Using proteomics of ovarian cancer to constrain a genome-scale metabolic model

Aim: Identify person-specific biomarkers for drug and treatment responses.

• Human-GEM.xml is the latest collection of a genome-scale model (GSM) of human metabolism by Robinson et al. 2020

• annotate_model.ipynb takes all of the reactions in the model and for each set of ENSGs looks up the corresponding protein identifier and name from Uniprot and associates it with that reaction.

• model_proteins.csv is the output from the Python script that matches model reactions to protein names and identifiers. The ReactionRule column can be used to check whether the reaction is catalyzed by a single protein, a protein complex or different isoforms.

• Human-GEM-annotated.xml is an instance of the GSM by Robinson et al. 2020 with further information included in the reaction name, reaction notes and reaction annotations.