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Anal Chem. 2019 Apr 2;91(7):4312-4316. doi: 10.1021/acs.analchem.8b05818. Epub 2019 Mar 13.

Visual and Semantic Enrichment of Analytical Chemistry Literature Searches by Combining Text Mining and Computational Chemistry.

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Center for Proteomics and Metabolomics , Leiden University Medical Center , Postzone S3-P, Postbus 9600, 2300 RC Leiden , The Netherlands.


The open-access scientific literature contains a wealth of information for meaningful text mining. However, this information is not always easy to retrieve. This technical note addresses the problem by a new flexible method combining in a single workflow existing resources for literature searches, text mining, and large-scale prediction of physicochemical and biological properties. The results are visualized as virtual mass spectra, chromatograms, or images in styles new to text mining but familiar to analytical chemistry. The method is demonstrated on comparisons of analytical-chemistry techniques and semantically enriched searches for proteins and their activities, but it may also be of general utility in experimental design, drug discovery, chemical syntheses, business intelligence, and historical studies. The method is realized in shareable scientific workflows using only freely available data, services, and software that scale to millions of publications and named chemical entities in the literature.

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