SBOL Visual Ontology (SBOL-VO)

The reference implementation of the SBOL Visual standard

SBOL Visual Ontology (SBOL-VO)

The SBOL Visual Ontology (SBOL-VO) provides a set of controlled terms to describe visual glyphs for genetic circuit designs. The terms are organised based on their descriptions in community-edited Markdown files. Terms are defined for recommended and alternative glyphs in addition to terms to represent generic glyphs. SBOL-VO consists of the following items.

  • A base term. The base term in the ontology is called “Glyph”.
  • Terms for glyphs. Examples include “AptamerGlyph”, “AssemblyScarGlyph” and “AssemblyScarGlyphAlternative”.
  • Properties. SBOL-VO includes object properties such as “hasGlyph” and “isAlternativeOf” to define the relationships between different terms.
  • Annotations. Terms are annotated using properties such as “defaultGlyph” and “recommended”.
  • Ontological axioms. Logical axioms restricting the use of SBOL-VO terms to specific biological roles and processes.

Browse

Browse the SBOL-VO terms via an HTML page.

The ontology can also be viewed after downloading and opening in an ontology editor, such as Protege.

Download

SBOL-VO is available as an RDF file. Click here to download the ontology.

Computational access: The SBOL-VO web service (SBOL-VO-WS)

An HTTP-based glyph service: The SBOL-VO web service(SBOL-VO-WS) has been developed to resolve SBOL-VO glyphs via an REST-based HTTP interface. The matching glyph is returned by using a term from the SBOL-Visual Ontology, the Sequence Ontology (SO) or the Systems Biology Ontology (SBO). The http://{SBOL-VO-WS}/glyph/{ONTOLOGY_TERM}"} REST interface returns glyphs. When a term from the SO or the SBO is used and there is no exact match, then a glyph is returned using the closest mathing parent term. The following example demonsrates retrieving the aptamer glyph by using the corresponding SBOL-VO or terms from the SO:

The web service returns the default PNG images. The PNG and SVG versions can be retrieved explicitly by appending “/svg” or “/png” to the query interface :

Mapping glyphs to terms from ontologies: Tools can also use the SBOL-VO-WS to get the mapping information and then to subsequently include glyphs, using the http://{SBOL-VO-WS}/mapping/{ONTOLOGY_TERM}"} interface. The mapping interface works similar to the glyph interface but it returns information in the JSON format. This interface includes information about the closest parent term, for which a glyph is assigned, and the parent term’s distance to the query term. URL examples below return information about AptamerGlyph.

Searching for glyphs: The SBOL-VO-WS can be used to search for glyphs using the http://{SBOL-VO-WS}/query/{ONTOLOGY_TERM}"} REST interface. This query interface is the reverse of the mapping interface and returns information about glyphs using a query term and for all its child terms. Glyphs are searched for by using a term from the SBOL-Visual Ontology, the Sequence Ontology or the Systems Biology Ontology. Examples:

Retrieving metadata about glyphs: The SBOL-VO-WS can also be used to retrieve metadata about SBOL Visual glyphs, using the for glyphs using the http://{SBOL-VO-WS}/metadata/{SBOL-VO-TERM}"} REST interface. Examples: