Associating biological context with protein-protein interactions through text mining at PubMed scale

Sosa, D., Hintzen, R., Xiong, B., de Giorgio, A., Fauqueur, J., Davies, M., Lever, J. and Altman, R. B. (2023) Associating biological context with protein-protein interactions through text mining at PubMed scale. Journal of Biomedical Informatics, 145, 104474. (doi: 10.1016/j.jbi.2023.104474) (PMID:37572825)

Abstract

Inferring knowledge from known relationships between drugs, proteins, genes, and diseases has great potential for clinical impact, such as predicting which existing drugs could be repurposed to treat rare diseases. Incorporating key biological context such as cell type or tissue of action into representations of extracted biomedical knowledge is essential for principled pharmacological discovery. Existing global, literature-derived knowledge graphs of interactions between drugs, proteins, genes, and diseases lack this essential information. In this study, we frame the task of associating biological context with protein-protein interactions extracted from text as a classification task using syntactic, semantic, and novel meta-discourse features. We introduce the Insider corpora, which are automatically generated PubMed-scale corpora for training classifiers for the context association task. These corpora are created by searching for precise syntactic cues of cell type and tissue relevancy to extracted regulatory relations. We report F1 scores of 0.955 and 0.862 for identifying relevant cell types and tissues, respectively, for our identified relations. By classifying with this framework, we demonstrate that the problem of context association can be addressed using intuitive, interpretable features. We demonstrate the potential of this approach to enrich text-derived knowledge bases with biological detail by incorporating cell type context into a protein-protein network for dengue fever.

• Item Type: Articles
• Additional Information: This research was supported by a grant to Stanford University from BenevolentAI.
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Lever, Dr Jake

Creator Roles

Lever, J.: Conceptualization, Methodology, Software, Writing – original draft, Writing – review and editing

• Authors: Sosa, D., Hintzen, R., Xiong, B., de Giorgio, A., Fauqueur, J., Davies, M., Lever, J., and Altman, R. B.
• College/School: College of Science and Engineering > School of Computing Science
• Journal Name: Journal of Biomedical Informatics
• Publisher: Elsevier
• ISSN: 1532-0464
• Published Online: 10 August 2023