Structure-based classification and ontology in chemistry

We analyze the different categories of structural classes in chemistry, presenting a list of patterns for features found in class definitions. We compare these patterns of class definition to tools which allow for automation of hierarchy construction within cheminformatics and within logic-based ontology technology, going into detail in the latter case with respect to the expressive capabilities of the Web Ontology Language and recent extensions for modelling structured objects. Finally we discuss the relationships and interactions between cheminformatics approaches and logic-based approaches.Systems that perform intelligent reasoning tasks on chemistry data require a diverse set of underlying computational utilities including algorithmic, statistical and logic-based tools. For the task of automatic structure-based classification of chemical entities, essential to managing the vast swathes of chemical data being brought online, systems which are capable of hybrid reasoning combining several different approaches are crucial. We provide a thorough review of the available tools and methodologies, and identify areas of open research.Recent years have seen an explosion in the availability of data throughout the natural sciences. Availability of data facilitates research through complex data-mining and knowledge discovery methods. However, with the information explosion, retrieving relevant information from these data has become much more difficult. Computational processing is essential to filter, retrieve and organise such data. Traditional large-scale data management methods in chemistry include chemical structure-based algorithmic and statistical methods for the construction of hierarchies and similarity landscapes. These techniques are essential not only for human consumption of data in the form of effective browsing and searching but also in scientific methods for interpreting underlying biological mechanisms and detecting bioactivity patterns associated with chemica