receiving medical counselling at the HDP postpartum clinic. Participants in the intervention group then received the educational pamphlet. One month later, both groups completed the questionnaire again (questionnaire #2). The primary outcome of this study was improvement in the global knowledge score at 1 month, reflecting improved understanding of the health risks of HDP. Secondary outcomes included retention of information, risk perception, satisfaction, and anxiety level. Results Of 137 eligible women, 57 were randomly assigned to the intervention group and 56, to the control group. Participants in both groups had similar baseline characteristics. Thirteen percent of participants did not complete questionnaire #2. The knowledge score was higher in the intervention group than the control group at 1 month, (88.2%; 95% confidence interval [CI] 26.37–28.32 and 71.3%; 95% CI 20.78–23.45, respectively [ P \textless0.0001]). No difference was seen in anxiety level between the groups (4.0 ± 1.00 vs. 3.8 ± 0.92; P = 0.6746). The intervention group was highly satisfied with the medical counselling they received (5.5 ± 0.84 out 6) and with the pamphlet (5.6 ± 0.66 out 6). Conclusion The educational pamphlet increased women's knowledge about future health risks of HDP without increasing anxiety and it may be helpful in promoting lifestyle changes necessary to modify these risks.

@article{cote-poirier_evaluation_2020,
	title = {Evaluation of {Complications} in {Postpartum} {Women} {Receiving} {Therapeutic} {Anticoagulation}},
	volume = {136},
	issn = {0029-7844},
	url = {https://journals.lww.com/greenjournal/fulltext/2020/08000/evaluation_of_complications_in_postpartum_women.26.aspx},
	abstract = {OBJECTIVE: 

To evaluate complications associated with early postpartum therapeutic anticoagulation.

METHODS:

A multicenter retrospective cohort study was done to evaluate the association between therapeutic anticoagulation postpartum and major complications (hemorrhagic and wound complications). Secondary outcomes included minor complications, risk factors associated with total complications (including the time to therapeutic anticoagulation resumption after delivery) and recurrent thrombotic events within 6 weeks postpartum.

RESULTS:

From 2003 to 2015, 232 consecutive women were treated with therapeutic anticoagulation within 96 hours postpartum; among those treated, 91 received unfractionated heparin, 138 received low-molecular-weight heparin, and three received other anticoagulants. The primary outcome, a composite of major hemorrhagic complications (requiring transfusion, hospitalization, volume resuscitation, transfer to intensive care unit, or surgery) and major wound complications, occurred in 7 of 83 (8.4\%) for cesarean deliveries and 9 of 149 (6.0\%) for vaginal deliveries (P=.490). Total complications (including major and minor hemorrhagic and wound complications) occurred in 13 of 83 (15.7\%) for cesarean deliveries compared with 9 of 149 (6.0\%) for vaginal deliveries (P=.016). When comparing cases associated with and without complications, the median delay before resuming anticoagulation was significantly shorter for both cesarean (12 vs 33 hours, P=.033) and vaginal deliveries (6 vs 19 hours, P=.006). For vaginal deliveries, 8 of 51 (15.7\%) women had complications when anticoagulation was started before 9.25 hours postpartum, compared with 1 of 98 (1.0\%) when started after 9.25 hours. For cesarean deliveries, 7 of 21 (33.3\%) of women experienced complications compared with 6 of 62 (9.7\%) if anticoagulation was started before or after 15.1 hours, respectively. Two (0.9\%) episodes of venous thromboembolism occurred within 6 weeks postpartum.

CONCLUSION:

Among postpartum women who received early therapeutic anticoagulation, major complications occurred in 8.4\% for cesarean deliveries and 6.0\% for vaginal deliveries. Complications were associated with earlier resumption of therapeutic anticoagulation, particularly before 9.25 hours for vaginal deliveries and before 15.1 hours for cesarean deliveries.},
	number = {2},
	journal = {Obstetrics \& Gynecology},
	author = {Côté-Poirier, Gabrielle and Bettache, Nazila and Côté, Anne-Marie and Mahone, Michèle and Morin, Francine and Cumyn, Annabelle and Bureau, Yves-André and Malick, Mandy and Sauvé, Nadine},
	year = {2020},
	keywords = {Journal Article},
}

OBJECTIVE: To evaluate complications associated with early postpartum therapeutic anticoagulation. METHODS: A multicenter retrospective cohort study was done to evaluate the association between therapeutic anticoagulation postpartum and major complications (hemorrhagic and wound complications). Secondary outcomes included minor complications, risk factors associated with total complications (including the time to therapeutic anticoagulation resumption after delivery) and recurrent thrombotic events within 6 weeks postpartum. RESULTS: From 2003 to 2015, 232 consecutive women were treated with therapeutic anticoagulation within 96 hours postpartum; among those treated, 91 received unfractionated heparin, 138 received low-molecular-weight heparin, and three received other anticoagulants. The primary outcome, a composite of major hemorrhagic complications (requiring transfusion, hospitalization, volume resuscitation, transfer to intensive care unit, or surgery) and major wound complications, occurred in 7 of 83 (8.4%) for cesarean deliveries and 9 of 149 (6.0%) for vaginal deliveries (P=.490). Total complications (including major and minor hemorrhagic and wound complications) occurred in 13 of 83 (15.7%) for cesarean deliveries compared with 9 of 149 (6.0%) for vaginal deliveries (P=.016). When comparing cases associated with and without complications, the median delay before resuming anticoagulation was significantly shorter for both cesarean (12 vs 33 hours, P=.033) and vaginal deliveries (6 vs 19 hours, P=.006). For vaginal deliveries, 8 of 51 (15.7%) women had complications when anticoagulation was started before 9.25 hours postpartum, compared with 1 of 98 (1.0%) when started after 9.25 hours. For cesarean deliveries, 7 of 21 (33.3%) of women experienced complications compared with 6 of 62 (9.7%) if anticoagulation was started before or after 15.1 hours, respectively. Two (0.9%) episodes of venous thromboembolism occurred within 6 weeks postpartum. CONCLUSION: Among postpartum women who received early therapeutic anticoagulation, major complications occurred in 8.4% for cesarean deliveries and 6.0% for vaginal deliveries. Complications were associated with earlier resumption of therapeutic anticoagulation, particularly before 9.25 hours for vaginal deliveries and before 15.1 hours for cesarean deliveries.

