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RegNum

Background

RegNum is a web application designed to store and manage phylogenetic definitions. Anyone will be able to store clade definitions in RegNum, although this application was originally designed to support the International Code of Phylogenetic Nomenclaure (PhyloCode). However, RegNum will offer the option to submit definitions that do not strictly follow the PhyloCode recommendations (e.g., in case of clades that correspond to species).

The International Code of Phylogenetic Nomenclaure (PhyloCode) is a formal set of rules governing phylogenetic nomenclature. It is designed to name the parts of the tree of life by explicit reference to phylogeny. The PhyloCode will be formally published in 2012, although the exact date has not yet been determined.

The PhyloCode grew out of a workshop at Harvard University in August 1998, where basic decisions were made about its scope and content. Many of the workshop participants, together with a few other people who subsequently joined the project, have served as an advisory body (see the PhyloCode preface for the history of development and a list of people involved). In 2004 The International Society for Phylogenetic Nomenclature was founded in Paris at the first society meeting.

The current draft of the PhyloCode represents several years of work and some rules may still be refined before the code is implemented. For example, the current draft governs only the naming of clades (see Dayrat et al., 2008) and rules governing species names may be added in future (see Cellinese et al., 2012). Since the code does not currently cover species names, the examples in the present draft use Linnaean binomials when species names are cited in the phylogenetic definitions of clade names.

We hope that many members of the scientific community will examine the draft PhyloCode and send suggestions for improvement. Although the code has initially been developed by a small group of people, it is intended for the benefit of all biologists who name clades or use clade names.

RegNum database

According to the PhyloCode, clade names should be registered in a database and published in peer-reviewed publications. To develop such a registry, an informatics project managed by Mikael Thollesson (Uppsala University) was launched and RegNum was originally developed with Java tools as part of a master thesis by Jonas Ekstedt. Currently, Nico Cellinese at University of Florida is developing the next version of RegNum with Ruby-on-Rails and MySQL. A RegNum prototype but it is still under construction. However, a beta release is scheduled in the Fall.

The source code can be found at https://github.com/FLMNH-Informatics/phyloregnum. For more information please contact Nico Cellinese: ncellinese(at)flmnh.ufl.edu.

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Page last modified on July 02, 2013, at 02:38 PM