Before revision:  Even in such a heavily simplified method, which disregards most of the dynamic aspects of biochemistry, one is faced with fundamental questions, such as how the chemical reaction systems should be reduced to a graph so that as much information as possible about the original network is retained. Vertices may represent either chemical substances, or reactions , or both .
After revision:  Even in such a heavily simplified method, which disregards most of the dynamic aspects of biochemistry, one is faced with fundamental questions, such as how the chemical reaction systems should be reduced to a graph so that as much information as possible from the original reaction system. In such graph representations, should the edges go between substrates and products, or substrates and substrates , or both .