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. 2017 Jun 5;8(1):18.
doi: 10.1186/s13326-017-0126-0.

Dead simple OWL design patterns

David Osumi-Sutherland  1 , Melanie Courtot  2 , James P Balhoff  3 , Christopher Mungall  4
Affiliations

Dead simple OWL design patterns

David Osumi-Sutherland et al. J Biomed Semantics. .

Abstract

Background: Bio-ontologies typically require multiple axes of classification to support the needs of their users. Development of such ontologies can only be made scalable and sustainable by the use of inference to automate classification via consistent patterns of axiomatization. Many bio-ontologies originating in OBO or OWL follow this approach. These patterns need to be documented in a form that requires minimal expertise to understand and edit and that can be validated and applied using any of the various programmatic approaches to working with OWL ontologies.

Results: Here we describe a system, Dead Simple OWL Design Patterns (DOS-DPs), which fulfills these requirements, illustrating the system with examples from the Gene Ontology.

Conclusions: The rapid adoption of DOS-DPs by multiple ontology development projects illustrates both the ease-of use and the pressing need for the simple design pattern system we have developed.

Keywords: Design pattern; OBO; OWL.

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Figures

Fig. 1
Fig. 1
DOS-DP for defining classes of transmembrane import (based on an example from the GO.) Panel A shows the DOS-DP using the OBO extension. Panel B shows the same pattern expressed using the core specification (classes, relations and vars fields omitted from panel B for brevity). In Panel A, annotations are specified using dedicated fields (def, name, xrefs). The mapping from these to OWL annotation properties is specified in the OBO extension schema. This mapping is made explicit in Panel B, using an annotation_property dictionary and the annotationProperty field in axiom specifications under annotations. Throughout both versions of the pattern, paired fields text and vars specify printf text and fillers respectively. The value field is used with the data_list_var def_xrefs to specify a list database_cross_reference annotations on the definition
Fig. 2
Fig. 2
Example pattern implementation. An example of a term, ‘leucine transport across the plasma membrane’, generated using the pattern in Fig. 1. Note the automated classification under ‘amino acid transport across the plasma membrane’, specified using the same pattern
See this image and copyright information in PMC

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