[October 17, 2000] 'Taxonomic Markup Language' is represented by "a DTD and some sample files demonstrating the use of XML for the storage and presentation of biological taxonomic information. There are also two XSL stylesheets for use with the sample files and a Perl program for converting data in Nexus format into valid XML."
"Systematists make use of biopolymer data and codified morphological data to reconstruct the branching phylogenies of groups of organisms. The hierarchical structure of these phylogenies lends itself readily to being description by XML. These phylogenies are created by algorithms that seek to minimize unnecessary assumptions (the rule of parsimony) or maximize the probability of a particular phylogeny occurring (the rule of maximum likelihood). A phylogenetic tree is therefor not a simple statement, but must be qualified by a wide variety of statistics which describe the degree to which the original data is explained by the tree and the statistical strength of particular configurations (Kitching et al., 1998). In addition to generating 'raw' phylogenies (the visual representations of which are variously known as dendrograms or cladograms), systematists also attempt to provide a nomenclatural system which, at least to some degree, reflects the patterns of relationship in the phylogeny. The document type definition (DTD) proposed here seeks to accomplish three things: (1) The description of the structure (topology) of a biological phylogeny. (2) The presentation of statistical metadata about the phylogeny. (3) The option of superimposing a Linnean taxonomy upon the phylogenetic structure. Note that while the DTD allows taxonomic units to be tagged in a Linnean manner, this is optional, since many practicing systematists do not routinely apply this type of classification or do so only at a very late stage in their research. This is especially true of situations in which species boundaries are not clear or in which the nature of sub-specific taxa is open to interpretation. ... An XML document type definition (DTD) is provided for the description of taxonomic relationships between organisms. Two XSL stylesheets for the graphical presentation of simple taxonomic trees are also provided." [From the article]
"Taxonomic Markup Language: Applying XML to Systematic Data." Bioinformatics 16/4 (2000), pages 406-407. 'An XML document type definition (DTD) is provided for the description of taxonomic relationships between organisms. Two XSL stylesheets for the graphical presentation of simple taxonomic trees are also provided.' [related version, source]
Contact: Ron Gilmour
See also 'XDELTA - Deriving an XML based format for Taxonomic Information', and the XML DTD. [cache]