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Process attributes in bio-ontologies.

Andrade AQ, Blondé W, Hastings J, Schulz S - BMC Bioinformatics (2012)

Bottom Line: 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 provide full definitions for process attributes at increasing levels of domain complexity.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria.

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.

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Related in: MedlinePlus

Comparison between different process qualities representations.
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Figure 4: Comparison between different process qualities representations.

Mentions: When analysed more deeply, process attributes as used in domain terminologies reveal themselves to be a loosely related set of descriptions, reifications and analogies used to communicate some characteristics of events in natural language. We provide in Figure 4 a comparison between SNOMED, PATO, VSO and the present approach.


Process attributes in bio-ontologies.

Andrade AQ, Blondé W, Hastings J, Schulz S - BMC Bioinformatics (2012)

Comparison between different process qualities representations.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3585786&req=5

Figure 4: Comparison between different process qualities representations.
Mentions: When analysed more deeply, process attributes as used in domain terminologies reveal themselves to be a loosely related set of descriptions, reifications and analogies used to communicate some characteristics of events in natural language. We provide in Figure 4 a comparison between SNOMED, PATO, VSO and the present approach.

Bottom Line: 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 provide full definitions for process attributes at increasing levels of domain complexity.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria.

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.

Show MeSH
Related in: MedlinePlus