Abstract

While I was investigating methods to construct 'controlled vocabularies' and 'ontologies', I created a set of 'ontological design patterns'. These engineering design patterns and terminologies specific to some protein families were represented within the object-oriented programming language CLOS (Common Lisp Object System). Within bioinformatics, 'ontologies' are represented on the World Wide Web (WWW) in terminology files that are tagged and marked up by the syntax and keywords of HTML or XML. Therefore, I specified, designed and partially implemented a compiler to translate specified 'controlled vocabularies' and 'ontologies' represented in CLOS and structured by 'ontological design patterns' into the language called 'Simple Hypertext Ontology Extension' (SHOE). First results show that a 'one-step-look-ahead' parser can automatically print the original CLOS version of the 'ontologies' into a file reorganised according to the SHOE syntax.

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