Pharmacology Data Discovery through Biomedical Literature Mining and Electronic Medical Records Text Mining

Publication

Binkheder S, Wu HY, Quinney SK, Zhang S, Zitu MM, Chiang CW, Wang L, Jones J, Li L. PhenoDEF: a corpus for annotating sentences with information of phenotype definitions in biomedical literature. J Biomed Semantics. 2022 Jun 11;13(1):17. doi: 10.1186/s13326-022-00272-6. Erratum in: J Biomed Semantics. 2022 Jul 20;13(1):20. doi: 10.1186/s13326-022-00275-3. PMID: 35690873; PMCID: PMC9188713.
Kolchinsky A, Lourenço A, Wu HY, Li L, Rocha LM. Extraction of pharmacokinetic evidence of drug-drug interactions from the literature. PLoS One. 2015 May 11;10(5):e0122199. doi: 10.1371/journal.pone.0122199. PMID: 25961290; PMCID: PMC4427505.
Zhang Y, Wu HY, Du J, Xu J, Wang J, Tao C, Li L, Xu H. Extracting drug-enzyme relation from literature as evidence for drug drug interaction. J Biomed Semantics. 2016 Mar 7;7:11. doi: 10.1186/s13326-016-0052-6. Erratum in: J Biomed Semantics. 2016 Apr 19;7:21. doi: 10.1186/s13326-016-0063-3. PMID: 26955465; PMCID: PMC4780188.
Wu HY, Karnik S, Subhadarshini A, Wang Z, Philips S, Han X, Chiang C, Liu L, Boustani M, Rocha LM, Quinney SK, Flockhart D, Li L. An integrated pharmacokinetics ontology and corpus for text mining. BMC Bioinformatics. 2013 Feb 1;14:35. doi: 10.1186/1471-2105-14-35. PMID: 23374886; PMCID: PMC3571923.
Wu HY, Lu D, Hyder M, Zhang S, Quinney SK, Desta Z, Li L. DrugMetab: An Integrated Machine Learning and Lexicon Mapping Named Entity Recognition Method for Drug Metabolite. CPT Pharmacometrics Syst Pharmacol. 2018 Nov;7(11):709-717. doi: 10.1002/psp4.12340. Epub 2018 Sep 29. PMID: 30033622; PMCID: PMC6263660.
Zhang Y, Wu HY, Xu J, Wang J, Soysal E, Li L, Xu H. Leveraging syntactic and semantic graph kernels to extract pharmacokinetic drug drug interactions from biomedical literature. BMC Syst Biol. 2016 Aug 26;10 Suppl 3(Suppl 3):67. doi: 10.1186/s12918-016-0311-2. PMID: 27585838; PMCID: PMC5009562.
Zhang S, Wu H, Wang L, Zhang G, Rocha LM, Shatkay H, Li L. Translational drug-interaction corpus. Database (Oxford). 2022 May 18;2022:baac031. doi: 10.1093/database/baac031. PMID: 35616099; PMCID: PMC9216474.
Wang Z, Kim S, Quinney SK, Guo Y, Hall SD, Rocha LM, Li L. Literature mining on pharmacokinetics numerical data: a feasibility study. J Biomed Inform. 2009 Aug;42(4):726-35. doi: 10.1016/j.jbi.2009.03.010. Epub 2009 Apr 2. PMID: 19345282; PMCID: PMC2737819.
Zitu MM, Zhang S, Owen DH, Chiang C, Li L. Generalizability of machine learning methods in detecting adverse drug events from clinical narratives in electronic medical records. Front Pharmacol. 2023 Jul 12;14:1218679. doi: 10.3389/fphar.2023.1218679. PMID: 37502211; PMCID: PMC10368879.
Nashed A, Zhang S, Chiang CW, Zitu M, Otterson GA, Presley CJ, Kendra K, Patel SH, Johns A, Li M, Grogan M, Lopez G, Owen DH, Li L. Comparative assessment of manual chart review and ICD claims data in evaluating immunotherapy-related adverse events. Cancer Immunol Immunother. 2021 Oct;70(10):2761-2769. doi: 10.1007/s00262-021-02880-0. Epub 2021 Feb 24. PMID: 33625533; PMCID: PMC10992210.