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Updated: Jun 14, 2026

A Knowledge Graph Approach to Elucidate the Role of Organellar Pathways in Disease via Biomedical Reports
Published on: October 13, 2023
Mining connections between chemicals, proteins, and diseases extracted from Medline annotations
Nancy C Baker1, Bradley M Hemminger
1School of Information and Library Science, University of North Carolina, Chapel Hill, NC, USA. nbaker@email.unc.edu
None:
The biomedical literature is an important source of information about the biological activity and effects of chemicals. We present an application that extracts terms indicating biological activity of chemicals from Medline records, associates them with chemical name and stores the terms in a repository called ChemoText. We describe the construction of ChemoText and then demonstrate its utility in drug research by employing Swanson's ABC discovery paradigm. We reproduce Swanson's discovery of a connection between magnesium and migraine in a novel approach that uses only proteins as the intermediate B terms. We validate our methods by using a cutoff date and evaluate them by calculating precision and recall. In addition to magnesium, we have identified valproic acid and nitric oxide as chemicals which developed links to migraine. We hypothesize, based on protein annotations, that zinc and retinoic acid may play a role in migraine. The ChemoText repository has promise as a data source for drug discovery.
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