semanticSBML - User exercises

    1. Build a model of the threonine pathway from the KEGG reaction IDs R00480, R02291, R01775, R01771, R01466 (two versions, with and without enzyme species). Hint: To add several reaction identifers you have to write every ID into a new line (without any commas, quotes or other signs).
    2. Annotate the model with the following IDs: (i) NCBI taxonomy ID 83333 for Escherichia coli ("model:is" qualifier); (ii) NCBI PubMed ID 11368770 for the article Chassagnole C, Fell DA, Rais B, Kudla B, Mazat JP. Control of the threonine-synthesis pathway in Escherichia coli: a theoretical and experimental approach. Biochem J. 2001 356(Pt 2):433-44. ("model:isDescribedBy" qualifier); (iii) KEGG pathway ID map00260 ("Bio:isVersionOf" qualifier).
    3. Display the model structure, check the model for correctness, and have a look at the element annotations.
    4. Save the model to disk
    5. Download the original threonine pathway model from Biomodels.net (BIOMD0000000066.xml) and compare it to your model (display the structures and find differences).
    1. Create an SBML model from the reactions: G6P <=> F6P and F6P + ATP <=> FBP + ADP. Choose "cell" as the compartment. (Please do not forget to type spaces between every reaction parameter. )
    2. Annotate all substances with MIRIAM annotations pointing to the ChEBI database.

      G6P: Glucose-6-phosphate;
      F6P: Fructose-6-phosphate;
      FBP: Fructose-1,6-bisphosphate;
      ATP: Adenosine triphosphate;
      ADP: Adenosine diphosphate

    3. Annotate the compartment with the SBO term for "physical compartment"
    4. Display the model and check it for correctness.
    5. Look up the KEGG reaction ID for the second reaction and build a second model "model_2" from this reaction, in the compartment "Cell" (with capital C).
    6. Merge the two models "model_1" and "model_2". Make sure that the two compartments "cell" and "Cell" are merged to a single compartment.
    7. Save the merged model to disk
  3. Create an SBML model from the KEGG pathway map for glycolysis (map00010).