Cedric Raguenaud

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.

The Prometheus taxonomic database

M.R. Pullen et al. (2000) have designed a new model of plant taxonomy (called Prometheus); it supports multiple overlapping classifications, and distinguishes the process of naming from classifying. The concepts identified in this taxonomic model necessitated the design of a new database model - the Prometheus Object-Oriented Model (POOM) - to represent and manipulate the data. POOM is an extended object-oriented model which emphasises relationships, thereby providing graph behaviour in an object-oriented database and providing an expressive means of defining relationships between objects. Additionally, the Object Query Language (OQL) is extended to the Prometheus Object-Oriented Language (POOL) in order to provide unified querying of object-oriented graph structures. This paper presents a taxonomic database system designed in terms of the concepts offered by POOM. Through examples we show how the representation of the semantics and processes of taxonomy, not possible using existing data models, can be supported. Example POOL queries highlight the need for the extended features for manipulating relationships, graph structures and complex objects such as are found in taxonomies.

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

Multiple overlapping classifications: issues and solutions

This paper discusses issues and solutions for supporting multiple overlapping classifications in database systems. These classifications are commonly found in science, although they are often ignored in computing applications for scientific data, and inappropriate solutions adopted as their replacement. Known database models and classification techniques offer some degree of support for multiple overlapping classifications, but do not fully support the basic features we have identified as necessary: trees/graphs, traceability, semantics of classifications, independence of classification and data, and identity of classifications. The approach to the problem adopted by the Prometheus project, based on an extended object-oriented database model and the independence of classification schemes from classified data, is presented and discussed.

The Prometheus database for taxonomy

This paper presents the work carried out in the Prometheus project and its motivation, taxonomy. Taxonomy presents challenges to common database systems. Because of its complexity and the necessary treatments applied to its data, common database model such as the relational, the object-oriented of even graph models are not able to support taxonomic applications fully. Our approach is the extension of a object-oriented database model with explicit relationships in order to support new features and thereby offer the necessary level of service for developing taxonomic applications.

Two approaches to representing multiple overlapping classifications: a comparison [plant taxonomy]

One of the tasks of plant taxonomy is the creation of classifications of organisms that allows the understanding of the evolutionary relationships between them. In this paper, we describe two different data models that have been designed to support two aspects of taxonomic work: the storage of the information and the visualisation of that information. We show that these two models are different because of their constraints and aims, and we compare their abilities using a number of typical tasks that users perform. We also show that, although different and able to perform different tasks, each of these models is well adapted to its purpose, and tight integration is difficult.