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Tawny-SBOL: Using ontologies to design and constrain genetic circuits

Lookup NU author(s): Dr Goksel Misirli, Dr Phillip Lord



This is the final published version of a conference proceedings (inc. abstract) that has been published in its final definitive form by CEUR-WS, 2017.

For re-use rights please refer to the publisher's terms and conditions.


© 2018 CEUR-WS. All rights reserved. Synthetic biology is a data-driven engineering discipline and designing novel genetic circuits often requires utilizing existing information where possible. Semantic Web technologies, and particularly ontologies, are important to formalize knowledge for computational design processes and to facilitate data interoperability. The Synthetic Biology Open Language has already emerged as a data standard and is based on RDF/XML. This language is ideal to represent information as graphs in which nodes and edges are defined using multiple properties. Terms from ontologies and controlled vocabularies are used to indicate the meaning of these multiple properties. Semantic representation of these nodes and edges would simplify both the representation of information and the querying of underlying information. Here, we present Tawny-SBOL as a domain specific language and a framework to address these issues. Tawny-SBOL is a proof-of-concept project, based on the Tawny-OWL ontology library, to specify genetic circuit designs. Users can query and potentially constrain these designs. As a result, designs can be evolved based on predefined requirements. Due to the native Clojure language support, users can extend Tawny-SBOL programmatically and work interactively.

Publication metadata

Author(s): Misirli G, Lord P

Editor(s): Matthew Horridge, Phillip Lord, Jennifer D. Warrender

Publication type: Conference Proceedings (inc. Abstract)

Publication status: Published

Conference Name: Proceedings of the 8th International Conference on Biomedical Ontology (ICBO 2017)

Year of Conference: 2017

Online publication date: 11/07/2018

Acceptance date: 02/04/2016

Date deposited: 09/08/2018

ISSN: 1613-0073

Publisher: CEUR-WS


Series Title: CEUR Workshop Proceedings