@inproceedings{fabry_questo_2020,
	address = {Bolzano, Italie},
	series = {{CEUR} {Workshop} {Proceedings}},
	title = {{QUESTO} – {An} ontology for questionnaires},
	volume = {2807},
	url = {https://hal.archives-ouvertes.fr/hal-03053318},
	booktitle = {{ICBO}{\textbar}{ODLS} 2020 {International} {Conference} on {Biomedical} {Ontologies} 2020},
	publisher = {CEUR-WS.org},
	author = {Fabry, Paul and Barton, Adrien and Ethier, Jean-François},
	month = sep,
	year = {2020},
	keywords = {Conference Paper, Directive information entity, Document, FRQS-Résumés et notes publiés, Information content entity, Questionnaire, ontologie},
	pages = {B.1--12},
}

@misc{cumyn_consentement_2019,
	type = {Présentation orale},
	title = {Le consentement à l'utilisation des données de santé pour la recherche : {CLARET}},
	author = {Cumyn, Annabelle and Barton, Adrien and Ethier, Jean-François},
	month = apr,
	year = {2019},
	keywords = {CLARET\_PRESENTATION\_PHASE1, FRQS-Présentations orales ou par affiche, Presentation},
}

@misc{barton_initiative_2019,
	address = {Québec, Canada},
	type = {Présentation par affiche},
	title = {Initiative {CLARET} : {Consentement} pour l'utilisation secondaire des données médicales en recherche},
	author = {Barton, Adrien and Cumyn, Annabelle and Dault, Roxanne and Cloutier, Anne-Marie and Ethier, Jean-François},
	month = jun,
	year = {2019},
	keywords = {CLARET\_AFFICHE\_PHASE1, FRQS-Présentations orales ou par affiche, Presentation},
}

@misc{cumyn_point_2019,
	address = {Québec, Canada},
	title = {Le point de vue des citoyens quant à l'utilisation des données de santé pour la recherche},
	author = {Cumyn, Annabelle and Barton, Adrien and Ethier, Jean-François},
	month = oct,
	year = {2019},
	keywords = {CLARET\_PRESENTATION\_PHASE1, FRQS-Présentations orales ou par affiche, Presentation},
}

@misc{ethier_learning_2019,
	address = {Vancouver, Canada},
	title = {Learning health systems: challenges and opportunities},
	author = {Ethier, Jean-François},
	year = {2019},
	keywords = {FRQS-Communications à titre de conférencier invité, Presentation},
}

@article{cumyn_informed_2019,
	title = {Informed consent within a learning health system: {A} scoping review},
	volume = {4},
	issn = {2379-6146},
	shorttitle = {Informed consent within a learning health system},
	url = {https://doi.org/10.1002/lrh2.10206},
	doi = {10.1002/lrh2.10206},
	abstract = {Introduction: A major consideration for the implementation of a learning health system (LHS) is consent from participants to the use of their data for research purposes. The main objective of this paper was to identify in the literature which types of consent have been proposed for participation in research observational activities in a LHS. We were particularly interested in understanding which approaches were seen as most feasible and acceptable and in which context, in order to inform the development of a Quebec-based LHS.
METHODS: Using a scoping review methodology, we searched scientific and legal databases as well as the gray literature using specific terms. Full-text articles were reviewed independently by two authors on the basis of the following concepts: (a) LHS and (b) approach to consent. The selected papers were imported in NVivo software for analysis in the light of a conceptual framework that distinguishes various, largely independent dimensions of consent.
RESULTS: A total of 93 publications were analysed for this review. Several studies reach opposing conclusions concerning the best approach to consent within a LHS. However, in the light of the conceptual framework we developed, we found that many of these results are distorted by the conflation between various characteristics of consent. Thus, when these characteristics are distinguished, the results mainly suggest the prime importance of the communication process, by contrast to the scope of consent or the kind of action required by participants (opt-in/opt-out). We identified two models of consent that were especially relevant for our purpose: metaconsent and dynamic consent.
CONCLUSIONS: Our review shows the importance of distinguishing carefully the various features of the consent process. It also suggests that the metaconsent model is a valuable model within a LHS, as it addresses many of the issues raised with regards to feasibility and acceptability. We propose to complement this model by adding the modalities of the information process to the dimensions relevant in the metaconsent process.},
	language = {eng},
	number = {2},
	journal = {Learning Health Systems},
	author = {Cumyn, Annabelle and Barton, Adrien and Dault, Roxanne and Cloutier, Anne-Marie and Jalbert, Rosalie and Ethier, Jean-François},
	month = dec,
	year = {2019},
	keywords = {CLARET\_ARTICLE\_PHASE1, FRQS-Documents revus et publiés, Journal Article, approaches to consent, claret, health data research, learning health system, metaconsent},
	pages = {e10206},
}

Introduction: A major consideration for the implementation of a learning health system (LHS) is consent from participants to the use of their data for research purposes. The main objective of this paper was to identify in the literature which types of consent have been proposed for participation in research observational activities in a LHS. We were particularly interested in understanding which approaches were seen as most feasible and acceptable and in which context, in order to inform the development of a Quebec-based LHS. METHODS: Using a scoping review methodology, we searched scientific and legal databases as well as the gray literature using specific terms. Full-text articles were reviewed independently by two authors on the basis of the following concepts: (a) LHS and (b) approach to consent. The selected papers were imported in NVivo software for analysis in the light of a conceptual framework that distinguishes various, largely independent dimensions of consent. RESULTS: A total of 93 publications were analysed for this review. Several studies reach opposing conclusions concerning the best approach to consent within a LHS. However, in the light of the conceptual framework we developed, we found that many of these results are distorted by the conflation between various characteristics of consent. Thus, when these characteristics are distinguished, the results mainly suggest the prime importance of the communication process, by contrast to the scope of consent or the kind of action required by participants (opt-in/opt-out). We identified two models of consent that were especially relevant for our purpose: metaconsent and dynamic consent. CONCLUSIONS: Our review shows the importance of distinguishing carefully the various features of the consent process. It also suggests that the metaconsent model is a valuable model within a LHS, as it addresses many of the issues raised with regards to feasibility and acceptability. We propose to complement this model by adding the modalities of the information process to the dimensions relevant in the metaconsent process.

