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. 2012 Sep 21;3 Suppl 2(Suppl 2):S5.
doi: 10.1186/2041-1480-3-S2-S5. Epub 2012 Sep 21.

Towards improving phenotype representation in OWL

Frank Loebe  1 , Frank Stumpf, Robert Hoehndorf, Heinrich Herre
Affiliations

Towards improving phenotype representation in OWL

Frank Loebe et al. J Biomed Semantics. .

Abstract

Background: Phenotype ontologies are used in species-specific databases for the annotation of mutagenesis experiments and to characterize human diseases. The Entity-Quality (EQ) formalism is a means to describe complex phenotypes based on one or more affected entities and a quality. EQ-based definitions have been developed for many phenotype ontologies, including the Human and Mammalian Phenotype ontologies.

Methods: We analyze formalizations of complex phenotype descriptions in the Web Ontology Language (OWL) that are based on the EQ model, identify several representational challenges and analyze potential solutions to address these challenges.

Results: In particular, we suggest a novel, role-based approach to represent relational qualities such as concentration of iron in spleen, discuss its ontological foundation in the General Formal Ontology (GFO) and evaluate its representation in OWL and the benefits it can bring to the representation of phenotype annotations.

Conclusion: Our analysis of OWL-based representations of phenotypes can contribute to improving consistency and expressiveness of formal phenotype descriptions.

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Figures

Figure 1
Figure 1
EQ model. In the schematic part, E stands for entity, Q for quality, and R for relational quality. Schema a) accounts for a simple (unary or non-relational) quality, while b) refers to relational qualities. The examples c) and d) correspond to those from the text. Example e) in parallel with d) is forestalling the problem of inter-modeler consistency from the Methods section. 'conc.' in d) and e) abbreviates concentration of.
Figure 2
Figure 2
Roles-as-properties: Ontological roles encoded as OWL properties. PB stands for phenotype bearer in the schematic part.
Figure 3
Figure 3
Roles-as-classes: Ontological roles modeled as classes in OWL.
Figure 4
Figure 4
Relator-based-quality: Relators characterized by qualities.
See this image and copyright information in PMC

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