Martin R. Pullan

The Prometheus Taxonomic Model: a practical approach to representing multiple classifications

A model for representing taxonomic data in a flexible and dynamic system capable of handling and comparing multiple simultaneous classifications is presented. The Prometheus Taxonomic Model takes as its basis the idea that a taxon can be circumscribed by the specimens or taxa of a lower rank which are said to belong to it. In this model alternative taxon concepts are therefore represented in terms of differing circumscriptions. This provides a more objective way of expressing taxonomic concepts than purely descriptive circumscriptions have been published. Using specimens as the fundamental elements of taxon circumscription also allows for the automatic naming of taxa based upon the distribution and priority of types within each circumscription, and by application of the International Code of Botanical Nomenclature. This approach effectively separates the process of naming taxa (nomenclature) from that of classification, and therefore enables the system to store multiple classifications. The derivation of the model, how it compares with other models, and the implications for the construction of global data sets and taxonomic working practice are discussed.

A Universal Character Model and Ontology of Defined Terms for Taxonomic Description

Taxonomists classify biological specimens into groups (taxa) on the basis of similarities between their observed features (‘characters’). The description of these ‘characters’ is therefore central to taxonomy, but there is currently no agreed model, defined terminology nor methodology for composing these descriptions. This lack of a common conceptual model, together with the individualistic working practices of taxonomists, means that descriptions are not composed consistently, and are not easy to interpret and re-use, nor are datasets comparable. The purpose of the Prometheus II project is to improve the interpretation and comparison of plant descriptions. To this end we propose a new conceptual model for unambiguously representing character descriptions, and have developed a controlled vocabulary as an ontology of defined terms, which will be used to describe specimens according to our character model.

In search of a functional flora—towards a greater integration of ecology and taxonomy

Large-scale biodiversity informatics projects will not properly address the needs of one important potential user group. Ecologists do not have ready access to datasets which allow them to assign plant species to functional types. We believe that information technology has developed sufficiently to allow taxonomists and ecologists to work together to address this need and develop specimen databases to combine taxonomic data with ecological and ecophysiological information so that this information will be assigned to the correct taxon in the future. Digital images provide a rapid and economical method of vouchering specimen data, reducing the need to store physical vouchers in herbaria.

The Prometheus Description Model: an examination of the taxonomic description-building process and its representation

A model for representing taxonomic descriptive data is presented. The model has been developed in response to the growing requirement for the global exchange of descriptive data. Meaningful exchange of data requires that data be represented in a form that can be consistently parsed and interpreted, requiring a common data model and the constrained and explicitly defined use of descriptive terms. The model presented here is divided into two parts that address both of these issues. A new data model for the representation and storage of taxonomic descriptive data is proposed that builds on and extends the best features of current descriptive data models and formats. An ontology-based model for defining and constraining the use of descriptive terms is also presented. The model is based on an analysis of current taxonomic working practices and the processes involved in generating a description. The model takes a specimen-oriented approach allowing descriptive data to be represented through a range of levels of abstraction from actual measurements of structures on a specimen to

Implementation of the Prometheus Taxonomic Model: a comparison of database models and query languages and an introduction to the Prometheus Object-Oriented Model

Types of databases commonly used for handling taxonomic data are compared. It is shown that none of the existing types of databases fully support the requirements of taxonomic data. The results of this comparison provide a rationale for the design and implementation of a new database system based on an Extended Object- Oriented model. The new model, the Prometheus Object-Oriented Model (POOM) and its query language Prometheus Object-Oriented Language (POOL), are discussed in relation to the requirements of taxonomic data and the Prometheus Taxonomic Data Model. POOM provides the ability to represent the semantics of relationships between data. This allows us to build the type of graph structures that are found in taxonomic hierarchies. In addition, the system can query and manipulate these graphs (POOL). These features have been used to improve the original Prometheus Taxonomic Data Model. These improvements and the advantages they offer are described and discussed.