@article{cumyn_education_2019,
	title = {Education {Research}-{GIM}},
	volume = {14},
	shorttitle = {{CJGIM}},
	url = {http://dx.doi.org/10.22374/cjgim.v14i3.322},
	number = {3},
	journal = {Canadian Journal of General Internal Medicine},
	author = {Cumyn, Annabelle and Card, Sharon E. and Gibson, Paul},
	month = aug,
	year = {2019},
	keywords = {Journal Article},
	pages = {13--29},
}

@article{cumyn_mapping_2019,
	title = {Mapping of essential content of an obstetric medicine curriculum from the perspective of two groups},
	volume = {14},
	url = {https://cjgim.ca/index.php/csim/article/view/322},
	abstract = {Background


Obstetric Medicine is an area of expertise within General Internal Medicine (GIM) in Canada. Essential content for clinical rotations for GIM residents was identified by subject-matter experts (N=204 items). However, this work did not address the perspective of curriculum stakeholders.


Methods


Members of the Canadian GIM Specialty Committee (GIMSC) were surveyed to obtain their perspective on essential content that GIM residents should acquire in Obstetric Medicine.


Results


GIMSC members (N=14) selected “core content” which reduced the initial content blueprint by 72\%. Some sections of the blueprint were left largely unchanged (e.g., hypertensive disorders of pregnancy), whereas others were removed entirely (e.g., transplant medicine).


Interpretation


GIMSC were more selective than Canadian Obstetric Internists in choosing the essential content for GIM residents, with a moderate overall agreement of 78\% (kappa coefficient of 0.53). Comparison of perspectives and content mapping may provide useful validity evidence for further work.},
	number = {3},
	urldate = {2019-11-22},
	journal = {Canadian Journal of General Internal Medicine},
	author = {Cumyn, Annabelle and Card, Sharon E. and Gibson, Paul},
	month = aug,
	year = {2019},
	keywords = {Journal Article},
	pages = {13--20},
}

Background Obstetric Medicine is an area of expertise within General Internal Medicine (GIM) in Canada. Essential content for clinical rotations for GIM residents was identified by subject-matter experts (N=204 items). However, this work did not address the perspective of curriculum stakeholders. Methods Members of the Canadian GIM Specialty Committee (GIMSC) were surveyed to obtain their perspective on essential content that GIM residents should acquire in Obstetric Medicine. Results GIMSC members (N=14) selected “core content” which reduced the initial content blueprint by 72%. Some sections of the blueprint were left largely unchanged (e.g., hypertensive disorders of pregnancy), whereas others were removed entirely (e.g., transplant medicine). Interpretation GIMSC were more selective than Canadian Obstetric Internists in choosing the essential content for GIM residents, with a moderate overall agreement of 78% (kappa coefficient of 0.53). Comparison of perspectives and content mapping may provide useful validity evidence for further work.

@article{ibrahim_radiomics_2019,
	series = {From {Basic} {Science} to {Clinical} {Imaging}},
	title = {Radiomics analysis for clinical decision support in nuclear medicine},
	volume = {49},
	issn = {0001-2998},
	url = {http://www.sciencedirect.com/science/article/pii/S0001299819300546},
	doi = {10.1053/j.semnuclmed.2019.06.005},
	abstract = {Radiomics – the high-throughput computation of quantitative image features extracted from medical imaging modalities- can be used to aid clinical decision support systems in order to build diagnostic, prognostic, and predictive models, which could ultimately improve personalized management based on individual characteristics. Various tools for radiomic features extraction are available, and the field gained a substantial scientific momentum for standardization and validation. Radiomics analysis of molecular imaging is expected to provide more comprehensive description of tissues than that of currently used parameters. We here review the workflow of radiomics, the challenges the field currently faces, and its potential for inclusion in clinical decision support systems to maximize disease characterization, and to improve clinical decision-making. We also present guidelines for standardization and implementation of radiomics in order to facilitate its transition to clinical use.},
	language = {en},
	number = {5},
	urldate = {2020-04-09},
	journal = {Seminars in Nuclear Medicine},
	author = {Ibrahim, Abdalla and Vallieres, Martin and Woodruff, Henry and Primakov, Sergey and Beheshti, Mohsen and Keek, Simon and Refaee, Turkey and Sanduleanu, Sebastian and Walsh, Sean and Morin, Olivier and Lambin, Philippe and Hustinx, Roland and Mottaghy, Felix M.},
	month = sep,
	year = {2019},
	note = {Number: 5
Reporter: Seminars in Nuclear Medicine},
	keywords = {Journal Article},
	pages = {438--449},
}

Radiomics – the high-throughput computation of quantitative image features extracted from medical imaging modalities- can be used to aid clinical decision support systems in order to build diagnostic, prognostic, and predictive models, which could ultimately improve personalized management based on individual characteristics. Various tools for radiomic features extraction are available, and the field gained a substantial scientific momentum for standardization and validation. Radiomics analysis of molecular imaging is expected to provide more comprehensive description of tissues than that of currently used parameters. We here review the workflow of radiomics, the challenges the field currently faces, and its potential for inclusion in clinical decision support systems to maximize disease characterization, and to improve clinical decision-making. We also present guidelines for standardization and implementation of radiomics in order to facilitate its transition to clinical use.

@inproceedings{toyoshima_linking_2019,
	address = {Graz, Autriche},
	title = {Linking image schemas with affordances: {An} ontological approach},
	volume = {2518},
	copyright = {All rights reserved},
	url = {http://ceur-ws.org/Vol-2518/paper-CAOS5.pdf},
	abstract = {Affordances and image schemas are two building blocks of cognitive and
behavioral modeling. In this paper, we present initial steps towards an extension of
our dispositional view of affordances and effectivities to image schemas. In
particular, we consider image schemas as mental patterns that are, in most cases,
about classes of affordances and effectivities.},
	booktitle = {Proceedings of the 5th {Joint} {Ontology} {Workshops} ({JOWO} 2019)},
	publisher = {CEUR Workshop Proceedings},
	author = {Toyoshima, Fumiaki and Barton, Adrien},
	editor = {Seppälä, Selja and Porello, Daniele},
	month = dec,
	year = {2019},
	keywords = {Conference Paper, ontologie},
	pages = {1--9},
}

Affordances and image schemas are two building blocks of cognitive and behavioral modeling. In this paper, we present initial steps towards an extension of our dispositional view of affordances and effectivities to image schemas. In particular, we consider image schemas as mental patterns that are, in most cases, about classes of affordances and effectivities.

