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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.

The notion of services, although intuitive and used in many domains, is difficult to define from an ontological point of view. However, a formal representation of services would be particularly relevant in the healthcare and social services domain to support domain ontology alignment. In this article we draw on previous ontological work about services to propose an adaptation focused on Basic Formal Ontology and ontologies from the biomedical domain. We provide definitions and axioms following the OBO Foundry methodology with a focus on informational entities. This ontological model is a first step towards a better integration of existing domain ontologies in a healthcare services framework.

We propose an axiomatic ontological framework for informational templates based on former works on slot-mereology. Templates and their parts can be filled by information content entities, but can exist even if unfilled. Thus, we represent templates as slots that can themselves have slots, where the "slot of" relation between slots can be interpreted as a parthood relation. Some slots of a slot are mandatory and need to be filled for the parent slot to be filled, whereas others are optional and do not have this restriction. The structure of a filler is also described by slots of a different nature. We discuss how parthood between slots can be connected with parthood between their fillers.

We take initial steps towards a meticulous analysis of functions (including the so-called "use function") within a recently proposed, unifying dispositional framework for realizable entities in Basic Formal Ontology (BFO). Our approach to function is strikingly characterized by an ontology of "extrinsic dispositions", which are realizable entities outside the BFO category of disposition. This work helps to articulate multiple possible senses of the term "function" within BFO and to deepen the understanding of the present BFO dispositional theory of function.

La pertinence de la métaphysique analytique a fait l'objet de critiques : Ladyman et Ross, par exemple, ont suggéré d'abandonner ce domaine. French et McKenzie ont défendu la métaphysique analytique en affirmant qu'elle développe des outils qui pourraient s'avérer utiles pour la philosophie de la physique. Dans cet article, nous montrons dans un premier temps que cette défense heuristique de la métaphysique peut être étendue au domaine scientifique de l'ontologie appliquée, qui utilise des théories et outils issus de la métaphysique analytique. Dans un deuxième temps, nous développons le parallèle que font French et McKenzie entre les mathématiques et la métaphysique pour montrer que l'ensemble du domaine de la métaphysique analytique, étant donné son utilité non seulement pour la philosophie mais également pour la science, devrait continuer à exister en tant que domaine largement autonome.

International audience; 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.

Part of the Bolzano Summer of Knowledge 2021 (BOSK); International audience; 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.

International audience; Social roles remain nebulous, although they are vital for an accurate understanding of the socioeconomic world. In this paper, we sketch out a dispositional approach to social roles by leveraging F. Loebe's account of social roles that is based on his tripartite classification of roles (relational, processual, and social): that is, social roles "aggregate" various relational and processual roles. More specifically, we articulate the thesis that socially relevant processual and relational roles are intimately connected with intrinsic and extrinsic dispositions, respectively. This aggregate and dispositional view of roles will serve as an initial step towards a full-fledged analysis of social roles and their contexts ("social contexts").

International audience; 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.

International audience; 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.

International audience; Introduced by Cass Sunstein and Richard Thaler, nudges have become an important tool in public policy, in particular for health-related interventions. This paper provides foundations to represent nudges in OBO Foundry ontologies. It defines a nudge as a function of an environment (or part thereof) that is designed to influence behavior, in order to contribute to the influencee's welfare or the society's welfare, and that is easily resistible. Nudges are distinguished from nudge-setting processes and nudge-activation processes.

International audience; QUESTO is an ontology formalizing questionnaires and related entities, such as the processes of administering the questionnaire or capturing the answers. It is built according to the OBO Foundry methodology and is a component of an ontological model that aims to enable interoperability between various clinical data sources in the context of a Learning Health System. This article presents the main entities of QUESTO and provides an example of its application: a relational data model is generated from the ontology and used to retrieve data from public health questionnaires stored in a REDCap database.

International audience; Sex and gender are important health determinants. It is therefore valuable to represent them in medical records. However, these entities are complex to define. In this paper we review some existing representations of sex and gender, with a special focus on the informational entities representing them. We detail our proposal for formalizing sex and gender informational entities according to the OBO Foundry methodology. In particular, we introduce classes enabling to represent information that may be either well-defined or ambiguous relatively to whether they represent sex or gender.

