Facing the huge amount of textual and terminological data in the life sciences, we present a theoretical basis for the linguistic analysis of chemical terms. Starting with organic compound names, we conduct a morpho-semantic deconstruction into morphemes and yield a semantic representation of the terms’ functional and structural properties. These semantic representations imply both the molecular structure of the named molecules and their class membership. A crucial feature of this analysis, which distinguishes it from all similar existing systems, is its ability to deal with terms that do not fully specify a structure as well as terms for generic classes of chemical compounds. Such ‘underspecified’ terms occur very frequently in scientific literature. Our approach will serve for the support of manual database curation and as a basis for text processing applications.