@misc{vallieres_medomics_2019,
	address = {Sherbrooke, Canada},
	title = {{MEDomics}: synergie entre analyse d’images médicales, apprentissage automatique, apprentissage profond, traitement automatique des langues naturelles et apprentissage distribué},
	language = {fr},
	author = {Vallieres, Martin},
	year = {2019},
	keywords = {Presentation},
}

@misc{fabry_labo_2019,
	address = {Buffalo, États-Unis},
	title = {{LABO}: an ontology for laboratory test prescription and reporting},
	abstract = {LABO is an ontology formalizing laboratory tests prescriptions and reporting documents. It is built according to the OBO Foundry methodology, and is a component of a core ontological model that aims to enable interoperability between various clinical data sources in the context of a Learning Health System.},
	language = {en},
	author = {Fabry, Paul and Barton, Adrien and Ethier, Jean-François},
	year = {2019},
	keywords = {FRQS-Présentations orales ou par affiche, Presentation, ontologie},
}

LABO is an ontology formalizing laboratory tests prescriptions and reporting documents. It is built according to the OBO Foundry methodology, and is a component of a core ontological model that aims to enable interoperability between various clinical data sources in the context of a Learning Health System.

@misc{barton_initiative_2018,
	address = {Québec, Canada},
	type = {Présentation par affiche},
	title = {Initiative {CLARET} : {Consentement} et {LittérAtie} pour la {Recherche} É{Thique}},
	author = {Barton, Adrien and Cumyn, Annabelle and Dault, Roxanne and Cloutier, Anne-Marie and Ethier, Jean-François},
	month = jun,
	year = {2018},
	keywords = {CLARET\_AFFICHE\_PHASE1, FRQS-Présentations orales ou par affiche, Presentation},
}

@misc{ethier_plateforme_2018,
	address = {Toronto, Canada},
	title = {Plateforme apprenante pour la recherche en santé et services sociaux — {PARS3} — {Learning} health and social services research platform},
	author = {Ethier, Jean-François},
	month = sep,
	year = {2018},
	keywords = {FRQS-Communications à titre de conférencier invité, Presentation},
}

@misc{beaudoin_initiative_2018,
	address = {Sherbrooke, Canada},
	type = {Présentation par affiche},
	title = {Initiative {CLARET} : consentement pour l'utilisation secondaire des données médicales en recherche},
	author = {Beaudoin, Andrée-Anne and Dault, Roxanne and Barton, Adrien and Cumyn, Annabelle and Cloutier, Anne-Marie and Ethier, Jean-François},
	month = sep,
	year = {2018},
	keywords = {CLARET\_AFFICHE\_PHASE1, FRQS-Présentations orales ou par affiche, Presentation},
}

@misc{dault_caracteriser_2018,
	address = {Longueuil, Canada},
	type = {Présentation par affiche},
	title = {Caractériser le processus de consentement à la recherche dans un système de santé apprenant},
	author = {Dault, Roxanne and Barton, Adrien and Cumyn, Annabelle and Cloutier, Anne-Marie and Ethier, Jean-François},
	month = apr,
	year = {2018},
	keywords = {CLARET\_AFFICHE\_PHASE1, FRQS-Présentations orales ou par affiche, Presentation},
}

@article{belzile_renal_2018,
	title = {Renal physiology and fluid and electrolyte disorders in pregnancy.},
	copyright = {Copyright (c) 2018. Published by Elsevier Ltd.},
	issn = {1532-1932 1521-6934},
	doi = {10.1016/j.bpobgyn.2018.11.008},
	abstract = {The majority of women are healthy entering pregnancy and do not require measurement of renal function or serum electrolytes. Clinicians must remain alert to the possibility of renal as well as fluid and electrolyte disorders in pregnancy, as the presenting complaints are often vague and mistaken for the normal physiology of pregnancy. In this chapter, our objectives are 1) to review  the renal physiology from a practical/clinical standpoint; 2) to provide the clinical obstetrician a case-based approach to fluid and electrolyte disorders commonly encountered in pregnancy; 3) to consolidate knowledge on renal physiology and fluid and electrolyte disorders in pregnancy with MCQs that are directly aligned with content; and 4) to highlight key practice points and present a research agenda.},
	language = {eng},
	journal = {Best practice \& research. Clinical obstetrics \& gynaecology},
	author = {Belzile, Maxime and Pouliot, Audrey and Cumyn, Annabelle and Cote, Anne Marie},
	month = dec,
	year = {2018},
	pmid = {30638905},
	keywords = {Diabetes insipidus, Hypokalemia, Hyponatremia, Journal Article, Pregnancy, Renal physiology},
}

The majority of women are healthy entering pregnancy and do not require measurement of renal function or serum electrolytes. Clinicians must remain alert to the possibility of renal as well as fluid and electrolyte disorders in pregnancy, as the presenting complaints are often vague and mistaken for the normal physiology of pregnancy. In this chapter, our objectives are 1) to review the renal physiology from a practical/clinical standpoint; 2) to provide the clinical obstetrician a case-based approach to fluid and electrolyte disorders commonly encountered in pregnancy; 3) to consolidate knowledge on renal physiology and fluid and electrolyte disorders in pregnancy with MCQs that are directly aligned with content; and 4) to highlight key practice points and present a research agenda.

@article{cumyn_role_2018,
	title = {Role of researchers in the ethical conduct of research: {A} discourse analysis from different stakeholder perspectives},
	volume = {0},
	issn = {1050-8422},
	shorttitle = {Role of {Researchers} in the {Ethical} {Conduct} of {Research}},
	url = {https://doi.org/10.1080/10508422.2018.1539671},
	doi = {10.1080/10508422.2018.1539671},
	abstract = {The ethical conduct of research rests largely on researchers, and as such, an understanding of how they perceive and enact their role in research is paramount. However, the literature around ethics and research mostly focuses on researchers’ perception of Research Ethics Boards (REB; also known as Institutional Review Boards) roles and functions. To fill that gap, we analyzed the perceptions of researchers, REB members, and influential parties (n = 40) about researchers’ role in the ethical conduct of research through discourse analysis. Three discourses emerged: researchers as reflective practitioners, protectors of participants, and technicians. Understanding the commonalities and differences among the discourses may foster a shared and compelling institutional research culture.},
	number = {0},
	urldate = {2019-04-29},
	journal = {Ethics \& Behavior},
	author = {Cumyn, Annabelle and Ouellet, Kathleen and Côté, Anne-Marie and Francoeur, Caroline and St-Onge, Christina},
	month = nov,
	year = {2018},
	keywords = {Journal Article, discourse analysis, ethical conduct of research, researchers},
	pages = {1--16},
}

The ethical conduct of research rests largely on researchers, and as such, an understanding of how they perceive and enact their role in research is paramount. However, the literature around ethics and research mostly focuses on researchers’ perception of Research Ethics Boards (REB; also known as Institutional Review Boards) roles and functions. To fill that gap, we analyzed the perceptions of researchers, REB members, and influential parties (n = 40) about researchers’ role in the ethical conduct of research through discourse analysis. Three discourses emerged: researchers as reflective practitioners, protectors of participants, and technicians. Understanding the commonalities and differences among the discourses may foster a shared and compelling institutional research culture.

