Ontology

The SBOL-OWL ontology provides a set of controlled terms that are used to describe genetic circuit designs using SBOL. Terms are included for the followings.

  • Descriptions of SBOL entities (e.g. “ComponentDefinition“) that are exchanged electronically. Constraints and validation rules that are enforced on SBOL entities are also captured as part of the ontology.
  • SBOL entities (e.g. “TopLevel“) that are not serialised but are used to group different SBOL entities. SBOL-OWL exposes these entities to semantic reasoning tools via parent-child relationships.
  • Terms (e.g. “inline“) that are used to restrict values of SBOL entities.
  • Properties (e.g. “sequence“) linking SBOL entities to accepted values.
  • Metadata terms (e.g. “Promoter“) for commonly used descriptions of design entities. Such terms may require the use of several SBOL entities and properties.

Browse

Browse the SBOL-OWL terms via an HTML page.

Download

SBOL-OWL is available in different formats.

Semantic reasoning

SBOL-OWL can be combined with any SBOL document to query genetic circuit designs using semantic queries. The sbolowl-sem Java application has been developed to facilitate this process. The resulting files can then be submitted to existing reasoners for semantic inferencing.

Using the sbolowl-sem Java library

usage: sbolowl_file sboldesign_file merged_file

  • sbolowl_file: The RDF version of the SBOL-OWL ontology
  • sboldesign_file: An SBOL file including genetic circuit designs
  • merged_file: The output file name

Example:
java -cp sbolowl-sem-1.0-SNAPSHOT-jar-with-dependencies.jar dissys.keele.ac.uk.RDFMerger sbol.rdf mapsto.rdf mapsto_sbolowl_consistent.rdf

Click here to access other examples.

Download sbol-sem

  • Click here to download the standalone sbol-sem Java library as a single file including all the dependencies.
  • Click here to download the sbol-sem Java library only. Dependencies are not included.