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A compiler to transfer controlled vocabularies and ontologies represented in an object-oriented programming language into text mark-up languages

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1 Author(s)
Reich, J.R. ; Dept. of Comput. Sci., Manchester Univ., UK

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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Bio-Informatics and Biomedical Engineering, 2000. Proceedings. IEEE International Symposium on

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