@article{cumyn_validation_2018,
	title = {Validation of content of clinical cases in obstetric medicine for a shared web-based educational tool},
	issn = {1753-495X},
	url = {https://journals.sagepub.com/doi/10.1177/1753495X18804744},
	doi = {10.1177/1753495X18804744},
	abstract = {Subsequent to the validation of a Canadian Curriculum blueprint for Obstetric Medicine (OM), the Canadian Consensus for a Curriculum in Obstetric Medicine (CanCOM) research group was approached to develop 20 cases to address gaps in clinical exposure during clinical rotations in OM. Forty-nine Obstetric Internists were identified and 43 confirmed their affiliation to the group. Participants (N = 22) reviewed the content of the CanCOM blueprint and identified curriculum content that they considered essential for a rotation for senior General Internal Medicine residents. This survey led to the creation of the CanCOM II essential content blueprint for General Internal Medicine. Following this step, a second subgroup of participants (N = 21) participated in a Delphi survey to identify the content that should be addressed by a teaching case for senior General Internal Medicine residents. A high-level of consensus was obtained for 13 topics and a moderate level for the 7 subsequent topics resulting in the creation of the CanCOM II clinical cases available at http://gemoq.ca/cancom-ii-clinical-case-databank/},
	language = {en},
	journal = {Obstetric Medicine},
	author = {Cumyn, Annabelle and Gibson, Paul},
	month = nov,
	year = {2018},
	keywords = {Journal Article},
	pages = {1753495X18804744},
}

Subsequent to the validation of a Canadian Curriculum blueprint for Obstetric Medicine (OM), the Canadian Consensus for a Curriculum in Obstetric Medicine (CanCOM) research group was approached to develop 20 cases to address gaps in clinical exposure during clinical rotations in OM. Forty-nine Obstetric Internists were identified and 43 confirmed their affiliation to the group. Participants (N = 22) reviewed the content of the CanCOM blueprint and identified curriculum content that they considered essential for a rotation for senior General Internal Medicine residents. This survey led to the creation of the CanCOM II essential content blueprint for General Internal Medicine. Following this step, a second subgroup of participants (N = 21) participated in a Delphi survey to identify the content that should be addressed by a teaching case for senior General Internal Medicine residents. A high-level of consensus was obtained for 13 topics and a moderate level for the 7 subsequent topics resulting in the creation of the CanCOM II clinical cases available at http://gemoq.ca/cancom-ii-clinical-case-databank/

@inproceedings{barton_what_2018,
	address = {Newcastle, Royaume-Uni},
	title = {What is a risk? {A} formal representation of risk of stroke for people with atrial fibrillation},
	volume = {2137},
	url = {http://ceur-ws.org/Vol-2137/paper_38.pdf},
	booktitle = {Proceedings of the 8th {International} {Conference} on {Biomedical} {Ontology}},
	author = {Barton, Adrien and Jansen, Ludger and Rosier, Arnaud and Ethier, Jean-François},
	year = {2018},
	keywords = {Conference Paper, FRQS-Résumés et notes publiés, ontologie},
	pages = {1--6},
}

@misc{cossette_reduction_2017,
	address = {San Antonio, États-Unis},
	title = {Reduction in potentially inappropriate medication use in elderly inpatients: a pragmatic randomized controlled trial},
	author = {Cossette, Benoit and Ethier, Jean-François and Joly-Mischlich, Thomas and Bergeron, Josée and Ricard, Geneviève and Brazeau, Serge and Caron, Mathieu and Germain, Olivier and Payette, Hélène and Kaczorowski, Janusz and Levine, Mitchell},
	year = {2017},
	keywords = {FRQS-Résumés et notes publiés, Presentation},
}

@misc{ethier_learning_2017,
	title = {The learning health and social services research platform ({PARS3}). {Truly} putting the patient at the core},
	author = {Ethier, Jean-François},
	year = {2017},
	keywords = {FRQS-Communications à titre de conférencier invité, Presentation},
}

@techreport{khnaisser_unified_2017,
	address = {Sherbrooke, Canada},
	type = {Technical {Report}},
	title = {Unified bitemporal historicization framework},
	shorttitle = {{UBHF}},
	language = {English},
	institution = {Université de Sherbrooke (GRIIS)},
	author = {Khnaisser, Christina and Lavoie, Luc and Burgun, Anita and Ethier, Jean-François},
	year = {2017},
	keywords = {FRQS-Rapports de recherche, Report},
}

@misc{ethier_recherche_2017,
	address = {Québec, Canada},
	title = {La recherche à partir des dossiers médicaux électroniques ({DMÉ}) dans un système de santé apprenant : défis et opportunités},
	url = {https://www.youtube.com/watch?v=SDVCKpSyYBE},
	author = {Ethier, Jean-François},
	year = {2017},
	keywords = {FRQS-Communications à titre de conférencier invité, Presentation},
}

@inproceedings{barton_two_2016,
	address = {Amsterdam, Pays-Bas},
	title = {The two ontological faces of velocity},
	volume = {283},
	url = {http://ebooks.iospress.com/volumearticle/44240},
	booktitle = {Formal {Ontology} in {Information} {Systems}. {Proceedings} of the 9th {International} {Conference} ({FOIS} 2016)},
	publisher = {IOS Press},
	author = {Barton, Adrien and Ethier, Jean-François},
	editor = {Ferrario, Roberta and Kuhn, Werner},
	year = {2016},
	keywords = {Book Section, FRQS-Contributions publiées à un ouvrage collectif ou aux chapitres d'un livre, ontologie},
	pages = {123--136},
}

@misc{taseen_prescribing_2016,
	address = {Oregon, États-Unis},
	title = {On prescribing drug prescriptions},
	author = {Taseen, Ryeyan and Ethier, Jean-François and Barton, Adrien},
	month = aug,
	year = {2016},
	keywords = {FRQS-Présentations orales ou par affiche, Presentation},
}