Nous proposons une taxonomie du jeu d’évasion complétée de définitions de termes-clés du domaine. Nous définissons un jeu d’évasion comme un jeu dans lequel des joueurs incarnent des personnages dans un environnement, où la consultation d’éléments externes au jeu n’est pas autorisée, et qui repose sur la découverte et la résolution de défis préétablis de natures différentes, afin d’accomplir un ou plusieurs objectifs. Nous définissons plusieurs sous-types du jeu d’évasion (grandeur nature, jeu vidéo, livre-jeu et jeu en boîte), ainsi que la notion-clé de « défi » et certains de ses sous-types. Cette définition exclut du champ du jeu d’évasion des formes de jeux partiellement similaires comme les soirées enquêtes, les chasses au trésor à distance, ainsi que certains jeux de société collaboratifs et jeux vidéo de réflexion. Nous discutons de la pertinence d’imposer un critère de contrainte temporelle dans la définition, ainsi que de la possibilité d’inclure ou non dans le champ du jeu d’évasion certains jeux de pistes et jeux vidéo de type « point-and-click » antérieurs à l’essor contemporain des jeux d’évasion. We propose a taxonomy of escape game completed with definitions of key terms in the domain. We define an escape game as a game in which players embody characters in an environment, where the consultation of elements external to the game is not allowed, that rests on discovering and completing predefined challenges of different natures, in order to accomplish one or several objectives. We define several subtypes of escape games (live game, video game, game book and game in a box), as well as the key notion of “challenge” and some of its subtypes. This definition excludes partially similar forms of games from the field of escape game, such as murder parties or armchair treasure hunts, as well as some collaborative board games and puzzle video games. We discuss whether or not to include in the field of escape games some scavenger hunts and point-and-click video games developed before the contemporary rise of escape games.

The medical world is replete with documents that ontologies can help to analyze and disambiguate. This paper provides a mereological analysis of such documents as structured by informational slots and fillers, completing recent work by our teams inspired by Bennett. It introduces the notion of adequate filling of an informational slot, and the representation of the layered structure of a document. An application is provided on the Prescription of drugs ontology (PDRO).

International audience; Functional parthood is relevant to the modeling of material objects and their complex interrelationships. For instance, it will be valuable for representingvarious kinds of objects in multi-layered biological reality. In this paper we sketch out a project to develop a dispositional approach to functional parthood based on a dispositional account of functions and a theory of parthood between dispositions.

International audience; We develop an affordance-based approach to a subkind of roles, namely roles that have a causal component and that involve an agent and an environment. This approach is based on a previous dispositional ontology of affordances and effectivities. More specifically, such roles are analyzed as identical to mereological sums of affordances or effectivities when they are realized. We illustrate this theory on the example of the roles of addresser (analyzed as a sum of effectivities when they are realized) and addressee (analyzed as a sum of affordances when they are realized). We discuss the import of this analysis for the category of role in the upper ontology Basic Formal Ontology (BFO), and the relation between this approach and Loebe's tripartition of roles.

International audience; Informational entities, such as words, can be used not only to make statements about the world, but also to direct actions. This happens when they describe actions, and those actions are then performed by some agents on the basis of this description. This paper investigates the characteristics of the relation of directedness and compliance and distinguishes between attempted, successful and maximal direction. It discusses the case when directive entities are synonymous or specialize one another.

LABO is an ontology formalizing laboratory test 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. This article presents LABO, distinguishing between directive entities and data items, and using the relations directs and is about to represent their connections with the relevant laboratory test processes.

Supplemental material, sj-pdf-1-eeg-10.1177_1556264621992214 for 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 by Annabelle Cumyn, Roxanne Dault, Adrien Barton, Anne-Marie Cloutier and Jean-François Ethier in Journal of Empirical Research on Human Research Ethics

International audience; Bennett proposed in 2013 a new mereological theory based on the decomposition of the parthood relation into two relations: having a slot and occupying that slot. Slot mereology can be used to represent the mereological structure of a variety of entities that can have the same part multiple times, including (but not only) structural universals. We show here that this theory is not compatible with a counting criterion that would enable us to count appropriately how many times a whole has a part. We propose news axioms to fix those flaws.

Additional file 2. Additional quotes from participants. The Additional file 2 presents additional citations from participants regarding reasons for liking or disliking each of the four consent options (Additional Table S2.1) as well as regarding reassuring factors and concerns cited towards each of the eight characteristics of the meta-consent model (Additional Table S2.2). Additional Table S2.1. Some reasons cited by our participants for liking or disliking each of the four consent options. Additional Table S2.2. Overview of some reassuring factors and concerns cited by our participants regarding each of the eight characteristics of the meta-consent model.

