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296 12 Building Bioinformatics Ontologies

We have already seen examples of including one XML file in another in

section 1.4. SBML is an example of an XSD schema that imports another. The

following shows how SBML imports the MathML schema:

<xsd:import

namespace=

"http://www.w3.org/1998/Math/MathML"

schemaLocation=

"http://www.w3.org/Math/XMLSchema/mathml2/mathml2.xsd"/>

Note that the URI of the MathML namespace is not the same as its URL.

Summary

• Reusing existing ontologies can save time and improve quality.


• However, reusing an existing ontology is not always appropriate. One
  must balance the risks against the advantages.


• There are three techniques for reusing an ontology:
  
  
  1. Copy the ontology
  
  
  2. Include the ontology
  
  
  3. Import the ontology
  
  
  
  

12.6 Designing the Concept Hierarchy

The most important part of any ontology is its concept hierarchy. The con-

cepts are the subjects and objects that appear in whatever statement of pur-

pose, glossaries, and usage examples one has available. Consider the medical

chart ontology. From the purpose and usage examples, one finds the follow-

ing terms: medical personnel, chart, event, patient, note, test, prescription,

operation, category, and admission. The following are examples of how these

concepts could be organized in a hierarchy for two ontology languages:

1. XML DTD.The concepts are organized according to how they will be ar-
   ranged in the document. The hierarchy is specified by giving the content
   model for each concept in terms of other concepts. The top-level concept
   of the medical chart ontology is the chart concept, which consists of a
   sequence of events for a patient, which can be admission, tests, prescrip-
   tions, or operations. Events are categorized using standard categories,