Philip Burton

XML is the appropriate format for semistructured data, that is, data with a natural tree structure. Trees are a special form of graphs, and a dialect of XML called GraphML now exists that provides a standard set of tags for describing them. To visualize or draw the graph we can use another XML dialect called SVG, or Scalable Vector Graphics. SVG is a language for describing two-dimensional graphics and graphical applications and is a dialect of XML. In this article we discuss the representation of tree-structured data using XML and GraphML. We visualize the data using SVG and transform the data between the various XML documents using Extensible Stylesheet Language Transformations (XSLT). Introduction A graph is simply a collection of nodes and edges and may be directed or undirected. In the case of a directed graph, an arrow connects the source to the target; for an... (more)

Using XSLT on Bioinformatic XML Data

For the biologist, the bioinformatic analysis of genes requires the compilation of tables of gene characteristics. To do this, data is often taken manually out of databases in an ad hoc fashion. Different databases (TIGR, MIPS, BLAIR, and NCBI, for example) give different outputs in different formats. We would like to be able to extract information from the databases in a common, structured file format in a way that allows for easy rearranging and processing of the data. The Extensible Markup Language (XML) is being used increasingly to represent semi-structured data and transmi... (more)