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Desiderata for domain reference ontologies in biomedicine.

Abstract：

:Domain reference ontologies represent knowledge about a particular part of the world in a way that is independent from specific objectives, through a theory of the domain. An example of reference ontology in biomedical informatics is the Foundational Model of Anatomy (FMA), an ontology of anatomy that covers the entire range of macroscopic, microscopic, and subcellular anatomy. The purpose of this paper is to explore how two domain reference ontologies--the FMA and the Chemical Entities of Biological Interest (ChEBI) ontology, can be used (i) to align existing terminologies, (ii) to infer new knowledge in ontologies of more complex entities, and (iii) to manage and help reasoning about individual data. We analyze those kinds of usages of these two domain reference ontologies and suggest desiderata for reference ontologies in biomedicine. While a number of groups and communities have investigated general requirements for ontology design and desiderata for controlled medical vocabularies, we are focusing on application purposes. We suggest five desirable characteristics for reference ontologies: good lexical coverage, good coverage in terms of relations, compatibility with standards, modularity, and ability to represent variation in reality.

journal_name

J Biomed Inform

journal_title

Journal of biomedical informatics

authors

Burgun A

doi

10.1016/j.jbi.2005.09.002

keywords:

subject

Has Abstract

pub_date

2006-06-01 00:00:00

pages

307-13

issue

3

eissn

1532-0464

issn

1532-0480

pii

S1532-0464(05)00099-7

journal_volume

39

pub_type

杂志文章

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