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

Abstract

Summary Pullan, M. R., Watson, M. F., Kennedy, J. B., Raguenaud, C. & Hyam, R.: The Prometheus Taxonomic Model: a practical approach to representing multiple classifications. – Taxon 49: 55‐75. 2000. – ISSN 0040‐0262. 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 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, and is more explicit than merely providing pointers to where 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.

DNA barcoding and taxonomy: dark taxa and dark texts

“…Because the taxonomic concepts in GBIF and BOLD are explicitly defined with respect to sets of specimens we can directly compare them, rather than rely on the possibly erroneous assumption that a given taxonomic name means the same thing in the two databases. Furthermore, as increasing numbers of type specimens are sequenced [15] we can more firmly associate names with sets of specimens, leading to a computable nomenclature where the name we assign to a set of specimens can be determined automatically [33]. Figure 6: Comparison of Morethia obscura in GBIF (top) with DNA barcodes from the same taxon in BOLD (bottom).…”

Unitary or unified taxonomy?

“…Attractive as a single and supposedly authoritative or preferred classification is to many users, multiple classifications and multiple taxonomic concepts, past and present, actually exist in the literature and in databases. In the Prometheus Taxonomic Model (Pullan et al 2000; and see www.prometheusdb.org), it was emphasized that Ytow et al 2001; Although the Prometheus project is not a Web site with taxonomic data, it demonstrates that specimen information underpinning taxonomic revisions can be incorporated into a taxonomic model to provide objective comparison of multiple classifications. The model was designed for botanists, specifically incorporating regulations in the Botanical Code, but the problem being addressed applies to all taxa.…”

Formalizing Botanical Taxonomies

“…One problem is that because of the size of modern taxonomies and the fact that usually many taxonomists contribute to a classification, it is difficult to oversee a single classification. Other problems are mentioned by Pullan et al (2000) who state that classifications must cope with "historical data, newly described taxa, new revisions and conflicting opinions".…”

“…The Prometheus project (Pullan et al, 2000) provides an object-oriented formalism for taxonomies that is implemented in an object database system (Prometheus, 2002). This implementation improves on prior attempts at implementing taxonomies which according to Berendsohn (1997) often suffer from "a frequent error of over-simplification of taxonomic data by non-taxonomist database designers" (quoted after Pullan et al (2000)).…”

“…If not, the reader is referred to Ganter & Wille (1999). Section 4 provides a short description of the Prometheus Project (Pullan et al, 2000), which is based on an object-relational modeling of taxonomies. Section 5 discusses some of the advantages and challenges involved in formalizing taxonomies with formal concept analysis.…”