An ontology co-design method for the co-creation of a continuous care ontology

Ontology engineering methodologies tend to emphasize the role of the knowledge engineer or require a very active role of domain experts. In this paper, a participatory ontology engineering method is described that holds the middle ground between these two 'extremes'. After thorough ethnographic research, an interdisciplinary group of domain experts closely interacted with ontology engineers and social scientists in a series of workshops. Once a preliminary ontology was developed, a dynamic care request system was built using the ontology. Additional workshops were organized involving a broader group of domain experts to ensure the applicability of the ontology across continuous care settings. The proposed method successfully actively engaged domain experts in constructing the ontology, without overburdening them. Its applicability is illustrated by presenting the co-created continuous care ontology. The lessons learned during the design and execution of the approach are also presented

Ontology-assisted database integration to support natural language processing and biomedical data-mining

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes of making computers understand medical natural language

Theorising disability: a practical and representative ontology of learning disability

This article contributes to the ongoing development of the theorisation of learning disability, focusing on the value of the ontological turn. We argue that while social theory has influenced understandings of disability within academia, particularly within disability studies, it has had a limited impact on the discursive and practical use of the term ‘learning disability’. How ‘learning disability’ is constructed is of direct consequence to the lives of people with learning disabilities. Owing to this, we present a practical and representative ontology of learning disability in order to progress the ontological turn into everyday understandings of disability. To do this, disability theory is discussed, critically appraised and progressed. We then outline how this new theorisation could be re-contextualised within policy, with a view to further re-contextualisation into practice and the everyday. It is hoped that this article will spark discussion regarding how the ontological turn can be used for change

Ontological and Epistemological Reflexivity: A Core Skill for Therapists

This paper develops the argument that a core skill needed to be an effective therapist is to have acquired an awareness of one’s own ontological and epistemological position in relation to one’s work as a therapist. In the same way that researchers need to develop reflexive awareness of their assumptions about what there is to know (ontology) and how they can come to know about it (epistemology), therapists need to be aware of their fundamental assumptions about human beings and the world they live in (ontology) as well as their beliefs about how best to develop an understanding of their clients and the meaning(s) of their experiences (epistemology). Regardless of which particular therapeutic model is adopted, the language used to talk about (and in) therapy, the kinds of questions asked of clients and the comments/interpretations offered, all presuppose and reinforce particular versions of human being and experiencing which are themselves not usually questioned or challenged during the course of therapy. In this paper it will be argued that it is essential that therapists are aware of their own fundamental assumptions about what it means to be human, and that they recognise their ontological and epistemological positions as positions that they are taking (rather than perceiving them to be self-evident truths). This is important for two reasons: i) if clients do not share the therapist’s assumptions (ie. their ‘model of the person’), the therapeutic work cannot proceed and be effective; ii) without such an awareness, therapists are at risk of unwittingly imposing their own model of the person upon the client which raises ethical issues

Controlled vocabularies in bioinformatics: A case study in the Gene Ontology

The automatic integration of information resources in the life sciences is one of the most challenging goals facing biomedical informatics today. Controlled vocabularies have played an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources secure in the knowledge that the same terms will also represent the same entities on all occasions of use. One of the most impressive achievements in this regard is the Gene Ontology (GO), which is rapidly acquiring the status of a de facto standard in the field of gene and gene product annotations, and whose methodology has been much intimated in attempts to develop controlled vocabularies for shared use in different domains of biology. The GO Consortium has recognized, however, that its controlled vocabulary as currently constituted is marked by several problematic features - features which are characteristic of much recent work in bioinformatics and which are destined to raise increasingly serious obstacles to the automatic integration of biomedical information in the future. Here, we survey some of these problematic features, focusing especially on issues of compositionality and syntactic regimentation

Towards a proteomics meta-classification

that can serve as a foundation for more refined ontologies in the field of proteomics. Standard data sources classify proteins in terms of just one or two specific aspects. Thus SCOP (Structural Classification of Proteins) is described as classifying proteins on the basis of structural features; SWISSPROT annotates proteins on the basis of their structure and of parameters like post-translational modifications. Such data sources are connected to each other by pairwise term-to-term mappings. However, there are obstacles which stand in the way of combining them together to form a robust meta-classification of the needed sort. We discuss some formal ontological principles which should be taken into account within the existing datasources in order to make such a metaclassification possible, taking into account also the Gene Ontology (GO) and its application to the annotation of proteins

Performing Gender: A Study of Gender Fluidity

The subjective quality of identity and the relativistic nature of gender are subjects that continue to bemuse and attract social scientists. In this study I examine gender fluidity – an inconsistent gender identity – within the framework of Western ontology. By analyzing narratives, I note that my informants recognize this gender identity as fluctuating feelings (which I call the feelings of gender) that influence how they perceive and interact with their bodies. Furthermore, I examine other important elements that may have influenced my informants\u27 understanding of their gender identities and bodies: upbringing, previous relationships and interactions, communities, and language

Dependence relationships between Gene Ontology terms based on TIGR gene product annotations

The Gene Ontology is an important tool for the representation and processing of information about gene products and functions. It provides controlled vocabularies for the designations of cellular components, molecular functions, and biological processes used in the annotation of genes and gene products. These constitute three separate ontologies, of cellular components), molecular functions and biological processes, respectively. The question we address here is: how are the terms in these three separate ontologies related to each other? We use statistical methods and formal ontological principles as a first step towards finding answers to this question

An Essay in Formal Ontology

As conceived by analytic philosophers ontology consists in the application of the methods of mathematical logic to the analysis of ontological discourse. As conceived by realist philosophers such as Meinong and the early Husserl, Reinach and Ingarden, it consists in the investigation of the forms of entities of various types. The suggestion is that formal methods be employed by phenomenological ontologists, and that phenomenological insights may contribute to the construction of adequate formal-ontological languages. The paper sketches an account of what might be involved in this new discipline, an account which is illustrated in application to the formal-ontological problems raised by negative states of affairs