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Open Access Highly Accessed Research article

Process attributes in bio-ontologies

André Q Andrade12, Ward Blondé1, Janna Hastings34 and Stefan Schulz15*

Author affiliations

1 Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria

2 School of Information Science, Federal University of Minas Gerais, Belo Horizonte, Brazil

3 Cheminformatics and Metabolism, European Bioinformatics Institute, Hinxton, UK

4 Swiss Centre for Affective Sciences, University of Geneva, Geneva, Switzerland

5 Institute for Medical Biometry and Medical Informatics, University Medical Center, Freiburg, Germany

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Citation and License

BMC Bioinformatics 2012, 13:217  doi:10.1186/1471-2105-13-217

Published: 28 August 2012

Abstract

Background

Biomedical processes can provide essential information about the (mal-) functioning of an organism and are thus frequently represented in biomedical terminologies and ontologies, including the GO Biological Process branch. These processes often need to be described and categorised in terms of their attributes, such as rates or regularities. The adequate representation of such process attributes has been a contentious issue in bio-ontologies recently; and domain ontologies have correspondingly developed ad hoc workarounds that compromise interoperability and logical consistency.

Results

We present a design pattern for the representation of process attributes that is compatible with upper ontology frameworks such as BFO and BioTop. Our solution rests on two key tenets: firstly, that many of the sorts of process attributes which are biomedically interesting can be characterised by the ways that repeated parts of such processes constitute, in combination, an overall process; secondly, that entities for which a full logical definition can be assigned do not need to be treated as primitive within a formal ontology framework. We apply this approach to the challenge of modelling and automatically classifying examples of normal and abnormal rates and patterns of heart beating processes, and discuss the expressivity required in the underlying ontology representation language. We provide full definitions for process attributes at increasing levels of domain complexity.

Conclusions

We show that a logical definition of process attributes is feasible, though limited by the expressivity of DL languages so that the creation of primitives is still necessary. This finding may endorse current formal upper-ontology frameworks as a way of ensuring consistency, interoperability and clarity.