title: Process attributes in bio-ontologies.
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.
authors.affiliation: Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria.
authors.forename: André Q
authors.initials: AQ
authors.lastname: Andrade
authors.forename: Ward
authors.initials: W
authors.lastname: Blondé
authors.forename: Janna
authors.initials: J
authors.lastname: Hastings
authors.forename: Stefan
authors.initials: S
authors.lastname: Schulz
mesh_terms: D035843:Biomedical Research; D007802:Language; D009626:Terminology as Topic