OBJECTIVE: Clinical practice guidelines (CPGs) for Integrated Traditional Chinese and Western Medicine (TCM and WM) are important medical documents used to assist medical decision-making and are of great significance for standardizing clinical pathways. However, due to the constraints of text format, it is difficult for Integrated TCM and WM CPGs to play a real role in medical practice. In addition, how to standardize the structure and semantic relationships between Integrated TCM and WM CPG knowledge, and realize the construction of computable, sharable and reliable CPGs, remains an urgent issue to be addressed. Therefore, we are proposing an ontology of CPGs for Integrated TCM and WM.
METHODS: We first initialized domain concepts and relationships to ensure the accuracy of the ontology knowledge structure. We then screened CPGs that meet the standards for Integrated TCM and WM, analyzed and classified the contents, and extracted the common structures. Based on the seven-step ontology construction method combined with inference-complement, referring to the representation methods and hierarchical relationships of terms and concepts in MeSH, ICD-10, SNOMED-CT, and other ontologies and terminology sets, we formed the concept structure and semantic relationship tables for the ontology. We also achieved the matching and mapping between the ontology and reference ontologies and term sets. Next, we defined the aspects and constraints of properties, selected multiple Integrated TCM and WM CPGs as instances to populate, and used ontology reasoning tools and formulated defined inference rules to reason and extend the ontology. Finally, we evaluated the performance of the ontology.
RESULTS: The content of the Integrated TCM and WM CPGs is divided into nine parts: basic information, background, development method, clinical question, recommendation, evidence, conclusion, result, and reason for recommendations. The Integrated TCM and WM CPG ontology has 152 classes and defines 90 object properties and 114 data properties, with a maximum classification depth of 4 layers. The terms of disease, drug and examination item names in the ontology have been standardized.
CONCLUSIONS: This study proposes an Integrated TCM and WM CPG ontology. The ontology adopts a modular design, which has both sharing and scaling ability, and can express rich guideline knowledge. It provides important support for the semantic processing and computational application of guideline documents.

