Analysing Names of Organic Chemical Compounds
From Morpho-Semantics to SMILES Strings and Classes
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Revision with unchanged content. The growing amount of data in the life sciences requires computer-aided methods to make full use of valuable resources. The identification and understanding of chemical terminology is a key to automated biochemical text processing. The authors present a linguistically motivated approach to analyse (semi-)systematic and underspecified names of organic chemical compounds. A morpho-semantic analysis is obtained via a Prolog grammar developed according to IUPAC nomenclature rules. This results in a detailed intermediate semantic representation coding the informatio...
Revision with unchanged content. The growing amount of data in the life sciences requires computer-aided methods to make full use of valuable resources. The identification and understanding of chemical terminology is a key to automated biochemical text processing. The authors present a linguistically motivated approach to analyse (semi-)systematic and underspecified names of organic chemical compounds. A morpho-semantic analysis is obtained via a Prolog grammar developed according to IUPAC nomenclature rules. This results in a detailed intermediate semantic representation coding the information about the compound structure which is contained in a name. The system described provides SMILES strings mapping names to their corresponding molecular structure and computes the chemical classes which the analysed term belongs to. This book gives an introduction to topics relevant for the linguistic analysis of biochemical terminology and presents a specific system to serve as a basis for future research in the BioNLP domain. It is directed towards researchers in the fields of life science, biochemistry, linguistics, and computer science dedicating their work to (semi-)automatic information processing.
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