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07.10.2020

Automating the Assignment of Systems Biology Onotology Terms

In her bachelor's thesis, Elisabeth Fritze suggests an automatic assignment of SBO terms for reactions.

Heatmap that displays the number of annotations for each SBO term (x-axis) in all 108 BiGG models (y-axis).

Annotations, such as the Systems Biology Ontology (SBO) terms, play an essential role in constructing computational models in SBML format. The thesis of Elisabeth Fritze aimed to automate SBO term annotation for reactions in SBML models. To this end, an annotation program was implemented in Python. In the process, Ms. Fritze also formulated a mapping between Enzyme Commission (EC) numbers to SBO terms to enable SBO terms to EC annotated reactions.

Additionally, the annotation script was tested on the 108 available models from the so-called BiGG database. This test showcased the gained diversity and specificity in SBO terms across the models. Thus, her bachelor thesis results provide additional context to models and can be seen as the first step for automated reaction analysis based on SBO terms.

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