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bioRxiv · 10.1101/499970

SBOL-OWL: An ontological approach for formal and semantic representation of synthetic genetic circuits

Misirli, G.·Taylor, R.·Goni-Moreno, A.·McLaughlin, J. A.·Myers, C.·Gennari, J. H.·Lord, P.·Wipat, A.
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Abstract

Standard representation of data is key for the reproducibility of designs in synthetic biology. The Synthetic Biology Open Language (SBOL) has already emerged as a data standard to represent genetic circuit designs, and it is based on capturing data using graphs. The language provides the syntax using a free text document which is accessible to humans only. Here, we provide SBOL-OWL, an ontology for a machine understandable definition of SBOL. This ontology acts as a semantic layer for genetic circuit designs. As a result, computational tools can understand the meaning of design entities in addition to parsing structured SBOL data. SBOL-OWL not only describes how genetic circuits can be constructed computationally, it also facilitates the use of several existing Semantic Web tooling for synthetic biology. Here, we demonstrate some of these features, for example, to validate designs and check for inconsistencies. Through the use of SBOL-OWL, queries are simplified and become more intuitive. Moreover, existing reasoners can be used to infer information about genetic circuit designs that cant be directly retrieved using existing querying mechanisms. This ontological representation of the SBOL standard provides a new perspective to the verification, representation and querying of information about synthetic genetic circuits and is important to incorporate complex design information via the integration of biological ontologies.

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Misirli, G., Taylor, R., Goni-Moreno, A., McLaughlin, J. A., Myers, C., Gennari, J. H., Lord, P., Wipat, A.. 2018-12-19. SBOL-OWL: An ontological approach for formal and semantic representation of synthetic genetic circuits. https://doi.org/10.1101/499970

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