A knowledge base of the chemical compounds of intermediary metabolism

This paper describes a publicly available knowledge base ofthe chemical compounds involved in intermediary metabolism.We consider the motivations for constructing a knowledge baseof metabolic compounds, the methodology by which it was constructed,and the information that it currently contains. Currently theknowledge base describes 981 compounds, listing for each: synonymsfor its name, a systematic name, CAS registry number, chemicalformula, molecular weight, chemical structure and two–dimensionaldisplay coordinates for the structure. The Compound KnowledgeBase (CompoundKB) illustrates several methodological principlesthat should guide the development of biological knowledge bases.I argue that biological datasets should be made available inmultiple representations to increase their accessibility toend users, and I present multiple representations of the CompoundKB(knowledge base, relational data base and ASN. 1 representations).I also analyze the general characteristics of these representationsto provide an understanding of their relative advantages anddisadvantages. Another principle is that the error rate of biologicaldata bases should be estimated and documented—this analysisis performed for the CompoundKB.