Development of an Intervention Setting Ontology for behaviour change: Specifying where interventions take place

Background: Contextual factors such as an intervention's setting are key to understanding how interventions to change behaviour have their effects and patterns of generalisation across contexts. The intervention's setting is not consistently reported in published reports of evaluations. Using ontologies to specify and classify intervention setting characteristics enables clear and reproducible reporting, thus aiding replication, implementation and evidence synthesis. This paper reports the development of a Setting Ontology for behaviour change interventions as part of a Behaviour Change Intervention Ontology, currently being developed in the Wellcome Trust funded Human Behaviour-Change Project. Methods: The Intervention Setting Ontology was developed following methods for ontology development used in the Human Behaviour-Change Project: 1) Defining the ontology's scope, 2) Identifying key entities by reviewing existing classification systems (top-down) and 100 published behaviour change intervention reports (bottom-up), 3) Refining the preliminary ontology by literature annotation of 100 reports, 4) Stakeholder reviewing by 23 behavioural science and public health experts to refine the ontology, 5) Assessing inter-rater reliability of using the ontology by two annotators familiar with the ontology and two annotators unfamiliar with it, 6) Specifying ontological relationships between setting entities and 7) Making the Intervention Setting Ontology machine-readable using Web Ontology Language (OWL) and publishing online. Results: The Intervention Setting Ontology consists of 72 entities structured hierarchically with two upper-level classes: Physical setting including Geographic location, Attribute of location (including Area social and economic condition, Population and resource density sub-levels) and Intervention site (including Facility, Transportation and Outdoor environment sub-levels), as well as Social setting. Inter-rater reliability was found to be 0.73 (good) for those familiar with the ontology and 0.61 (acceptable) for those unfamiliar with it. Conclusion: The Intervention Setting Ontology can be used to code information from diverse sources, annotate the setting characteristics of existing intervention evaluation reports and guide future reporting

Development of an Intervention Setting Ontology for behaviour change: Specifying where interventions take place.

Background: Contextual factors such as an intervention's setting are key to understanding how interventions to change behaviour have their effects and patterns of generalisation across contexts. The intervention's setting is not consistently reported in published reports of evaluations. Using ontologies to specify and classify intervention setting characteristics enables clear and reproducible reporting, thus aiding replication, implementation and evidence synthesis. This paper reports the development of a Setting Ontology for behaviour change interventions as part of a Behaviour Change Intervention Ontology, currently being developed in the Wellcome Trust funded Human Behaviour-Change Project. Methods: The Intervention Setting Ontology was developed following methods for ontology development used in the Human Behaviour-Change Project: 1) Defining the ontology's scope, 2) Identifying key entities by reviewing existing classification systems (top-down) and 100 published behaviour change intervention reports (bottom-up), 3) Refining the preliminary ontology by literature annotation of 100 reports, 4) Stakeholder reviewing by 23 behavioural science and public health experts to refine the ontology, 5) Assessing inter-rater reliability of using the ontology by two annotators familiar with the ontology and two annotators unfamiliar with it, 6) Specifying ontological relationships between setting entities and 7) Making the Intervention Setting Ontology machine-readable using Web Ontology Language (OWL) and publishing online. Re sults: The Intervention Setting Ontology consists of 72 entities structured hierarchically with two upper-level classes: Physical setting including Geographic location, Attribute of location (including Area social and economic condition, Population and resource density sub-levels) and Intervention site (including Facility, Transportation and Outdoor environment sub-levels), as well as Social setting. Inter-rater reliability was found to be 0.73 (good) for those familiar with the ontology and 0.61 (acceptable) for those unfamiliar with it. Conclusion: The Intervention Setting Ontology can be used to code information from diverse sources, annotate the setting characteristics of existing intervention evaluation reports and guide future reporting

Automated extension of biomedical ontologies

Developing and extending a biomedical ontology is a very demanding process, particularly because biomedical knowledge is diverse, complex and continuously changing and growing. Existing automated and semi-automated techniques are not tailored to handling the issues in extending biomedical ontologies. This thesis advances the state of the art in semi-automated ontology extension by presenting a framework as well as methods and methodologies for automating ontology extension specifically designed to address the features of biomedical ontologies.The overall strategy is based on first predicting the areas of the ontology that are in need of extension and then applying ontology learning and ontology matching techniques to extend them. A novel machine learning approach for predicting these areas based on features of past ontology versions was developed and successfully applied to the Gene Ontology. Methods and techniques were also specifically designed for matching biomedical ontologies and retrieving relevant biomedical concepts from text, which were shown to be successful in several applications.O desenvolvimento e extensão de uma ontologia biomédica é um processo muito exigente, dada a diversidade, complexidade e crescimento contínuo do conhecimento biomédico. As técnicas existentes nesta área não estão preparadas para lidar com os desafios da extensão de uma ontologia biomédica. Esta tese avança o estado da arte na extensão semi-automática de ontologias, apresentando uma framework assim como métodos e metodologias para a automação da extensão de ontologias especificamente desenhados tendo em conta as características das ontologias biomédicas. A estratégia global é baseada em primeiro prever quais as áreas da ontologia que necessitam extensão, e depois usá-las como enfoque para técnicas de alinhamento e aprendizagem de ontologias, com o objectivo de as estender. Uma nova estratégia de aprendizagem automática para prever estas áreas baseada em atributos de antigas versões de ontologias foi desenvolvida e testada com sucesso na Gene Ontology. Foram também especificamente desenvolvidos métodos e técnicas para o alinhamento de ontologias biomédicas e extracção de conceitos relevantes de texto, cujo sucesso foi demonstrado em várias aplicações.Fundação para a Ciência e a Tecnologi