The Global Burden of Animal Diseases (GBADs) programme aims to assess the impact of animal health on agricultural animals, livestock production systems and associated communities worldwide. As part of the objectives of GBADs\'Animal Health Ontology theme, the programme reviewed conceptual frameworks, ontologies and classification systems in biomedical science. The focus was on data requirements in animal health and the connections between animal health and human and environmental health. In May 2023, the team conducted searches of recognised repositories of biomedical ontologies, including BioPortal, Open Biological and Biomedical Ontology Foundry, and Ontology Lookup Service, to identify animal and livestock ontologies and those containing relevant concepts. Sixteen ontologies were found, covering topics such as surveillance, anatomy and genetics. Notable examples include the Animal Trait Ontology for Livestock, the Animal Health Surveillance Ontology, the National Center for Biotechnology Information Taxonomy and the Uberon Multi-Species Anatomy Ontology. However, some ontologies lacked class definitions for a significant portion of their classes. The review highlights the need for domain evidence to support proposed models, critical appraisal of external ontologies before reuse, and external expert reviews along with statistical tests of agreements. The findings from this review informed the structural framework, concepts and rationales of the animal health ontology for GBADs. This animal health ontology aims to increase the interoperability and transparency of GBADs data, thereby enabling estimates of the impacts of animal diseases on agriculture, livestock production systems and associated communities globally.
Le programme \" Impact mondial des maladies animales \" (GBADs) vise à évaluer l\'impact de la santé animale sur les animaux d\'élevage, les systèmes de production animale et les communautés liées à ce secteur d\'activités dans le monde. Afin de définir une ontologie de la santé animale répondant aux objectifs du GBADs, le programme a procédé à un examen des cadres conceptuels, des ontologies et des systèmes de classification actuellement appliqués en sciences biomédicales. Il s\'agissait de définir les besoins en données dans le domaine de la santé animale ainsi que les connexions entre la santé animale, la santé publique et la santé environnementale. En mai 2023, l\'équipe a procédé à des recherches dans des référentiels reconnus d\'ontologies biomédicales, notamment BioPortal, Open Biological and Biomedical Ontology Foundry et Ontology Lookup Service, afin de recenser les ontologies relatives aux animaux et au bétail ainsi que celles contenant des concepts pertinents. Seize ontologies ont été relevées, couvrant des thèmes tels que la surveillance, l\'anatomie et la génétique. Parmi les exemples notables on peut citer : Animal Trait Ontology for Livestock (ontologie dédiée aux caractères phénotypiques des animaux d\'élevage), Animal Health Surveillance Ontology (ontologie dédiée à la surveillance de la santé animale), National Center for Biotechnology Information Taxonomy (la base de données Taxonomie du Centre américain pour les informations biotechnologiques), et Uberon Multi-Species Anatomy Ontology (ontologie anatomique représentant diverses espèces animales). Il a cependant été constaté que certaines ontologies ne disposent pas de définitions de classes pour une grande partie des classes qui les composent. L\'examen a souligné l\'importance d\'étayer les modèles proposés par des données issues des spécialités en question, de procéder à une évaluation critique des ontologies externes avant de les réutiliser et de faire effectuer des examens complémentaires par des experts externes ainsi que des tests statistiques de concordance. Les résultats de cette étude ont apporté des éléments permettant de définir le cadre structurel, les concepts et les principes de l\'ontologie relative à la santé animale destinée au GBADs. Cette ontologie de la santé animale vise à accroître l\'interopérabilité et la transparence des données du GBADs, ce qui permet d\'effectuer des estimations de l\'impact des maladies animales sur l\'agriculture, les systèmes de production animale et les communautés associées à ce secteur d\'activités à l\'échelle mondiale.
El programa sobre el impacto global de las enfermedades animales (GBADs) tiene como objetivo evaluar el impacto de la sanidad animal en los animales de granja, los sistemas de producción ganadera y las comunidades conexas en todo el mundo. Como parte de los objetivos en torno al tema de la ontología de la sanidad animal del GBADs, el programa revisó marcos conceptuales, ontologías y sistemas de clasificación en el ámbito de la ciencia biomédica. Se hizo hincapié en los requisitos de datos sobre la sanidad animal y en las conexiones entre la sanidad animal y la salud humana y ambiental. En mayo de 2023, el equipo realizó búsquedas en repositorios reconocidos de ontologías biomédicas, como BioPortal, Open Biological and Biomedical Ontology Foundry y Ontology Lookup Service, para identificar no solo ontologías animales y ganaderas, sino también aquellas que incluyeran conceptos relevantes. En este sentido, se encontraron dieciséis ontologías, que abarcan temas como vigilancia, anatomía y genética. Entre los ejemplos más destacados figuran Animal Trait Ontology for Livestock (Ontología de Características Animales para el Ganado), Animal Health Surveillance Ontology (Ontología de Vigilancia de la Sanidad Animal), National Center for Biotechnology Information Taxonomy (la base de datos Taxonomía del Centro Nacional para la Información Biotecnológica) y Uberon Multi-Species Anatomy Ontology (Ontología Anatómica de Especies Múltiples). Sin embargo, algunas ontologías carecían de definiciones para una parte significativa de sus clases. La revisión pone de relieve la necesidad de contar con datos probatorios del ámbito en cuestión que respalden los modelos propuestos, una evaluación crítica de las ontologías externas antes de su reutilización y revisiones de expertos externos junto con pruebas estadísticas de los acuerdos. Los resultados de esta revisión han servido de base para el marco estructural, los conceptos y los fundamentos de la ontología de la sanidad animal para el GBADs. Esta ontología pretende aumentar la interoperabilidad y la transparencia de los datos del GBADs, permitiendo así estimar el impacto de las enfermedades animales en la agricultura, los sistemas de producción ganadera y las comunidades conexas en todo el mundo.

Ontologies and terminologies serve as the backbone of knowledge representation in biomedical domains, facilitating data integration, interoperability, and semantic understanding across diverse applications. However, the quality assurance and enrichment of these resources remain an ongoing challenge due to the dynamic nature of biomedical knowledge. In this editorial, we provide an introductory summary of seven articles included in this special supplement issue for quality assurance and enrichment of biological and biomedical ontologies and terminologies. These articles span a spectrum of topics, such as development of automated quality assessment frameworks for Resource Description Framework (RDF) resources, identification of missing concepts in SNOMED CT through logical definitions, and developing a COVID interface terminology to enable automatic annotations of COVID-19 related Electronic Health Records (EHRs). Collectively, these contributions underscore the ongoing efforts to improve the accuracy, consistency, and interoperability of biomedical ontologies and terminologies, thus advancing their pivotal role in healthcare and biomedical research.

