Knowledge-based generalization of metabolic networks: a practical study.
The complex process of genome-scale metabolic network reconstruction involves semi-automatic reaction inference, analysis, and refinement through curation by human experts. Unfortunately, decisions by experts are hampered by the complexity of the network, which can mask errors in the inferred network. In order to aid an expert in making sense out of the thousands of reactions in the organism's metabolism, we developed a method for knowledge-based generalization that provides a higher-level view of the network, highlighting the particularities and essential structure, while hiding the details. In this study, we show the application of this generalization method to 1,286 metabolic networks of organisms in Path2Models that describe fatty acid metabolism. We compare the generalised networks and show that we successfully highlight the aspects that are important for their curation and comparison.
Inria/Université Bordeaux/CNRS Joint Project-Team, MAGNOME F-33405 Talence, France.
Anna
A
Zhukova
David J
DJ
Sherman
D000465:Algorithms; D001185:Artificial Intelligence; D003198:Computer Simulation; D057225:Data Mining / Q000379:methods*; D003628:Database Management Systems; D030562:Databases, Protein; D005227:Fatty Acids / Q000378:metabolism*; D016015:Logistic Models; D055442:Metabolome / Q000502:physiology*; D008954:Models, Biological; D025941:Protein Interaction Mapping / Q000379:methods*; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D014584:User-Computer Interface
D005227:Fatty Acids