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288 12 Building Bioinformatics Ontologies

The choice of ontology language will be highly dependent on the purpose

of the ontology. As a first step one should choose among the four major

approaches: one of the three main groups or the combination of the first

and third groups. For the medical chart example, the intention is for the

ontology to be used for 10 years. This is a good argument for either RDF

or OWL because it is difficult to convert from an XML DTD or schema to

RDF or OWL. The fact that notes can be added to other entries is another

argument in favor of RDF or OWL, both of which are designed for annotating

resources that are stored elsewhere. So there are very good reasons why one

would choose RDF or OWL for the medical chart ontology. Since the purpose

of the development project focuses on data representation and not on logic

and reasoning, none of the more sophisticated features of OWL are needed.

Therefore this ontology should use the combined approach. This will make

the medical charts accessible to tools that are based on XML alone. This is

an advantage in the shortterm. In the longterm, the compatibility with RDF

allows one to take advantage of Semantic Web tools as they become available.

Summary

• The major ontology languages used today can be classified as follows:
  
  
  • Basic XML
    
    
    • XML DTD
    
    
    • XSD
    
    
    
    
  
  
  • XML Topic Maps
  
  
  • Semantic Web
    
    
    • RDF
    
    
    • OWL
      
      
      1. OWL Lite
      
      
      2. OWL-DL
      
      
      3. OWL Full
      
      
      
      
    
    
    
    
  
  
  
  


• It is possible to use an approach that is compatible with XML DTD, XSD,
  RDF, and the OWL languages.

12.3 Ontology Development Tools

Having chosen an ontology language or approach, the next step is to choose

a suitable development tool. Unfortunately, such tools seldom refer to them-