1. Prometheus II: Capturing and Relating Character Concept Definitions in Plant Taxonomy The Biological Problem Concepts describe objects and people invariably use names to refer to these concepts. However, using names as a shorthand for an underlying concept has the following problems: concept bounds will vary from person to person multiple concepts may be associated with the same term different names can refer to the same concept concept definitions are rarely explicitly recorded In taxonomy the descriptive concepts are called characters. However, the application of the term character is imprecise as it can refer to parts of organisms (e.g. leaf), attributes of organisms (e.g. plant height), or attributes of parts of organisms (e.g. leaf shape). These problems mean that there is no verifiable basis for the comparison of concepts across multiple bodies of data from different sources. This is hampering the advancement of our understanding of the form, function and taxonomic relationships of the organisms around us. NAPIER UNIVERSITYRBGE http://www.soc.napier.ac.uk/dosghttp://www.rbge.org.uk Jessie Kennedy Gordon Russell Martin Pullan Cédric Raguenaud Alan Cannon Mark Watson Trevor Paterson Sarah McDonald PUBLICATION: McDonald, S. M., Raguenaud C., Pullan M. R., Kennedy J. B., Russell, G. & Watson, M. F. The Prometheus II Description Model: an objective approach to representing taxonomic descriptions. Submitted to Taxon on 14th June 2002. Email: prometheus@rbge.org.ukWeb: http://www.prometheusdb.org Achievements to Date Completed an assessment of user requirements, by conducting interviews with Royal Botanic Garden staff Compiled several data sets for prototype testing using descriptive data from Umbelliferae and Bacillariophyceae obtained from new specimen descriptions and from published descriptions in Floras and monographs Constructed abstract data model (see Model 1 below) Constructed and tested two prototypes Tasks to be completed in the next year Design and test Model 2 for incorporating term definitions into Model 1 Develop the user interface by conducting research at the Royal Botanic Garden Edinburgh Build a comprehensive plant character glossary from published work and consultation with taxonomists at the Royal Botanic Garden Edinburgh Develop and test a prototype for Model 2 Fig. 1 shows that specimens have a description according to some author and publication. Descriptions are composed of several description units, each of which is a collection of description elements regarding some structure of the specimen. Each description element (or “character”) specifies a plant structure, property and state or value. These are recorded using the appropriate terms. The Prometheus approach emphasises the definition of terms and requires each use of a term to be placed into a context determined by the definition. Fig. 2 shows how the four kinds of term used to make up a description element are defined as defined terms. n n Defined As n n Structure Term Property Term Qualitative State Term Unit Term Term Defined Structure Defined Qualitative State Defined Unit Defined Term Assigned To n Defined As Defined Property Defined As n Modifier Term Defined Modifier Fig. 2 Description Structure Fig. 1 Defined Structure Defined Property Defined Units Value Description Property Description Value Description Unit Defined Qualitative State n Description State Description Author n n Description Unit the Author Specimen n the Description Description Units Description Element n The above screenshot shows a prototype interface for entering taxonomic data into the Prometheus system. This interface is generated from a terminology specific to the particular plant group being described. It allows a user to record the characters describing a specimen as well as recording definitions for all terms used within those characters. Taxonomists will be able to extend their terminologies as and when required.