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Taxon Concept

2005-08-08

As part of the Stratigraphy.net initiative, the TaxonConcept system as a tool to help resolve taxonomic ambiguities in biostratigraphy was created. Its workflow is based on the principles of 'open nomenclature' (Bengtson, 1988; Matthews, 1973).
This allows to work with taxonomic classifications that are uncertain, or where several versions exist. The system allows to store and compare differing taxonomic opinions of either authors of print publications or registered users. The discussion process is recorded in a change log which follows the operating principles of a wiki.

To keep track of the literature sources cited, TaxonConcept features a project literature database with an import and export interface to literature database software (e.g. BibTex, EndNote).
The conceptual distinction in the development of this database between species descriptions (species atlas) and their taxonomic classification (taxonomic database) is new and useful in that it permits us to separate the description of types, which do not change with time, from their taxonomic classification, which is always liable to change .
This modular architecture of the system makes it perfectly suitable for earth science projects as beneath the already available taxon related information, such as images, species descriptions or biostratigraphy, project specific modules can easily be integrated.

Taxonomy and open nomenclature

Ideally names of organisms are unique and representative for exactly one organism or species.
However, in practice there is no common agreement on the classification of organisms. In contrary, the use of a organism name may rather represent a taxonomic interpretation, depending on e.g. the nationality, trainer, knowledge and experience of the scientist. Thus researchers often disagree on the identity of the organisms studied. It is even possible that scientists who use the same name actually mean a completely different organism.

One of the rare studies where this effect has been shown was the "el Kef blind study"(Lipps, 1997). Scientists simultaneously executed faunal counts on the same sample source. They compared the results of this blind test in order to clarify some open questions on the nature of the K/T transition.
Surprisingly, due to completely different taxonomic opinions, the results of the counts could hardly been compared. (Keller, 1997)
Therefore, scientist who use organism names should exactly define what they mean while applying a name.

The technique of the open nomenclature was originally introduced by Richter (1948) to enable researchers to comment the identification of a specimen which cannot exactly be determined. For a detailed introduction see: Matthews, 1973, Bengtson, 1988. Several signs have been introduced, which can be used as part of the taxon name.
For example the use of the question mark in the name Agenus? album would indicate a uncertainty at the genus level.

In addition to such an judgment of an author of his own material, synonymy lists offer the possibility for a critical review of previous publications on the discussed taxon. Here, additional signs can be used in order to discuss other authors determinations. For example a synonym list entry

v 1895 Agenus album Aulus. -Bruno, Monogr. Agenidae, S.12 Taf. 3 Fig. 2.

expresses that the author has seen (v=vidimus) the material which relate to the cited work and the author agrees on this determination. In contrast the entry:

non 1895 Agenus album Aulus. -Bruno, Monogr. Agenidae, S.12 Taf. 3 Fig. 2.

expresses that the cited species (or its illustration at page 12, plate 3, respectively) cannot be compared with the discussed species (non).

The above examples of synonymy list entries show how synonymy lists and the use of the open nomenclature can perfectly be used to compare and discuss taxonomic opinions.
TaxonConcept offers the possibility to store synonymy lists which are either already published or are provided by system users. The comparison and discussion of these taxonomic opinions can be used as starting point to reach a taxonomic consensus within a working group or project, which can later be published online or by print media.

Systematics, taxon diagnosis and illustrations

Beneath the basic taxon information such as taxon names, authors and date of publication, of course taxon diagnosis (from publications or system users), comments can be entered to the system. Additionally, a image upload module can be used to provide taxon illustrations.

TaxonConcept further offers a advanced management of the systematics. The data model for systematics is based on the "Nested Set Model" of Celko(1996) which is already being used by the Stratigraphy.Net project Huber et al., (2003) for the hierarchical organisation of stratigraphic units. Systematics of taxa also serves to ease navigation within the system, the interactive 'taxon navigator' an explorer like user frontend allows user friendly search and navigation features.

Stratigraphy

As integral part of the stratigraphy.net information system, TaxonConcept offers the possibility to store taxon related stratigraphic data.
The current version supports the definition of absolute ages for uppermost and lowermost occurrence datums of the taxon (LAD, FAD) as well as relative correlation of the range of a taxon to e.g. biostartigraphic, magnetostratigraphic or chronostratiographic units.
Correlation is supported by one of the Stratigraphy.Net's core modules, which has been integrated to TaxonConcept. It allows the input of data on stratigraphic units, eg. their (biostratigraphic) definition and literature based ages as well as the construction of biostratigraphic zonations such as eg. the Berggren (1995) zonation of planktonic foraminifera can be done by this module. See (Huber at al. (2003) for details on the background technology) The application of these methods as age models on eg. sediment cores is scheduled for the next version of TaxonConcept

Ecology

Scheduled for a revision later this year. This module will allow to store ecological parameters.

Project and user management, Wiki features

Generally, TaxonConcept is a project centred tool, which means projects members can use TaxonConcept to define their common taxonomic consensus, for example to define the taxonomic frame work for their biostratigraphic studies. User privileges are therefore managed separately within each project.
TaxonConcept offers advanced information protection features. Users can assign different levels of data privacy to each infomation category. Data can be protected and reserved for private usage or can be published in various levels. Data protection levels currently are:

  • Data is for private use only
  • Allow usage of data for project members
  • Allow usage of data for all TaxonConcept users
  • Data is published (will appear on the project portals as well as on the common search results page)

Additionally user privileges are organized by user groups. Currently 2 user groups can be defined: normal users which have privileges to enter taxon related data and modify their entries. Editors, which can additionally supervise the discussion process and edit the so called 'taxon card', which is a Fossilium Catalogus style summary of the taxonomic consensus, which can be used for online publication. In order to have as little restrictions as possible for the system user, in many parts of the system so called wiki features have been integrated and changes are tracked by the system and can be undone if necessary.

Reference management

Proper reference management is essential for each scientific information management system. Therefore, TaxonConcept offers a literature management database with an import and export interface to literature database software (e.g. BibTex, EndNote).

Interfaces to other databases

Currently TaxonConcept offers the possibility to directly link search results with numerical and observational data from the PANGAEA database operated by the WDC-MARE. Scheduled for later this year, exchange with external databases and projects e.g. CHRONOS, GBIFor Genbank. This module will enable e.g. TaxonConcept entries to be published in the GBIF network, link TaxonConcept data sets to molecular databases or to query taxon related data sets in PANGAEA.

References:

Bengtson, Peter: Open Nomenclature, Palaeontology, Volume 31, Part 1, 1988, Pages 223-227.

Celko, Joe: A Look at SQL Trees, DBMS Magazine, March 1996, http://www.dbmsmag.com/9603d06.html

Huber, Robert, Jens Klump and Stefan Götz: A tree for rocks--hierarchies in stratigraphic databases, Computers & Geosciences, Volume 29, Issue 7, August 2003, Pages 921-928.

Keller, Gerta: Analysis of El Kef blind test I, Marine Micropaleontology, Volume 29, Issue 2, January 1997, Pages 89-93.

Lipps, Jere H.: The cretaceous-tertiary boundary: The El Kef blind test, Marine Micropaleontology, Volume 29, Issue 2, January 1997, Pages 65-66.

Matthews, S.C.: Notes on open Nomenclature and on synonymy lists, Palaeontology, Volume 16, Part 4, 1973, Pages 713-719.

Richter, R.: Einführung in die Zoologische Nomenklatur, Kramer, Frankfurt a. Main, 1948, 252 Pages.

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