Analysing names of organic chemical compounds : from morpho-semantics to SMILES strings and classes

Abstract

The linguistic analysis of chemical terminology is a key to biochemical text processing and semi-automatic database curation. The system described analyses systematic and semi-systematic names of chemical compounds, class terms, and also otherwise underspecified names by means of a morpho-semantic grammar developed according to IUPAC nomenclature. It yields an intermediate semantic representation which describes the information encoded in a name. Our tool provides SMILES strings for the mapping of names to their molecule structure and also classifies the analysed terms. It was implemented in Prolog as a prototype and a basis for further development to support research in the life sciences.