Bottom-up construction of ontologies

Presents a particular way of building ontologies that proceeds in a bottom-up fashion. Concepts are defined in a way that mirrors the way their instances are composed out of smaller objects. The smaller objects themselves may also be modeled as being composed. Bottom-up ontologies are flexible through the use of implicit and, hence, parsimonious part-whole and subconcept-superconcept relations. The bottom-up method complements current practice, where, as a rule, ontologies are built top-down. The design method is illustrated by an example involving ontologies of pure substances at several levels of detail. It is not claimed that bottom-up construction is a generally valid recipe; indeed, such recipes are deemed uninformative or impossible. Rather, the approach is intended to enrich the ontology developer's toolki

Storing the wisdom: chemical concepts and chemoinformatics

The purpose of the paper is to examine the nature of chemical concepts, and the ways in which they are applied in chemoinformatics systems. An account of concepts in philosophy and in the information sciences leads to an analysis of chemical concepts, and their representation. The way in which concepts are applied in systems for information retrieval and for structure–property correlation are reviewed, and some issues noted. Attention is focused on the basic concepts or substance, reaction and property, on the organising concepts of chemical structure, structural similarity, periodicity, and on more specific concepts, including two- and three-dimensional structural patterns, reaction types, and property concepts. It is concluded that chemical concepts, despite (or perhaps because of) their vague and mutable nature, have considerable and continuing value in chemoinformatics, and that an increased formal treatment of concepts may have value in the future

Storing the wisdom: chemical concepts and chemoinformatics

The purpose of the paper is to examine the nature of chemical concepts, and the ways in which they are applied in chemoinformatics systems. An account of concepts in philosophy and in the information sciences leads to an analysis of chemical concepts, and their representation. The way in which concepts are applied in systems for information retrieval and for structure–property correlation are reviewed, and some issues noted. Attention is focused on the basic concepts or substance, reaction and property, on the organising concepts of chemical structure, structural similarity, periodicity, and on more specific concepts, including two- and three-dimensional structural patterns, reaction types, and property concepts. It is concluded that chemical concepts, despite (or perhaps because of) their vague and mutable nature, have considerable and continuing value in chemoinformatics, and that an increased formal treatment of concepts may have value in the future