Limits...
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.

Show MeSH

Related in: MedlinePlus

The heart beating process as represented in ECG.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3585786&req=5

Figure 1: The heart beating process as represented in ECG.

Mentions: The OWL model is built around the two classes: heart beating process and heart cycle. Whereas the former is a homomereous entity (there are parts of heart beating processes, which are, again heart beating processes) [16], the latter refers to the events that occur from the beginning of one heartbeat to the beginning of the next. A sequence of members of the class heart_cycle constitutes all members of the class heart_beating_process. If we cut a temporal region, which spans over a minute of this beating process we can count the number of full heart cycles that take place in that time period. The class heart_cycle has common properties to every cyclical process; and the heart beating process, which for any given period of time consists of a fiat collection of heart cycles. The generic classes were named “single cycle” and “aggregate of cycles and their parts”, respectively. This can be seen in Figure 1 and 2. We relate the cycles and the aggregate using the BioTop[17] relation “hasGranularPart”, since our goal is to relate collectives (aggregate of cycles) and the grains (the cycles themselves) that compose it [18].


Process attributes in bio-ontologies.

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

The heart beating process as represented in ECG.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: The heart beating process as represented in ECG.
Mentions: The OWL model is built around the two classes: heart beating process and heart cycle. Whereas the former is a homomereous entity (there are parts of heart beating processes, which are, again heart beating processes) [16], the latter refers to the events that occur from the beginning of one heartbeat to the beginning of the next. A sequence of members of the class heart_cycle constitutes all members of the class heart_beating_process. If we cut a temporal region, which spans over a minute of this beating process we can count the number of full heart cycles that take place in that time period. The class heart_cycle has common properties to every cyclical process; and the heart beating process, which for any given period of time consists of a fiat collection of heart cycles. The generic classes were named “single cycle” and “aggregate of cycles and their parts”, respectively. This can be seen in Figure 1 and 2. We relate the cycles and the aggregate using the BioTop[17] relation “hasGranularPart”, since our goal is to relate collectives (aggregate of cycles) and the grains (the cycles themselves) that compose it [18].

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