A Literature Based Approach to Define the Scope of Biomedical Ontologies: A Case Study on a Rehabilitation Therapy Ontology

TL;DR

This paper presents a literature-based method for defining the scope of a biomedical rehabilitation therapy ontology, aiming to reduce expert effort and bias in ontology development.

Contribution

It introduces an alternative approach that uses literature corpus analysis and information extraction to bootstrap and scope the ontology, reducing reliance on expert elicitation.

Findings

Four approaches to building a suitable corpus are discussed.

The method helps define the ontology's scope efficiently.

Initial terminology and competencies are derived from literature analysis.

Abstract

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 ontologists 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.