Saturday, March 15, 2008

RDF Schemas and directed graphs

In yesterday's blog I provided a Perl script that transformed an RDF Schema and which was used to produce a schematic of the Neoplasm Classification.

Today, I want to go back and review the relationship between RDF Schemas and directed graphs and to provide a rationale for why this is possible and to provide you with some tools you might need to do this for your own RDF Schemas.

RDF (Resource Description Framework) is a syntax and logic for making computer parsable statements that have meaning. RDF uses the familiar tagging syntax of XML, so all RDF documents are also XML documents.

Meaning, in the informatics field, is achieved when a datum and a description of the datum (a metadatum) are bound to an identified object. This is the "triple" that underlies all of RDF.

Here is a data/metadata pair:

<date>March 15, 2008</data>

This kind of data/matadata pair, common to XML, has no meaning because it is not bound to an identified object.

Now consider:

Ides of March occurs on <date>March 15, 2008</data>

This gets a little closer to an RDF statement (with meaning) because the data/metadata pair are assigned to an object (Ides of March).

RDF has a formal way of defining objects [and their properties, which we won't discuss here]. This is called RDF Schema. You can think of RDF Schema as a dictionary for the terms in an RDF data document. RDF Schema is written in RDF syntax. This means that all RDF Schemas are RDF documents and consist of statments in the form of triples.

For today, the important point about RDF Schemas is that they create logical relationships among objects in a domain that can be translated into directed graphs (graphs consisting of connected nodes and arcs and directions for the arcs).

An example of two RDF statements:

<rdfs:Class rdf:ID="Fibrous_tissue">

<rdfs:Class rdf:ID="Mesoderm_primitive">

Every class of object is a subclass of another class of object. A Perl script, such as the one that I provided yesterday, can parse and RDF Schema and transform it into a GraphViz script. This is a type of poor-man's metaprogramming (using a programming language to generate programs in another programming language). GraphViz is a free, open source graphic scripting language that renders a wide range of graphic representations for specified object relationships.

Information on GraphViz is available at:

RDF is the syntax and logic underlying the semantic web, and every serious informatician must learn to use RDF. There are quite a few books and articles written on RDF. My book, Ruby Programming for Medicine and Biology , has a large section on RDF with some examples showing how to build and use RDF Schemas and RDF documents. In my opinion, Ruby is a better language that Perl or Python for dealing with RDF logic. Also, based on my limited ability to survey all of the literature, it would seem that a really good book that explains RDF and provides good examples for building RDF documents and drawing useful inferences from multiple RDF documents, has not been written. When I find one, I'll let you know.

- Jules Berman

key words: RDF Schema, triple, triples, ontology, digraph
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