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This paper discusses the uncertainty in the automation of knowledge building from heterogeneous raw datasets. Ontologies play a critical role in such a process by providing a well consolidated support to link and semantically integrate datasets via interoperability, as well as semantic enrichment and annotations. By adopting Semantic Web technology, the resulting ecosystem is fully machine consumable. However, while the manual alignment of concepts from different vocabularies is reasonable at a small scale, fully automatic mechanisms are required once the target system scales up, leading to a significant uncertainty.
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