Self-organizing ontology of biochemically relevant small molecules

To address this, we present a formal framework based on Semantic Web technologies for the automatic design of chemical ontology which can be used for automated classification of novel entities. We demonstrate the automatic self-assembly of a structure-based chemical ontology based on 60 MeSH and 40 ChEBI chemical classes. This ontology is then used to classify 200 compounds with an accuracy of 92.7%. We extend these structure-based classes with molecular feature information and demonstrate the utility of our framework for classification of functionally relevant chemicals. Finally, we discuss an iterative approach that we envision for future biochemical ontology development.We conclude that the proposed methodology can ease the burden of chemical data annotators and dramatically increase their productivity. We anticipate that the use of formal logic in our proposed framework will make chemical classification criteria more transparent to humans and machines alike and will thus facilitate predictive and integrative bioactivity model development.Over the hundreds of years of biochemical research, humanity has encountered myriads of chemical entities with countless combinations of functional groups that imparted upon their bearers distinct reactivities and properties. According to the structure-activity relationship (SAR) principle, grouping these entities into structure- and property-based classes within a larger chemical ontology (formal logical specification of a chemical hierarchy conceptualization) can enable the recapitulation of or improvements in the prediction of their biological functionality and chemical reactivity patterns, thus providing indispensable assistance in understanding the molecular nature of metabolism, toxicity, and bioactivity [1,2]. In addition to this, the assignment of individual chemical entities to a given class within a chemical ontology or hierarchy may facilitate the inference of the potential anticipated roles and properties of these en