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SBOL Visual 2 Ontology.

Göksel Mısırlı1, Jacob Beal2, Thomas E Gorochowski3

  • 1School of Computing and Mathematics, Keele University, Keele, Staffordshire ST5 5BG, U.K.

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|April 2, 2020
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Summary
This summary is machine-generated.

Standardizing genetic designs requires consistent visual representations. The SBOL Visual 2 Ontology provides rules for mapping genetic elements to standardized glyphs, simplifying tool development and integration in synthetic biology.

Keywords:
glyphsontologystandardizationsynthetic biologyvisualization

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Area of Science:

  • Synthetic Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Standardized visual representations are crucial for genetic design and interpretation.
  • The Synthetic Biology Open Language (SBOL) Visual standard uses glyphs for genetic parts and relationships.
  • Current tools lack a standardized method for mapping biological concepts to SBOL Visual glyphs.

Purpose of the Study:

  • To introduce the SBOL Visual 2 Ontology, a machine-accessible resource for mapping genetic elements to SBOL Visual glyphs.
  • To provide a standardized approach for the implementation and maintenance of relationships between biological concepts and their visual representations.
  • To facilitate the development of visualization tools and integration with existing synthetic biology standards.

Main Methods:

  • Development of the SBOL Visual 2 Ontology, a rule-based system for glyph mapping.
  • Creation of a web service to accompany the ontology.
  • Integration of the ontology with existing biological ontologies and standards.

Main Results:

  • A comprehensive, machine-accessible ontology for mapping genetic parts, molecules, and interactions to SBOL Visual glyphs.
  • A web service enabling computational searching for suitable glyphs and simplifying visualization tool development.
  • Facilitation of integration with other synthetic biology standards and ontologies.

Conclusions:

  • The SBOL Visual 2 Ontology standardizes the visual representation of genetic designs, improving clarity and interoperability.
  • This resource simplifies the creation and maintenance of visualization tools for synthetic biology.
  • It promotes consistency and facilitates the integration of diverse biological data and standards.