@phdthesis{khnaisser_methode_2016,
	address = {Sherbrooke, Canada},
	type = {Mémoire de maitrise},
	title = {Méthode de construction d'entrepôt de données temporalisé pour un système informationnel de santé},
	url = {http://savoirs.usherbrooke.ca/handle/11143/8386},
	abstract = {Des systèmes informationnels de santé (SIS) ont été mis en place au cours des 20 dernières
années pour soutenir les processus de soins, les tâches administratives et les activités de
recherche ainsi que pour assurer la gestion raisonnée des établissements de santé. Un entrepôt
de données (ED) doit être créé à partir de nombreuses sources de données hétérogènes afin de
rendre les données exploitables d’une façon uniforme au sein des SIS. La temporalisation de
cet entrepôt est rapidement devenue un enjeu crucial afin de garder les traces de l’évolution
des données et d’améliorer la prise de décision clinique. L’entrepôt de données temporalisé
(EDT) requiert l’application de règles systématiques afin de garantir l’intégrité et la qualité
des données. Générer le schéma temporel d’un EDT est une tâche complexe. Plusieurs
questions se posent dès lors, dont celles-ci : (a) Quel modèle temporel est le mieux adapté à
l’automatisation de la construction d’un EDT (plus particulièrement dans le domaine de la
santé)? (b) Quelles propriétés peut-on garantir formellement, suite à cette construction?
D’une part, le volume du schéma de données nécessite d’importantes ressources humaines et
financières, et d’autre part, plusieurs modèles temporels existent, mais ils ne sont pas
formalisés ou non généraux. Les concepteurs s’en remettent donc le plus souvent à des règles
de pratiques variées, floues, incomplètes et non validées. Dans ce travail, un cadre de
référence permettant de formaliser, de généraliser et d’opérationnaliser des modèles
temporels est défini. Deux modèles : BCDM et TRM sont présentés selon le cadre de
référence avec leurs contraintes d’intégrité, leurs algorithmes de construction et une liste des
prolongements requis. Il en résulte qu’il est désormais possible de s’affranchir des règles de
pratique imprécises et de temporaliser un entrepôt en se fondant sur une méthode rigoureuse
aux propriétés démontrables basées sur des critères fondamentaux (théorie relationnelle), des
critères de conception reconnus et explicites (normalisation).},
	language = {fr},
	urldate = {2016-07-21},
	school = {Université de Sherbrooke},
	author = {Khnaisser, Christina and {Lavoie L (dir.) et Ethier J-F (dir.)}},
	collaborator = {Lavoie, Luc and Ethier, Jean-François},
	year = {2016},
	doi = {http://hdl.handle.net/11143/8386},
	keywords = {FRQS-Thèses et mémoires, Thesis},
}

Des systèmes informationnels de santé (SIS) ont été mis en place au cours des 20 dernières années pour soutenir les processus de soins, les tâches administratives et les activités de recherche ainsi que pour assurer la gestion raisonnée des établissements de santé. Un entrepôt de données (ED) doit être créé à partir de nombreuses sources de données hétérogènes afin de rendre les données exploitables d’une façon uniforme au sein des SIS. La temporalisation de cet entrepôt est rapidement devenue un enjeu crucial afin de garder les traces de l’évolution des données et d’améliorer la prise de décision clinique. L’entrepôt de données temporalisé (EDT) requiert l’application de règles systématiques afin de garantir l’intégrité et la qualité des données. Générer le schéma temporel d’un EDT est une tâche complexe. Plusieurs questions se posent dès lors, dont celles-ci : (a) Quel modèle temporel est le mieux adapté à l’automatisation de la construction d’un EDT (plus particulièrement dans le domaine de la santé)? (b) Quelles propriétés peut-on garantir formellement, suite à cette construction? D’une part, le volume du schéma de données nécessite d’importantes ressources humaines et financières, et d’autre part, plusieurs modèles temporels existent, mais ils ne sont pas formalisés ou non généraux. Les concepteurs s’en remettent donc le plus souvent à des règles de pratiques variées, floues, incomplètes et non validées. Dans ce travail, un cadre de référence permettant de formaliser, de généraliser et d’opérationnaliser des modèles temporels est défini. Deux modèles : BCDM et TRM sont présentés selon le cadre de référence avec leurs contraintes d’intégrité, leurs algorithmes de construction et une liste des prolongements requis. Il en résulte qu’il est désormais possible de s’affranchir des règles de pratique imprécises et de temporaliser un entrepôt en se fondant sur une méthode rigoureuse aux propriétés démontrables basées sur des critères fondamentaux (théorie relationnelle), des critères de conception reconnus et explicites (normalisation).

@inproceedings{madar_targeting_2016,
	address = {Ottawa, Canada},
	title = {Targeting gaps in the quality of care for patients with diabetes in community chronic care programs},
	author = {Madar, Houssein Mohamed and Brown, C and Baillargeon, J-P and Langlois, M-F},
	month = oct,
	year = {2016},
	keywords = {Conference Paper},
}