Automatic disease progression prediction models require large amounts of training data, which are seldom available, especially when it comes to rare diseases. A possible solution is to integrate data from different medical centres. Nevertheless, various centres often follow diverse data collection procedures and assign different semantics to collected data. Ontologies, used as schemas for interoperable knowledge bases, represent a state-of-the-art solution to homologate the semantics and foster data integration from various sources. This work presents the BrainTeaser Ontology (BTO), an ontology that models the clinical data associated with two brain-related rare diseases (ALS and MS) in a comprehensive and modular manner. BTO assists in organizing and standardizing the data collected during patient follow-up. It was created by harmonizing schemas currently used by multiple medical centers into a common ontology, following a bottom-up approach. As a result, BTO effectively addresses the practical data collection needs of various real-world situations and promotes data portability and interoperability. BTO captures various clinical occurrences, such as disease onset, symptoms, diagnostic and therapeutic procedures, and relapses, using an event-based approach. Developed in collaboration with medical partners and domain experts, BTO offers a holistic view of ALS and MS for supporting the representation of retrospective and prospective data. Furthermore, BTO adheres to Open Science and FAIR (Findable, Accessible, Interoperable, and Reusable) principles, making it a reliable framework for developing predictive tools to aid in medical decision-making and patient care. Although BTO is designed for ALS and MS, its modular structure makes it easily extendable to other brain-related diseases, showcasing its potential for broader applicability.Database URL  https://zenodo.org/records/7886998 .

Background: Investigating and enhancing the effectiveness of behaviour change interventions requires detailed and consistent specification of all aspects of interventions. We need to understand not only their content, that is the specific techniques, but also the source, mode, schedule, and style in which this content is delivered. Delivery style refers to the manner by which content is communicated to intervention participants. This paper reports the development of an ontology for specifying the style of delivery of interventions that depend on communication. This forms part of the Behaviour Change Intervention Ontology, which aims to cover all aspects of behaviour change intervention scenarios. Methods: The Style of Delivery Ontology was developed following methods for ontology development used in the Human Behaviour-Change Project, with seven key steps: 1) defining the scope of the ontology, 2) identifying key entities and developing their preliminary definitions by reviewing 100 behaviour change intervention evaluation reports and existing classification systems, 3) refining the ontology by piloting the ontology through annotations of 100 reports, 4) stakeholder review by eight behavioural science and public health experts, 5) inter-rater reliability testing through annotating 100 reports using the ontology, 6) specifying ontological relationships between entities, and 7) disseminating and maintaining the ontology. Results: The resulting ontology is a five-level hierarchical structure comprising 145 unique entities relevant to style of delivery. Key areas include communication processes, communication styles, and attributes of objects used in communication processes. Inter-rater reliability for annotating intervention evaluation reports was α=0.77 (good) for those familiar with the ontology and α=0.62 (acceptable) for those unfamiliar with it. Conclusions: The Style of Delivery Ontology can be used for both annotating and describing behaviour change interventions in a consistent and coherent manner, thereby improving evidence comparison, synthesis, replication, and implementation of effective interventions.

Technology remains enmeshed in our daily lives and given its continuing presence in clinical practice and rapid technological proliferation; it becomes relevant for nurses to examine techno-onto-epistemology in relation to the discipline of nursing. This is critical considering the intersection of technology and nursing remains an area of ongoing discussion revealing a need for further philosophical reflection. To this end, this paper sought to examine the philosophy of technology from the engineering and humanities perspectives to contribute to the discussion regarding its intersection with the onto-epistemology of nursing. Although technology seems to be constantly present in nursing practice, two opposing perspectives reflecting a love-hate relationship is highlighted: technological optimism (promotes technology) and technological romanticism (dissuades technology). Based on Mitcham\'s interpretation of \'mutual relationship\' and \'being-with\', a potential way to break away from the binary perspectives is to view the intersection of/relationship between technology and nursing as being on a continuum rather than entirely monolithic entities. Caring is presented as multidimensional reflecting actions and attitudes. Arguably, some caring actions may intersect with the engineering perspective to suggest that technology can support nurses in their roles, that is, by imitating some of what nurses do, but not to replace them. From the humanities perspective, technology is presented as a way of being with humans exercising control over what technology has to offer. Put together, it is clearly time to break away from the love-hate relationship between nursing and technology. Although this emphasises a great need to build the technological competency of nurses, there is an even greater call for nurses to reflect on and voice the epistemological, ontological, axiological, and ethical issues that the application of technology raises for the discipline.

