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Continuation-like semantics for modeling structural process anomalies

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 aberra...

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Autor principal: Grewe, Niels
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3448524/
https://www.ncbi.nlm.nih.gov/pubmed/23046705
http://dx.doi.org/10.1186/2041-1480-3-S2-S8
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author Grewe, Niels
author_facet Grewe, Niels
author_sort Grewe, Niels
collection PubMed
description 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.
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spelling pubmed-34485242012-09-24 Continuation-like semantics for modeling structural process anomalies Grewe, Niels J Biomed Semantics Proceedings 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. BioMed Central 2012-09-21 /pmc/articles/PMC3448524/ /pubmed/23046705 http://dx.doi.org/10.1186/2041-1480-3-S2-S8 Text en Copyright ©2012 Grewe; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Proceedings
Grewe, Niels
Continuation-like semantics for modeling structural process anomalies
title Continuation-like semantics for modeling structural process anomalies
title_full Continuation-like semantics for modeling structural process anomalies
title_fullStr Continuation-like semantics for modeling structural process anomalies
title_full_unstemmed Continuation-like semantics for modeling structural process anomalies
title_short Continuation-like semantics for modeling structural process anomalies
title_sort continuation-like semantics for modeling structural process anomalies
topic Proceedings
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3448524/
https://www.ncbi.nlm.nih.gov/pubmed/23046705
http://dx.doi.org/10.1186/2041-1480-3-S2-S8
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