Mapping Nanomedicine Terminology in the Regulatory Landscape

A common terminology is essential in any field of science and technology for a mutual understanding among different communities of experts and regulators, harmonisation of policy actions, standardisation of quality procedures and experimental testing, and the communication to the general public. It also allows effective revision of information for policy making and optimises research fund allocation. In particular, in emerging scientific fields with a high innovation potential, new terms, descriptions and definitions are quickly generated, which are then ambiguously used by stakeholders having diverse interests, coming from different scientific disciplines and/or from various regions. The application of nanotechnology in health -often called nanomedicine- is considered as such emerging and multidisciplinary field with a growing interest of various communities. In order to support a better understanding of terms used in the regulatory domain, the Nanomedicines Working Group of the International Pharmaceutical Regulators Forum (IPRF) has prioritised the need to map, compile and discuss the currently used terminology of regulatory scientists coming from different geographic areas. The JRC has taken the lead to identify and compile frequently used terms in the field by using web crawling and text mining tools as well as the manual extraction of terms. Websites of 13 regulatory authorities and clinical trial registries globally involved in regulating nanomedicines have been crawled. The compilation and analysis of extracted terms demonstrated sectorial and geographical differences in the frequency and type of nanomedicine related terms used in a regulatory context. Finally 31 relevant and most frequently used terms deriving from various agencies have been compiled, discussed and analysed for their similarities and differences. These descriptions will support the development of harmonised use of terminology in the future. The report provides necessary background information to advance the discussion among stakeholders. It will strengthen activities aiming to develop harmonised standards in the field of nanomedicine, which is an essential factor to stimulate innovation and industrial competitiveness.JRC.F.2-Consumer Products Safet

Proceedings of the 15th ISWC workshop on Ontology Matching (OM 2020)

15th International Workshop on Ontology Matching co-located with the 19th International Semantic Web Conference (ISWC 2020)International audienc

Lipoprotein ontology: a formal representation of Lipoproteins

Lipoproteins serve as a mode of transport for the uptake, storage and metabolism of lipids. Dysregulation in lipoprotein metabolism, known as dyslipidaemia, is strongly correlated to various diseases such as cardiovascular disease. Lipoprotein Ontology provides a formal representation of lipoprotein concepts and relationships that can be used to support the intelligent retrieval of information, faciliate collaboration between research groups, and provide the basis for the development of tools for the diagnosis and treatment of dyslipidaemia

A medical ultrasound reporting system based on domain ontology

Ultrasound reports are produced in different ways by radiologists. These variations in reporting style could impact on the value of the report and the way it is interpreted, which in turn may have implications for patients’ management and decision making. As the images produced will not give the whole view of the examination, it is vital that a high quality and standardised ultrasound report is produced. In addition to their medical value, ultrasound reports contain a lot of important information that can be very useful in research and education. Reports can contain a variety of terms or heterogeneous terminologies used for describing similar findings. This research project aims to develop a medical ultrasound reporting system that uses domain ontology as its knowledge base to support the generation of standardised reports as well as Rhetorical Structure Theory (RST) to transform free text reports to the preferred structured and standardised format. The domain ontology will specifically focus on abdominal ultrasound scanning which includes both the anatomy and pathology of the organs in the abdominal area. The ontology was developed using an ontology reuse methodology where terms from the sample reports were mapped to existing biomedical ontologies. It is anticipated that a standardised report based on domain ontology will improve the quality of ultrasound reports and encourage its implementation

Génération automatique d'alignements complexes d'ontologies

Le web de données liées (LOD) est composé de nombreux entrepôts de données. Ces données sont décrites par différents vocabulaires (ou ontologies). Chaque ontologie a une terminologie et une modélisation propre ce qui les rend hétérogènes. Pour lier et rendre les données du web de données liées interopérables, les alignements d'ontologies établissent des correspondances entre les entités desdites ontologies. Il existe de nombreux systèmes d'alignement qui génèrent des correspondances simples, i.e., ils lient une entité à une autre entité. Toutefois, pour surmonter l'hétérogénéité des ontologies, des correspondances plus expressives sont parfois nécessaires. Trouver ce genre de correspondances est un travail fastidieux qu'il convient d'automatiser. Dans le cadre de cette thèse, une approche d'alignement complexe basée sur des besoins utilisateurs et des instances communes est proposée. Le domaine des alignements complexes est relativement récent et peu de travaux adressent la problématique de leur évaluation. Pour pallier ce manque, un système d'évaluation automatique basé sur de la comparaison d'instances est proposé. Ce système est complété par un jeu de données artificiel sur le domaine des conférences.The Linked Open Data (LOD) cloud is composed of data repositories. The data in the repositories are described by vocabularies also called ontologies. Each ontology has its own terminology and model. This leads to heterogeneity between them. To make the ontologies and the data they describe interoperable, ontology alignments establish correspondences, or links between their entities. There are many ontology matching systems which generate simple alignments, i.e., they link an entity to another. However, to overcome the ontology heterogeneity, more expressive correspondences are sometimes needed. Finding this kind of correspondence is a fastidious task that can be automated. In this thesis, an automatic complex matching approach based on a user's knowledge needs and common instances is proposed. The complex alignment field is still growing and little work address the evaluation of such alignments. To palliate this lack, we propose an automatic complex alignment evaluation system. This system is based on instances. A famous alignment evaluation dataset has been extended for this evaluation