A global network of biomedical relationships derived from text

Bioinformatics
Bethany Percha, Russ B Altman

Abstract

The biomedical community's collective understanding of how chemicals, genes and phenotypes interact is distributed across the text of over 24 million research articles. These interactions offer insights into the mechanisms behind higher order biochemical phenomena, such as drug-drug interactions and variations in drug response across individuals. To assist their curation at scale, we must understand what relationship types are possible and map unstructured natural language descriptions onto these structured classes. We used NCBI's PubTator annotations to identify instances of chemical, gene and disease names in Medline abstracts and applied the Stanford dependency parser to find connecting dependency paths between pairs of entities in single sentences. We combined a published ensemble biclustering algorithm (EBC) with hierarchical clustering to group the dependency paths into semantically-related categories, which we annotated with labels, or 'themes' ('inhibition' and 'activation', for example). We evaluated our theme assignments against six human-curated databases: DrugBank, Reactome, SIDER, the Therapeutic Target Database, OMIM and PharmGKB. Clustering revealed 10 broad themes for chemical-gene relationships, 7 for chemical-...Continue Reading

References

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Citations

Jun 28, 2019·PLoS Computational Biology·Sid KiblawiMark Craven
May 23, 2019·Nucleic Acids Research·Chih-Hsuan WeiZhiyong Lu
Nov 28, 2019·Briefings in Bioinformatics·Jussi Paananen, Vittorio Fortino
Jul 16, 2019·Genomics & Informatics·Mina GachlooJingbo Xia
Aug 27, 2019·Frontiers in Pharmacology·Debleena GuinRitushree Kukreti
Sep 29, 2020·Frontiers in Cell and Developmental Biology·Nadeesha PereraFrank Emmert-Streib
Dec 21, 2020·Briefings in Bioinformatics·Shuangjia ZhengZhangming Niu
Dec 22, 2020·Briefings in Bioinformatics·Apurva BadkasThomas Sauter
Jul 9, 2020·Computational and Structural Biotechnology Journal·David N Nicholson, Casey S Greene
Dec 16, 2020·BMC Medical Informatics and Decision Making·Li ZhangCui Tao
Apr 13, 2021·Expert Opinion on Drug Discovery·Finlay MacLean
May 21, 2021·Briefings in Bioinformatics·Thomas GaudeletJake P Taylor-King
Jul 14, 2020·Journal of Proteome Research·Xiangxiang ZengFeixiong Cheng
Sep 9, 2021·Medical Reference Services Quarterly·Tariq Rahaman
Dec 2, 2021·Briefings in Bioinformatics·Margaret G GuoRuss B Altman

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