CellDesigner Help

SBO (Systems Biology Ontology)

"The Systems Biology Ontology is a set of controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modelling."

http://www.ebi.ac.uk/sbo/main/

CellDesigner can save the SBO Term automatically.

To save a model with SBO Terms

  1. In the Menu, select Edit – SBO Term Value.
  2. Select Save with SBOTerm Value option.
  3. When you save, SBO Terms will automatically be allocated and written in the model file.

An example of SBO Terms in the XML file

  1. In the Menu, click File – New.
  2. In the New Document dialog, click OK.
  3. From the Macro Toolbar, select the Inhibition icon (Inhibition icon).
  4. Click on the Draw Area.
  5. A diagram expressing the inhibition is drawn.
    Macro (Inhibition)
  6. In the Menu, click File – Save.
  7. Launch an XML-capable web browser or an text editor to open the XML file you have just saved.
  8. Listed below are elements with the sboTerm property.
    • <model metaid="untitled" id="untitled" sboTerm="SBO:0000231">
    • <compartment metaid="default" id="default" size="1" units="volume" sboTerm="SBO:0000240"/>
    • <species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0" sboTerm="SBO:0000240">
    • <species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0" sboTerm="SBO:0000240">
    • <reaction metaid="re1" id="re1" reversible="false" sboTerm="SBO:0000231">
    • <speciesReference metaid="CDMT00002" sboTerm="SBO:0000003" species="s1">
    • <speciesReference metaid="CDMT00003" sboTerm="SBO:0000003" species="s1">
    • <modifierSpeciesReference metaid="CDMT00004" sboTerm="SBO:0000003" species="s2">
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