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Continuation-like semantics for modeling structural process anomalies
- Source :
- Journal of Biomedical Semantics, Vol 3, Iss Suppl 2, p S8 (2012), Journal of Biomedical Semantics
- Publication Year :
- 2012
- Publisher :
- BMC, 2012.
-
Abstract
- Background Biomedical ontologies usually encode knowledge that applies always or at least most of the time, that is in normal circumstances. But for some applications like phenotype ontologies it is becoming increasingly important to represent information about aberrations from a norm. These aberrations may be modifications of physiological structures, but also modifications of biological processes. Methods To facilitate precise definitions of process-related phenotypes, such as delayed eruption of the primary teeth or disrupted ocular pursuit movements, I introduce a modeling approach that draws inspiration from the use of continuations in the analysis of programming languages and apply a similar idea to ontological modeling. This approach characterises processes by describing their outcome up to a certain point and the way they will continue in the canonical case. Definitions of process types are then given in terms of their continuations and anomalous phenotypes are defined by their differences to the canonical definitions. Results The resulting model is capable of accurately representing structural process anomalies. It allows distinguishing between different anomaly kinds (delays, interruptions), gives identity criteria for interrupted processes, and explains why normal and anomalous process instances can be subsumed under a common type, thus establishing the connection between canonical and anomalous process-related phenotypes. Conclusion This paper shows how to to give semantically rich definitions of process-related phenotypes. These allow to expand the application areas of phenotype ontologies beyond literature annotation and establishment of genotype-phenotype associations to the detection of anomalies in suitably encoded datasets.
- Subjects :
- Theoretical computer science
Computer Networks and Communications
Computer science
Semantics (computer science)
Process (engineering)
Health Informatics
Type (model theory)
ENCODE
computer.software_genre
lcsh:Computer applications to medicine. Medical informatics
Computer Science Applications
Open Biomedical Ontologies
Continuation
Proceedings
Norm (artificial intelligence)
Identity (object-oriented programming)
lcsh:R858-859.7
Data mining
computer
Information Systems
Subjects
Details
- Language :
- English
- ISSN :
- 20411480
- Volume :
- 3
- Database :
- OpenAIRE
- Journal :
- Journal of Biomedical Semantics
- Accession number :
- edsair.doi.dedup.....1198aa1f5f11a247805adce7844c241f