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For: Lim S, Kang J. Chemical-gene relation extraction using recursive neural network. Database (Oxford) 2018;2018:5042822. [PMID: 29961818 PMCID: PMC6014134 DOI: 10.1093/database/bay060] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/25/2018] [Indexed: 11/14/2022]
Number Cited by Other Article(s)
1
Yu B, Zhao Y, Jiang L, Zhou J, Xu H, Lei L, Xu L, Wang X, Bu S. Network pharmacology and experimental validation of Compound Kushen Powder for the treatment of diarrhea in vivo. Vet Anim Sci 2025;28:100443. [PMID: 40206406 PMCID: PMC11979447 DOI: 10.1016/j.vas.2025.100443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2025]  Open
2
Saad E, Kishk S, Ali-Eldin A, Saleh AI. SB-AGT: A stochastic beam search-enhanced attention-based Gumbel tree framework for drug-drug interaction extraction from biomedical literature. Comput Biol Med 2025;189:110011. [PMID: 40086288 DOI: 10.1016/j.compbiomed.2025.110011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2024] [Revised: 02/27/2025] [Accepted: 03/06/2025] [Indexed: 03/16/2025]
3
Zhang Y, Sui X, Pan F, Yu K, Li K, Tian S, Erdengasileng A, Han Q, Wang W, Wang J, Wang J, Sun D, Chung H, Zhou J, Zhou E, Lee B, Zhang P, Qiu X, Zhao T, Zhang J. A comprehensive large scale biomedical knowledge graph for AI powered data driven biomedical research. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2023.10.13.562216. [PMID: 38168218 PMCID: PMC10760044 DOI: 10.1101/2023.10.13.562216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
4
He J, Li F, Li J, Hu X, Nian Y, Xiang Y, Wang J, Wei Q, Li Y, Xu H, Tao C. Prompt Tuning in Biomedical Relation Extraction. JOURNAL OF HEALTHCARE INFORMATICS RESEARCH 2024;8:206-224. [PMID: 38681754 PMCID: PMC11052745 DOI: 10.1007/s41666-024-00162-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 02/09/2024] [Accepted: 02/19/2024] [Indexed: 05/01/2024]
5
Huang MS, Han JC, Lin PY, You YT, Tsai RTH, Hsu WL. Surveying biomedical relation extraction: a critical examination of current datasets and the proposal of a new resource. Brief Bioinform 2024;25:bbae132. [PMID: 38609331 PMCID: PMC11014787 DOI: 10.1093/bib/bbae132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 11/06/2023] [Accepted: 03/02/2023] [Indexed: 04/14/2024]  Open
6
Whitton J, Hunter A. Automated tabulation of clinical trial results: A joint entity and relation extraction approach with transformer-based language representations. Artif Intell Med 2023;144:102661. [PMID: 37783549 DOI: 10.1016/j.artmed.2023.102661] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/05/2023] [Accepted: 09/04/2023] [Indexed: 10/04/2023]
7
Ai X, Kavuluru R. End-to-End Models for Chemical-Protein Interaction Extraction: Better Tokenization and Span-Based Pipeline Strategies. IEEE INTERNATIONAL CONFERENCE ON HEALTHCARE INFORMATICS. IEEE INTERNATIONAL CONFERENCE ON HEALTHCARE INFORMATICS 2023;2023:610-618. [PMID: 38274947 PMCID: PMC10809256 DOI: 10.1109/ichi57859.2023.00108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
8
Bokharaeian B, Dehghani M, Diaz A. Automatic extraction of ranked SNP-phenotype associations from text using a BERT-LSTM-based method. BMC Bioinformatics 2023;24:144. [PMID: 37046202 PMCID: PMC10099837 DOI: 10.1186/s12859-023-05236-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 03/17/2023] [Indexed: 04/14/2023]  Open
9
Kumar A, Sharaff A. ABEE: automated bio entity extraction from biomedical text documents. DATA TECHNOLOGIES AND APPLICATIONS 2022. [DOI: 10.1108/dta-04-2022-0151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
10
Hou Y, Xia Y, Wu L, Xie S, Fan Y, Zhu J, Qin T, Liu TY. Discovering drug-target interaction knowledge from biomedical literature. Bioinformatics 2022;38:5100-5107. [PMID: 36205562 DOI: 10.1093/bioinformatics/btac648] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 07/19/2022] [Indexed: 12/24/2022]  Open
11
Nicholson DN, Himmelstein DS, Greene CS. Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts. BioData Min 2022;15:26. [PMID: 36258252 PMCID: PMC9578183 DOI: 10.1186/s13040-022-00311-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 09/17/2022] [Indexed: 02/04/2023]  Open
12
Kim H, Sung M, Yoon W, Park S, Kang J. Full-text chemical identification with improved generalizability and tagging consistency. Database (Oxford) 2022;2022:6726385. [PMID: 36170114 PMCID: PMC9518746 DOI: 10.1093/database/baac074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/11/2022] [Accepted: 08/22/2022] [Indexed: 11/14/2022]
13
