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Hierarchically structured ontological terms can now be adopted to query sequences and to describe genes and their products at different levels of knowledge and specificity [ 1].
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First, as can be noted in Table 1, it is difficult to get appropriate parameters automatically that can be adopted to all queries.
For query semantic extension, latent semantic analysis is adopted to discover the latent semantic relationships between queries and ontology semantic features, and ontology semantic graph is used to represent the query.
Moreover, K-D tree was adopted to organize the samples to accelerate neighbor query in 3D space during the above modeling process.
By integrating the above two different approaches, the following steps were adopted to predict the side effects of the query drug d.
When "gap" exists in the metabolic pathways, reciprocal-best-hit search was adopted to identify orthologues using experimentally verified protein sequence as query.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com