@phdthesis{camirand_lemyre_sur_2016,
	address = {Sherbrooke, Canada},
	type = {Thèse de doctorat},
	title = {Sur des estimateurs et des tests non-paramétriques pour des distributions et copules conditionnelles},
	url = {https://savoirs.usherbrooke.ca/handle/11143/9517},
	abstract = {Pour modéliser un vecteur aléatoire en présence d'une co-variable, on peut d'abord faire appel à la fonction de répartition conditionnelle. En effet, cette dernière contient toute l'information ayant trait au comportement du vecteur étant donné une valeur prise par la co-variable. Il peut aussi être commode de séparer l'étude du comportement conjoint du vecteur de celle du comportement individuel de chacune de ses composantes. Pour ce faire, on utilise la copule conditionnelle, qui caractérise complètement la dépendance conditionnelle régissant les différentes associations entre les variables. Dans chacun des cas, la mise en oeuvre d'une stratégie d'estimation et d'inférence s'avère une étape essentielle à leur utilisant en pratique. Lorsqu'aucune information n'est disponible a priori quant à un choix éventuel de modèle, il devient pertinent d'opter pour des méthodes non-paramétriques. Le premier article de cette thèse, co-écrit par Jean-François Quessy et moi-même, propose une façon de ré-échantillonner des estimateurs non-paramétriques pour des distributions conditionnelles. Cet article a été publié dans la revue Statistics and Computing. En autres choses, nous y montrons comment obtenir des intervalles de confiance pour des statistiques s'écrivant en terme de la fonction de répartition conditionnelle. Le second article de cette thèse, co-écrit par Taoufik Bouezmarni, Jean-François Quessy et moi-même, s'affaire à étudier deux estimateurs non-paramétriques de la copule conditionnelles, proposés par Gijbels et coll. en présence de données sérielles. Cet article a été soumis dans la revue Statistics and Probability Letters. Nous identifions la distribution asymptotique de chacun de ces estimateurs pour des données mélangeantes. Le troisième article de cette thèse, co-écrit par Taoufik Bouezmarni, Jean-François Quessy et moi-même, propose une nouvelle façon d'étudier les relations de causalité entre deux séries chronologiques. Cet article a été soumis dans la revue Electronic Journal of Statistics. Dans cet article, nous utilisons la copule conditionnelle pour caractériser une version locale de la causalité au sens de Granger. Puis, nous proposons des mesures de causalité basées sur la copule conditionnelle. Le quatrième article de cette thèse, co-écrit par Taoufik Bouezmarni, Anouar El Ghouch et moi-même, propose une méthode qui permette d'estimer adéquatement la copule conditionnelle en présence de données incomplètes. Cet article a été soumis dans la revue Scandinavian Journal of Statistics. Les propriétés asymptotiques de l'estimateur proposé y sont aussi étudiées. Finalement, la dernière partie de cette thèse contient un travail inédit, qui porte sur la mise en oeuvre de tests statistiques permettant de déterminer si deux copules conditionnelles sont concordantes. En plus d'y présenter des résultats originaux, cette étude illustre l'utilité des techniques de ré-échantillonnage développées dans notre premier article.},
	school = {Université de Sherbrooke},
	author = {Camirand Lemyre, Félix},
	year = {2016},
	keywords = {Copule conditionnelle, Covariable, Rho de Spearman, Tau de Kendall, Thesis},
}

Pour modéliser un vecteur aléatoire en présence d'une co-variable, on peut d'abord faire appel à la fonction de répartition conditionnelle. En effet, cette dernière contient toute l'information ayant trait au comportement du vecteur étant donné une valeur prise par la co-variable. Il peut aussi être commode de séparer l'étude du comportement conjoint du vecteur de celle du comportement individuel de chacune de ses composantes. Pour ce faire, on utilise la copule conditionnelle, qui caractérise complètement la dépendance conditionnelle régissant les différentes associations entre les variables. Dans chacun des cas, la mise en oeuvre d'une stratégie d'estimation et d'inférence s'avère une étape essentielle à leur utilisant en pratique. Lorsqu'aucune information n'est disponible a priori quant à un choix éventuel de modèle, il devient pertinent d'opter pour des méthodes non-paramétriques. Le premier article de cette thèse, co-écrit par Jean-François Quessy et moi-même, propose une façon de ré-échantillonner des estimateurs non-paramétriques pour des distributions conditionnelles. Cet article a été publié dans la revue Statistics and Computing. En autres choses, nous y montrons comment obtenir des intervalles de confiance pour des statistiques s'écrivant en terme de la fonction de répartition conditionnelle. Le second article de cette thèse, co-écrit par Taoufik Bouezmarni, Jean-François Quessy et moi-même, s'affaire à étudier deux estimateurs non-paramétriques de la copule conditionnelles, proposés par Gijbels et coll. en présence de données sérielles. Cet article a été soumis dans la revue Statistics and Probability Letters. Nous identifions la distribution asymptotique de chacun de ces estimateurs pour des données mélangeantes. Le troisième article de cette thèse, co-écrit par Taoufik Bouezmarni, Jean-François Quessy et moi-même, propose une nouvelle façon d'étudier les relations de causalité entre deux séries chronologiques. Cet article a été soumis dans la revue Electronic Journal of Statistics. Dans cet article, nous utilisons la copule conditionnelle pour caractériser une version locale de la causalité au sens de Granger. Puis, nous proposons des mesures de causalité basées sur la copule conditionnelle. Le quatrième article de cette thèse, co-écrit par Taoufik Bouezmarni, Anouar El Ghouch et moi-même, propose une méthode qui permette d'estimer adéquatement la copule conditionnelle en présence de données incomplètes. Cet article a été soumis dans la revue Scandinavian Journal of Statistics. Les propriétés asymptotiques de l'estimateur proposé y sont aussi étudiées. Finalement, la dernière partie de cette thèse contient un travail inédit, qui porte sur la mise en oeuvre de tests statistiques permettant de déterminer si deux copules conditionnelles sont concordantes. En plus d'y présenter des résultats originaux, cette étude illustre l'utilité des techniques de ré-échantillonnage développées dans notre premier article.

@incollection{khnaisser_data_2015,
	series = {Communications in {Computer} and {Information} {Science}},
	title = {Data warehouse design methods review: {Trends}, challenges and future directions for the healthcare domain},
	copyright = {©2015 Springer International Publishing Switzerland},
	isbn = {978-3-319-23200-3 978-3-319-23201-0},
	shorttitle = {Data {Warehouse} {Design} {Methods} {Review}},
	url = {http://link.springer.com/chapter/10.1007/978-3-319-23201-0_10},
	language = {en},
	number = {539},
	urldate = {2015-09-15},
	booktitle = {New {Trends} in {Databases} and {Information} {Systems}},
	publisher = {Springer International Publishing},
	author = {Khnaisser, Christina and Lavoie, Luc and Diab, Hassan and Ethier, Jean-François},
	editor = {Morzy, Tadeusz and Valduriez, Patrick and Bellatreche, Ladjel},
	year = {2015},
	note = {DOI 10.1007/978-3-319-23201-0\_10},
	keywords = {Artificial Intelligence (incl. Robotics), Bioinformatics, Book Section, Data Mining and Knowledge Discovery, Database Management, FRQS-Contributions publiées à un ouvrage collectif ou aux chapitres d'un livre, Information Storage and Retrieval, Information Systems Applications (incl. Internet), Medical Informatics, Secondary data use, clinical data warehouse, data warehouse design},
	pages = {76--87},
}

@misc{khnaisser_architecture_2015,
	address = {Sherbrooke, Canada},
	type = {Présentation par affiche},
	title = {Architecture et méthode de construction d’entrepôts de données au coeur des systèmes informationnels régionaux de santé.},
	author = {Khnaisser, Christina and Lavoie, Luc and Diab, Hassan and Ethier, Jean-François},
	year = {2015},
	keywords = {FRQS-Présentations orales ou par affiche, Presentation},
}

