Reconciling users' needs and formal requirements: issues in developing a reusable ontology for medicine

Abstract

A common language, or terminology, for representing what clinicians have said and done is an important requirement for individual clinical systems, and it is a pre-requisite for integrating disparate applications in a distributed telematic healthcare environment. Formal representations based on description logics or closely related formalisms are increasingly used for representing medical terminologies. GALEN's experience in using one such formalism raises two major issues, as follows: how to make ontologies based on description logics easy to use and understand for both clinicians and applications developers; what features are required of the ontology and description logic if they are to achieve their aims. Based on our experience we put forward four contentions: two relating to each of these two issues, as follows: that natural language generation is essential to make a description logic based ontology accessible to users; that the description logic based ontology should be treated as an "assembly language" and accessed via "intermediate representations" oriented to users and "perspectives" adapting it to specific applications; that independence and reuse are best supported by partitioning the subsumption hierarchy of elementary concepts into orthogonal taxonomies, each of which forms a pure tree in which the branches at each level are disjoint but nonexhaustive subconcepts of the parent concept; that the expressivity of the description logic must include support for transitive relations despite the computational cost, and that this computational cost is acceptable in practice. The authors argue that these features will be necessary, though by no means sufficient, for the development of any large reusable ontology for medicine.

AIM: a personal view of where I have been and where we might be going

“…The layered architecture and Intermediate Representation have proved very effective at making the technology accessible [106,118]. (One might ask why it took us so long to apply what was well known in other knowledge acquisition tasks and even taught in our own classes, but that is another story.…”

“…Simple language generation proved essential to presenting compositional terminologies, at least for GALEN [10,106,127,138]. However, the world of language processing, information retrieval and information extraction have remained remarkably separate from the world of ontologies motivated by logical classification.…”

Modularisation of domain ontologies implemented in description logics and related formalisms including OWL

“…In our experience, violation of this principle almost always indicates that tacit information is concealed which makes later extension and maintenance difficult. Furthermore, this approach to normalisation or "untangling" has proved easy to explain to new ontology developers and has been one of the key strategies to support loosely coupled development [11]. Interestingly, Gu and her colleagues have independently proposed post hoc decomposition into disjoint trees as a means to improve maintainability of large ontologies represented in frame systems with multiple inheritance [2].…”

“…Interestingly, Gu and her colleagues have independently proposed post hoc decomposition into disjoint trees as a means to improve maintainability of large ontologies represented in frame systems with multiple inheritance [2]. We have no comparative data on effort for maintenance, but the combination of normalisation and the user of intermediate representations [9,11] has allowed us to develop and maintain a large ontology (~30,000 concepts) in a loosely coupled cooperative team consisting at times of up to nine centres in seven countries. The central maintenance and integration effort has been reduced to roughly ten per cent of the total.…”

Experimental analysis of some computation rules in a simple parallel reasoning system for the ALC description logic

“…Logics from this class have a reasonable expressivity and are, in many cases, decidable. Hence, they have been successfully applied in various domains, such as software engineering (Devanbu and Jones, 1997), object databases (Calvanese et al, 1999), control in manufacturing (Rychtyckyj, 1996), action planning in robotics (De Giacomo et al, 1996), medical expert systems (Rector et al, 1998) and also the Semantic Web (Semantic Web, 2001). DLs generally provide the semantics of knowledge bases for systems constructed in the areas mentioned.…”