sbol-visual-ontology

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”.

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.

Development

The Python code to generate the ontology is maintained by Goksel Misirli and is available at the sbol-visual-ontology GitHub repository.

Are you intersted in contributing?

If you are interested in contributing, please see below and get in touch with the developers of this repository.

Prerequisites

• Make sure you have git and python3 installed. Then install owlready2 and rdflib python libraries.

  pip3 install owlready2
  pip3 install rdflib
  

• Also make sure you jave Maven and Java installed to update the autogenerated HTML version.

• Download the SBOL-Visual project

  git clone https://github.com/SynBioDex/SBOL-visual.git
  

  and place it at the same level with the SBOL-Visual-Ontology folder. The parent working folder should look like below: ```

• Parent working folder
  • SBOL-visual
  • sbol-visual-ontology ```
• The edit the python scripts under markdown-to-owl scripts. The main file to execute is Application.py and the changes to the ontology can be done via Ontology.py.

Updating the HTML documentation

SBOL-VO has an HTML version that is automatically created from the ontology using LODE.

• Download a forked copy of LODE and run it:

  git clone https://github.com/dissys/LODE.git
  cd LODE
  mvn clean jetty:run
  

• Open a web browser and save the output from the following URL as sbol-vo.html, into the sbol-visual-ontology folder, replacing the existing file.

  http://localhost:8080/lode/extract?url=https://dissys.github.io/sbol-visual-ontology/sbol-vo.rdf
  

• Finally, run the following line to update the autogenerated HTML.

  cd sbol-vo-update-doc
  mvn exec:java -Dexec.mainClass="uk.ac.keele.dissys.sbolvo.html.App" 
  

Submitting changes

Note: Update instructions are adapted from https://github.com/SynBioDex/SBOL-visual.

Updates should be made in a branch or a separate fork on GitHub. To do this, follow standard git branching or forking procedure.

Here is an example of git commands to achieve this:

git clone https://github.com/dissys/sbol-visual-ontology.git
git pull origin master # MAKE SURE NO ONE HAS MADE ANYMORE CHANGES
git checkout -b <newBranch> # CREATE NEW BRANCH

Make your edits and use the following commands to add them to your own GitHub branch.

git add <filesYouChanged>
git commit
git push origin <newBranch>

Synching changes with the SBOL-Visual repository

These changes will then be uploaded to SBOL-visual ontology v2 directory after the changes are reviewed and incorporated. Alternatively, please follow the insructions at https://github.com/SynBioDex/SBOL-visual to incorporate the changes to the https://github.com/SynBioDex/SBOL-visual/tree/master/Ontology/v2 folder directly.