@misc{khnaisser_etude_2015,
	address = {Sherbrooke, Canada},
	type = {Présentation par affiche},
	title = {Étude comparative des modèles temporels {BCDM} et {DDLM} dans le contexte d’entrepôt de données.},
	author = {Khnaisser, Christina and Lavoie, Luc and Burgun, Anita and Ethier, Jean-François},
	year = {2015},
	keywords = {FRQS-Présentations orales ou par affiche, Presentation},
}

@inproceedings{khnaisser_data_2015-1,
	title = {Data {Warehouse} {Design} {Methods} {Review}: {Trends}, {Challenges} and {Future} {Directions} for the {Healthcare} {Domain}},
	isbn = {978-3-319-23201-0},
	abstract = {In secondary data use context, traditional data warehouse design methods don't address many of today's challenges; particularly in the healthcare domain were semantics plays an essential role to achieve an effective and implementable heterogeneous data integration while satisfying core requirements. Forty papers were selected based on seven core requirements: data integrity, sound temporal schema design, query expressiveness, heterogeneous data integration, knowledge/source evolution integration, traceability and guided automation. Proposed methods were compared based on twenty-two comparison criteria. Analysis of the results shows important trends and challenges, among them (1) a growing number of methods unify knowledge with source structure to obtain a well-defined data warehouse schema built on semantic integration; (2) none of the published methods cover all the core requirements as a whole and (3) their potential in real world is not demonstrated yet.},
	booktitle = {New {Trends} in {Databases} and {Information} {Systems}},
	publisher = {Springer International Publishing},
	author = {Khnaisser, Christina and Lavoie, Luc and Diab, Hassan and Ethier, Jean-François},
	editor = {Morzy, Tadeusz and Valduriez, Patrick and Bellatreche, Ladjel},
	year = {2015},
	keywords = {Conference Paper},
	pages = {76--87},
}

In secondary data use context, traditional data warehouse design methods don't address many of today's challenges; particularly in the healthcare domain were semantics plays an essential role to achieve an effective and implementable heterogeneous data integration while satisfying core requirements. Forty papers were selected based on seven core requirements: data integrity, sound temporal schema design, query expressiveness, heterogeneous data integration, knowledge/source evolution integration, traceability and guided automation. Proposed methods were compared based on twenty-two comparison criteria. Analysis of the results shows important trends and challenges, among them (1) a growing number of methods unify knowledge with source structure to obtain a well-defined data warehouse schema built on semantic integration; (2) none of the published methods cover all the core requirements as a whole and (3) their potential in real world is not demonstrated yet.

@inproceedings{mcgilchrist_transform_2015,
	address = {San Francisco, États-Unis},
	title = {{TRANSFoRm}: {Connectivity} infrastructure to embed {eCRFs} into {EHRs}},
	booktitle = {{AMIA} {CRI} 2015},
	author = {McGilchrist, Mark M. and Curcin, Vasa and Ethier, Jean-François and Arvanitis, Theodoros N. and Delaney, Brendan C.},
	year = {2015},
	keywords = {Conference Paper, FRQS-Résumés et notes publiés},
}

@inproceedings{lim_choi_keung_semantic_2015,
	address = {San Francisco, États-Unis},
	title = {Semantic enrichment of {CDISC} operational data model},
	url = {http://wrap.warwick.ac.uk/70272/},
	booktitle = {{AMIA} {Joint} {Summits} on {Translational} {Science} proceedings {AMIA} {Summit} on {Translational} {Science}},
	publisher = {American Medical Informatics Association},
	author = {Lim Choi Keung, Sarah Niukyun and Zhao, Lei and Ethier, Jean-François and Curcin, Vasa and Burgun, Anita and Delaney, B. C. and Arvanitis, Theodoros N.},
	year = {2015},
	keywords = {Conference Paper, FRQS-Résumés et notes publiés},
}

@misc{ethier_learning_2015,
	address = {Montréal, Canada},
	title = {Learning {Health} {Systems} — {LHS}: {La} recherche translationnelle sous l'angle des données de santé pragmatiques provenant du terrain},
	author = {Ethier, Jean-François},
	year = {2015},
	keywords = {FRQS-Communications à titre de conférencier invité, Presentation},
}

@misc{khnaisser_generation_2014,
	address = {Sherbrooke, Canada},
	type = {Présentation par affiche},
	title = {Génération automatisée de schémas relationnels bitemporels dans un contexte d’entrepôt de données},
	author = {Khnaisser, Christina and Lavoie, Luc and Burgun, Anita and Ethier, Jean-François},
	year = {2014},
	keywords = {FRQS-Présentations orales ou par affiche, Presentation},
}

@inproceedings{barton_cardiovascular_2014,
	title = {The {Cardiovascular} {Disease} {Ontology}},
	url = {https://www.researchgate.net/publication/269404044_The_Cardiovascular_Disease_Ontology},
	urldate = {2017-08-23},
	booktitle = {Proceedings of the eighth conference ({FOIS} 2014).{Conference} on {Formal} {Ontology} in {Information} {Systems}, {Rio} de {Janeiro}, {Brésil}.},
	publisher = {IOS Press},
	author = {Barton, Adrien and Rosier, Arnaud and Burgun, Anita and Ethier, Jean-François},
	year = {2014},
	keywords = {Conference Paper, FRQS-Résumés et notes publiés},
	pages = {409--414},
}

@misc{curcin_semantic_2014,
	address = {Lisbonne, Portugal},
	title = {Semantic approach to achieving interoperability between clinical care and clinical research},
	url = {http://wrap.warwick.ac.uk/id/eprint/70294},
	author = {Curcin, Vasa and Arvanitis, Theodoros N. and Ethier, Jean-François and Fraczkowsk, Kazimierz and Kazienko, Przemyslaw and Brodka, Piotr and Andreasson, Anna and Blizniuk, Grzegorz and Lim Choi Keung, Sarah Niukyun and Zhao, Lei and Misiaszek, Andrzej and McGilchrist, Mark M. and Delaney, B. C. and Burgun, Anita},
	year = {2014},
	keywords = {FRQS-Présentations orales ou par affiche, Presentation},
}

@misc{ecarot_optimal_2014,
	address = {Phoenix, États-Unis},
	title = {Optimal resources allocation for distributed and connected {Clouds}},
	author = {Ecarot, Thibaud and Zeghlache, D. and Brandily, C.},
	year = {2014},
	keywords = {Presentation},
}