Additional file 1. Additional methodology information. The Additional file 1 presents details on the composition of the eight focus groups (Additional Table S1.1), a description of the meta-consent model as we defined it in our study (Additional Tables S1.2, S1.3 and S1.4) as well as the tools used with our focus group participants (Additional Tables S1.5 and S1.6). Additional Table S1.1. Focus groups’ composition. Additional Table S1.2. Meta-consent model: Set of data content characteristics {X}. Additional Table S1.3. Meta-consent model: Set of contextual characteristics {Y}. Additional Table S1.4. Meta-consent model: Set of consent choices {Z}. Additional Table S1.5. Characteristics defining categories of research projects in our meta-consent model as presented to the focus group participants. Additional Table S1.6. Example of predefining categories of research projects for which focus group participants had to express their meta-consent preferences.

International audience; In lieu of an abstract, here is a brief excerpt of the content: La métaphysique est parfois caractérisée comme l’étude de la nature fondamentale de la réalité. À ce titre, elle semble l’une des branches les plus prototypiques de la philosophie dite «théorique», et donc résolument à l’opposé de la philosophie dite «pratique». Pourtant, une discipline à visée pratique utilise largement la métaphysique: l’ontologie appliquée. Cette discipline trouve son origine dans l’accélération contemporaine de la production de données à l’échelle mondiale. De nombreux systèmes d’information ont été développés pour produire et traiter ces données, mais l’échange d’information entre systèmes reste encore souvent difficile. La diversité des formats de données utilisées constitue une première difficulté, d’ordre technique. Mais il existe également une seconde difficulté, d’ordre sémantique. Une base de données est en effet développée par une communauté humaine pour répondre à certains besoins propres ; elle présente donc souvent un défaut de systématicité due à ses idiosyncrasies, ainsi que ses propres ambiguïtés – voire incohérences. Il est par conséquent difficile d’assurer la conservation de la signification de données lors de leur transmission d’un système à un autre: on dit qu’il y a un défaut d’«interopérabilité sémantique». L’ontologie appliquée est une discipline visant à développer de manière systématique des catégorisations générales (nommées «ontologies appliquées» ou «ontologies») qui permettent de pallier ce défaut. Une ontologie appliquée définit les catégories d’entités pertinentes à un domaine du savoir, et énonce des axiomes formels clarifiant les relations entre ces entités. Il existe ainsi des ontologies appliquées de domaines aussi variés que la médecine, la biologie, la géographie, l’ingénierie ou le commerce, ainsi que de leurs sous-domaines. Une ontologie appliquée 88 Deuxième partie–La dimension épistémologique de la philosophie pratique 88 peut être représentée sous forme de fichier informatique – le format OWL (Web Ontological Language) étant aujourd’hui fréquemment utilisé 1 . Une ontologie appliquée vise ainsi à décrire systématiquement les entités d’un domaine particulier. Mais le terme «ontologie» est également utilisé dans le domaine philosophique – soit comme synonyme de«métaphysique», soit pour désigner la branche de la métaphysique qui étudie l’être, ou ce qui est. Le développement d’ontologies appliquées en sciences de l’information pose donc des problèmes très similaires à ceux qui sont classiquement abordés par l’ontologie philosophique – et il est largement reconnu que cette dernière a beaucoup à apporter à l’ontologie appliquée. Cela est particulièrement vrai de l’ontologie philosophique dite «analytique», qui met l’accent sur la précision et la clarté de l’argumentation , et emploie fréquemment des méthodes formelles. On peut donc s’interroger sur le statut philosophique de l’ontologie appliquée ; étant donné sa visée applicative, on peut notamment se demander s’il s’agit d’une forme de philosophie pratique. Pour analyser cette question, une première partie clarifiera les relations entre l’ontologie philosophique et l’ontologie appliquée. Une deuxième partie présentera les fondements philosophiques de la OBO Foundry, un ensemble d’ontologies appliquées biomédicales. Une troisième partie mettra en évidence la valeur pratique des ontologies appliquées, en montrant comment les distinctions établies par les ontologies de la OBO Foundry permettent d’éviter certaines erreurs communes dans la classification de l’information médicale. Enfin, une quatrième partie examinera, à la lumière des parties précédentes, les connexions entre ontologie appliquée et philosophie pratique.