Literature DB >> 32422651

Recent advances in biomedical literature mining.

Sendong Zhao1, Chang Su2, Zhiyong Lu3, Fei Wang1.   

Abstract

The recent years have witnessed a rapid increase in the number of scientific articles in biomedical domain. These literature are mostly available and readily accessible in electronic format. The domain knowledge hidden in them is critical for biomedical research and applications, which makes biomedical literature mining (BLM) techniques highly demanding. Numerous efforts have been made on this topic from both biomedical informatics (BMI) and computer science (CS) communities. The BMI community focuses more on the concrete application problems and thus prefer more interpretable and descriptive methods, while the CS community chases more on superior performance and generalization ability, thus more sophisticated and universal models are developed. The goal of this paper is to provide a review of the recent advances in BLM from both communities and inspire new research directions.
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Entities:  

Keywords:  Biomedical Literature Mining; Deep Learning; Natural Language Processing

Mesh:

Year:  2021        PMID: 32422651      PMCID: PMC8138828          DOI: 10.1093/bib/bbaa057

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN: 1467-5463            Impact factor:   11.622


  112 in total

1.  Toward Routine Automatic Pathway Discovery from On-line Scientific Text Abstracts.

Authors: 
Journal:  Genome Inform Ser Workshop Genome Inform       Date:  1999

2.  GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data.

Authors:  Andrey Rzhetsky; Ivan Iossifov; Tomohiro Koike; Michael Krauthammer; Pauline Kra; Mitzi Morris; Hong Yu; Pablo Ariel Duboué; Wubin Weng; W John Wilbur; Vasileios Hatzivassiloglou; Carol Friedman
Journal:  J Biomed Inform       Date:  2004-02       Impact factor: 6.317

3.  Investigation into biomedical literature classification using support vector machines.

Authors:  Nalini Polavarapu; Shamkant B Navathe; Ramprasad Ramnarayanan; Abrar ul Haque; Saurav Sahay; Ying Liu
Journal:  Proc IEEE Comput Syst Bioinform Conf       Date:  2005

4.  Identifying plausible adverse drug reactions using knowledge extracted from the literature.

Authors:  Ning Shang; Hua Xu; Thomas C Rindflesch; Trevor Cohen
Journal:  J Biomed Inform       Date:  2014-07-19       Impact factor: 6.317

5.  Literature-based discovery of new candidates for drug repurposing.

Authors:  Hsih-Te Yang; Jiun-Huang Ju; Yue-Ting Wong; Ilya Shmulevich; Jung-Hsien Chiang
Journal:  Brief Bioinform       Date:  2017-05-01       Impact factor: 11.622

6.  Detection of IUPAC and IUPAC-like chemical names.

Authors:  Roman Klinger; Corinna Kolárik; Juliane Fluck; Martin Hofmann-Apitius; Christoph M Friedrich
Journal:  Bioinformatics       Date:  2008-07-01       Impact factor: 6.937

7.  A linguistic rule-based approach to extract drug-drug interactions from pharmacological documents.

Authors:  Isabel Segura-Bedmar; Paloma Martínez; César de Pablo-Sánchez
Journal:  BMC Bioinformatics       Date:  2011-03-29       Impact factor: 3.169

8.  AuDis: an automatic CRF-enhanced disease normalization in biomedical text.

Authors:  Hsin-Chun Lee; Yi-Yu Hsu; Hung-Yu Kao
Journal:  Database (Oxford)       Date:  2016-06-07       Impact factor: 3.451

9.  Extracting chemical-protein interactions from literature using sentence structure analysis and feature engineering.

Authors:  Pei-Yau Lung; Zhe He; Tingting Zhao; Disa Yu; Jinfeng Zhang
Journal:  Database (Oxford)       Date:  2019-01-01       Impact factor: 3.451

10.  Drug-Drug Interaction Extraction via Convolutional Neural Networks.

Authors:  Shengyu Liu; Buzhou Tang; Qingcai Chen; Xiaolong Wang
Journal:  Comput Math Methods Med       Date:  2016-01-31       Impact factor: 2.238

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  11 in total

Review 1.  Artificial Intelligence-Based Pharmacovigilance in the Setting of Limited Resources.

Authors:  Likeng Liang; Jifa Hu; Gang Sun; Na Hong; Ge Wu; Yuejun He; Yong Li; Tianyong Hao; Li Liu; Mengchun Gong
Journal:  Drug Saf       Date:  2022-05-17       Impact factor: 5.228

2.  pubmedKB: an interactive web server for exploring biomedical entity relations in the biomedical literature.

Authors:  Peng-Hsuan Li; Ting-Fu Chen; Jheng-Ying Yu; Shang-Hung Shih; Chan-Hung Su; Yin-Hung Lin; Huai-Kuang Tsai; Hsueh-Fen Juan; Chien-Yu Chen; Jia-Hsin Huang
Journal:  Nucleic Acids Res       Date:  2022-05-10       Impact factor: 19.160

3.  Distantly supervised biomedical relation extraction using piecewise attentive convolutional neural network and reinforcement learning.

Authors:  Tiantian Zhu; Yang Qin; Yang Xiang; Baotian Hu; Qingcai Chen; Weihua Peng
Journal:  J Am Med Inform Assoc       Date:  2021-11-25       Impact factor: 7.942

4.  Information-incorporated Gaussian graphical model for gene expression data.

Authors:  Huangdi Yi; Qingzhao Zhang; Cunjie Lin; Shuangge Ma
Journal:  Biometrics       Date:  2021-02-12       Impact factor: 1.701

5.  Automated extraction of genes associated with antibiotic resistance from the biomedical literature.

Authors:  Andre Brincat; Markus Hofmann
Journal:  Database (Oxford)       Date:  2022-01-29       Impact factor: 4.462

Review 6.  Literature Mining and Mechanistic Graphical Modelling to Improve mRNA Vaccine Platforms.

Authors:  Lorena Leonardelli; Giuseppe Lofano; Gianluca Selvaggio; Silvia Parolo; Stefano Giampiccolo; Danilo Tomasoni; Enrico Domenici; Corrado Priami; Haifeng Song; Duccio Medini; Luca Marchetti; Emilio Siena
Journal:  Front Immunol       Date:  2021-09-07       Impact factor: 7.561

Review 7.  Self-Attention-Based Models for the Extraction of Molecular Interactions from Biological Texts.

Authors:  Prashant Srivastava; Saptarshi Bej; Kristina Yordanova; Olaf Wolkenhauer
Journal:  Biomolecules       Date:  2021-10-27

8.  DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules.

Authors:  Eryk Kropiwnicki; Alexander Lachmann; Daniel J B Clarke; Zhuorui Xie; Kathleen M Jagodnik; Avi Ma'ayan
Journal:  BMC Bioinformatics       Date:  2022-02-19       Impact factor: 3.307

Review 9.  Literature Mining of Disease Associated Noncoding RNA in the Omics Era.

Authors:  Jian Fan
Journal:  Molecules       Date:  2022-07-23       Impact factor: 4.927

Review 10.  AI-based language models powering drug discovery and development.

Authors:  Zhichao Liu; Ruth A Roberts; Madhu Lal-Nag; Xi Chen; Ruili Huang; Weida Tong
Journal:  Drug Discov Today       Date:  2021-06-30       Impact factor: 7.851

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