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Ontology usage in Omics Standards Initiatives: Pros and Cons of enriching XML data formats with controlled vocabulary terms EMAIL-ADDRESSES

This paper is available in a repository.
This paper is available in a repository.

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Postprint: policy unknown
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Abstract

Motivation: We here review a method of XML data enrichment with controlled vocabularies (CV) in light of end-user compliance. We outline the reasons that made major standard initiatives in proteomics and metabolomics use this data enrichment scheme on omics data in favor of more formal approaches, e.g. description logics (DL) knowledge bases. We show that in comparison to other knowledge representation formalisms , the list of prerequisite skills on the user-side and the learning threshold is significantly lower, making the approach feasible for bioinformaticians with average skill levels, i.e. basic XML knowledge. Additionally our approach allows to source out the 'business logics' from the terminology into external rules. This enables the successive and encapsulated addition of semantics in a flexible way. We feel our approach contributes to increase the amount of potential users, enabling them to participate in a peer-produced standards development process.