This article presents experience in construction the National Unified Terminological System (NUTS) with an ontological structure based on international Unified Medical Language System (UMLS). UMLS has been adapted and enriched with formulations from national directories, relationships, extracted from the texts of scientific articles and electronic health records, and weight coefficients.

Administrable dose form can be obtained after (no-)transformation from pharmaceutical dose form. Building on the creation of a small ontology of 428 pharmaceutical dose forms from EDQM to support alignment with other dose form ontologies (SNOMED-CT, RxNorm), the present study is focused on a simple ontology of 308 administrable dose forms, 27 Intended Sites and an intermediary level of 65 dose form groupers. The ontology was created after 432 pharmaceutical dose forms, 65 combined pharmaceutical dose forms and 73 combined terms were linked by EDQM to administrable dose forms during the UNICOM project. The article describes these resources, the resulting ontology, the differences between its top-level concepts and the source\'s. It presents the protocol for a validation study through expert review, as a preparation for use case studies.

BACKGROUND: Integrating information from data sources representing different study designs has the potential to strengthen evidence in population health research. However, this concept of evidence \"triangulation\" presents a number of challenges for systematically identifying and integrating relevant information. These include the harmonization of heterogenous evidence with common semantic concepts and properties, as well as the priortization of the retrieved evidence for triangulation with the question of interest.
RESULTS: We present Annotated Semantic Queries (ASQ), a natural language query interface to the integrated biomedical entities and epidemiological evidence in EpiGraphDB, which enables users to extract \"claims\" from a piece of unstructured text, and then investigate the evidence that could either support, contradict the claims, or offer additional information to the query. This approach has the potential to support the rapid review of preprints, grant applications, conference abstracts, and articles submitted for peer review. ASQ implements strategies to harmonize biomedical entities in different taxonomies and evidence from different sources, to facilitate evidence triangulation and interpretation.
METHODS: ASQ is openly available at https://asq.epigraphdb.org and its source code is available at https://github.com/mrcieu/epigraphdb-asq under GPL-3.0 license.

BACKGROUND: Within the Open Biological and Biomedical Ontology (OBO) Foundry, many ontologies represent the execution of a plan specification as a process in which a realizable entity that concretizes the plan specification, a \"realizable concretization\" (RC), is realized. This representation, which we call the \"RC-account\", provides a straightforward way to relate a plan specification to the entity that bears the realizable concretization and the process that realizes the realizable concretization. However, the adequacy of the RC-account has not been evaluated in the scientific literature. In this manuscript, we provide this evaluation and, thereby, give ontology developers sound reasons to use or not use the RC-account pattern.
RESULTS: Analysis of the RC-account reveals that it is not adequate for representing failed plans. If the realizable concretization is flawed in some way, it is unclear what (if any) relation holds between the realizable entity and the plan specification. If the execution (i.e., realization) of the realizable concretization fails to carry out the actions given in the plan specification, it is unclear under the RC-account how to directly relate the failed execution to the entity carrying out the instructions given in the plan specification. These issues are exacerbated in the presence of changing plans.
CONCLUSIONS: We propose two solutions for representing failed plans. The first uses the Common Core Ontologies \'prescribed by\' relation to connect a plan specification to the entity or process that utilizes the plan specification as a guide. The second, more complex, solution incorporates the process of creating a plan (in the sense of an intention to execute a plan specification) into the representation of executing plan specifications. We hypothesize that the first solution (i.e., use of \'prescribed by\') is adequate for most situations. However, more research is needed to test this hypothesis as well as explore the other solutions presented in this manuscript.