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Data from this study also are available from the Assembling the Fungal Tree of Life (AFTOL) Structural and Biochemical Database
Data from this study are available from the Assembling the Fungal Tree of Life (AFTOL) Structural and Biochemical Database: http://aftol.umn.edu.edu
Patients with routine laboratory measurements of C-reactive protein, albumin and calcium were obtained by systematically searching the North Glasgow biochemical database system.
In the case of RHA1, although annotated, several degradation pathways of various xenobiotics were missing from the Kyoto Encyclopaedia of Genes and Genomes (KEGG) (the primary biochemical database used [ 25]) and they were added to the model using literature data and other online databases [ 26, 27] to account for its catabolic ability.
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In a paper published in Nature Chemical Biology, the scientists write, "Currently, most publicly available biochemical databases do not provide quantitative probabilities or confidence measures for existing annotations.
'DB' designates priority ranking by presence in chemical and biochemical databases.
When investigating endogenous metabolites, it is important to utilize biochemical databases like KEGG and to boost them accordingly.
Different bits of data have been put into context, i.e., annotated, establishing valuable sources of information in the form of chemical and biochemical databases.
Additionally, biochemical databases often contain numerous duplicate compounds [40] and these were identified by Standard InChIKey [41] comparison and removed for computational efficiency.
When the study was restricted to species included in the respective biochemical databases, the Vitek YBC and API ID 32C systems performed adequately with positive identification rates of 87.3 and 76.8%, respectively.
Here we present Metabolic In silico Network Expansions (MINEs) that utilize the Biochemical Network Integrated Network Explorer BNICEE) [29, 30] to expand on general biochemical databases as well as organism-specific databases for Escherichia coli and yeast.
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