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A literature based approach to define the scope of biomedical ontologies: A case study on a rehabilitation therapy ontology

Lookup NU author(s): Mohammad Halawani, Dr Rob Forsyth, Dr Phillip Lord

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This is the final published version of a conference proceedings (inc. abstract) that has been published in its final definitive form by CEUR-WS, 2017.

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Abstract

© 2018 CEUR-WS. All rights reserved. In this article, we investigate our early attempts at building an ontology describing rehabilitation therapies following brain injury. These therapies are wide-ranging, involving interventions of many different kinds. As a result, these therapies are hard to describe. As well as restricting actual practice, this is also a major impediment to evidence-based medicine as it is hard to meaningfully compare two treatment plans. Ontology development requires significant effort from both ontolo-gists and domain experts. Knowledge elicited from domain experts forms the scope of the ontology. The process of knowledge elicitation is expensive, consumes experts’ time and might have biases depending on the selection of the experts. Various methodologies and techniques exist for enabling this knowledge elicitation, including community groups and open development practices. A related problem is that of defining scope. By defining the scope, we can decide whether a concept (i.e. term) should be represented in the ontology. This is the opposite of knowledge elicitation, in the sense that it defines what should not be in the ontology. This can be addressed by pre-defining a set of competency questions. These approaches are, however, expensive and time-consuming. Here, we describe our work toward an alternative approach, bootstrapping the ontology from an initially small corpus of literature that will define the scope of the ontology, expanding this to a set covering the domain, then using information extraction to define an initial terminology to provide the basis and the competencies for the ontology. Here, we discuss four approaches to building a suitable corpus that is both sufficiently covering and precise.


Publication metadata

Author(s): Halawani MK, Forsyth R, Lord P

Editor(s): Matthew Horridge, Phillip Lord, Jennifer D. Warrender

Publication type: Conference Proceedings (inc. Abstract)

Publication status: Published

Conference Name: Proceedings of the 8th International Conference on Biomedical Ontology (ICBO 2017)

Year of Conference: 2017

Online publication date: 11/07/2018

Acceptance date: 02/04/2016

Date deposited: 09/08/2018

ISSN: 1613-0073

Publisher: CEUR-WS

URL: http://ceur-ws.org/Vol-2137/paper_30.pdf

Series Title: CEUR Workshop Proceedings


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