Updating Annotation

This section explains updating annotations by providing feedback to the saved recommendations. Details of getting recommendation are demonstrated in Basic Usage and Getting Recommendation.

First, let’s get recommendations for two species: A and SAM.

$ recommend_species BIOMD0000000190.xml --species A SAM --outfile species_rec.csv
...
Analyzing 2 species...

Annotation recommended for 2 species:
[A, SAM]

Recommendations saved as:
/Users/amas/species_rec.csv

Once recommendations are saved, you will see a comma-separated value (CSV) file in the following format:

In the above, the existing column displays whether the annotation exists in the model file (1 means it exists, 0 otherwise). Now, you can choose to leave the value of the UPDATE ANNOTATION column (nothing will happen for that value); or, you can replace ignore with add and keep with delete to make changes. Below, user chose to add CHEBI:59789 to the existing annotation of SAM and delete existing annotation of A:

Once the table is updated, you can run the update_annotation command to update annotation of the SBML model, using BIOMD0000000190.xml (original model file) and species_rec.csv (recommendation file with user feedback):

$ update_annotation BIOMD0000000190.xml species_rec.csv new_model.xml
...
Updated model file saved as:
/Users/amas/new_model.xml

Then, you will see that the annotations have been updated in the new model file.