He J, Li F, Hu X, Li J, Nian Y, Wang J, Xiang Y, Wei Q, Xu H, Tao C. Chemical-Protein Relation Extraction with Pre-trained Prompt Tuning. PROCEEDINGS. IEEE INTERNATIONAL CONFERENCE ON HEALTHCARE INFORMATICS 2022;2022:608-609. [PMID: 37664001 PMCID: PMC10474649 DOI: 10.1109/ichi54592.2022.00120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
14
Brincat A, Hofmann M. Automated extraction of genes associated with antibiotic resistance from the biomedical literature. Database (Oxford) 2022;2022:6520791. [PMID: 35134132 PMCID: PMC9263533 DOI: 10.1093/database/baab077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 09/21/2021] [Accepted: 11/22/2021] [Indexed: 11/15/2022]
15
Zanoli R, Lavelli A, Löffler T, Perez Gonzalez NA, Rinaldi F. An annotated dataset for extracting gene-melanoma relations from scientific literature. J Biomed Semantics 2022;13:2. [PMID: 35045882 PMCID: PMC8772125 DOI: 10.1186/s13326-021-00251-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 08/27/2021] [Indexed: 11/10/2022]  Open
16
Bhasuran B. BioBERT and Similar Approaches for Relation Extraction. Methods Mol Biol 2022;2496:221-235. [PMID: 35713867 DOI: 10.1007/978-1-0716-2305-3_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
17
Pourreza Shahri M, Kahanda I. Deep semi-supervised learning ensemble framework for classifying co-mentions of human proteins and phenotypes. BMC Bioinformatics 2021;22:500. [PMID: 34656098 PMCID: PMC8520253 DOI: 10.1186/s12859-021-04421-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022]  Open
18
Warikoo N, Chang YC, Hsu WL. LBERT: Lexically aware Transformer-based Bidirectional Encoder Representation model for learning universal bio-entity relations. Bioinformatics 2021;37:404-412. [PMID: 32810217 DOI: 10.1093/bioinformatics/btaa721] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 06/30/2020] [Accepted: 08/13/2020] [Indexed: 11/13/2022]  Open
19
Shao Y, Li H, Gu J, Qian L, Zhou G. Extraction of causal relations based on SBEL and BERT model. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021;2021:6133143. [PMID: 33570092 PMCID: PMC7904051 DOI: 10.1093/database/baab005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 01/19/2021] [Accepted: 01/26/2021] [Indexed: 11/15/2022]
20
Cui F, Yue Y, Zhang Y, Zhang Z, Zhou HS. Advancing Biosensors with Machine Learning. ACS Sens 2020;5:3346-3364. [PMID: 33185417 DOI: 10.1021/acssensors.0c01424] [Citation(s) in RCA: 261] [Impact Index Per Article: 52.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
21
A multi-feature fusion model for Chinese relation extraction with entity sense. Knowl Based Syst 2020. [DOI: 10.1016/j.knosys.2020.106348] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
22
Lee J, Yoon W, Kim S, Kim D, Kim S, So CH, Kang J. BioBERT: a pre-trained biomedical language representation model for biomedical text mining. Bioinformatics 2020;36:1234-1240. [PMID: 31501885 PMCID: PMC7703786 DOI: 10.1093/bioinformatics/btz682] [Citation(s) in RCA: 1412] [Impact Index Per Article: 282.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/29/2019] [Accepted: 09/05/2019] [Indexed: 12/15/2022]  Open
23
Liu X, Fan J, Dong S. Document-Level Biomedical Relation Extraction Leveraging Pretrained Self-Attention Structure and Entity Replacement: Algorithm and Pretreatment Method Validation Study. JMIR Med Inform 2020;8:e17644. [PMID: 32469325 PMCID: PMC7314385 DOI: 10.2196/17644] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/02/2020] [Accepted: 03/19/2020] [Indexed: 01/26/2023]  Open
24
Döring K, Qaseem A, Becer M, Li J, Mishra P, Gao M, Kirchner P, Sauter F, Telukunta KK, Moumbock AFA, Thomas P, Günther S. Automated recognition of functional compound-protein relationships in literature. PLoS One 2020;15:e0220925. [PMID: 32126064 PMCID: PMC7053725 DOI: 10.1371/journal.pone.0220925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 01/29/2020] [Indexed: 11/18/2022]  Open
25
Lee J, Yoon W, Kim S, Kim D, Kim S, So CH, Kang J. BioBERT: a pre-trained biomedical language representation model for biomedical text mining. BIOINFORMATICS (OXFORD, ENGLAND) 2020;36:1234-1240. [PMID: 31501885 DOI: 10.48550/arxiv.1901.08746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/29/2019] [Accepted: 09/05/2019] [Indexed: 05/20/2023]
26
Lung PY, He Z, Zhao T, Yu D, Zhang J. Extracting chemical-protein interactions from literature using sentence structure analysis and feature engineering. Database (Oxford) 2019;2019:5280305. [PMID: 30624652 PMCID: PMC6323317 DOI: 10.1093/database/bay138] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 12/04/2018] [Accepted: 12/06/2018] [Indexed: 12/14/2022]
27
Antunes R, Matos S. Extraction of chemical-protein interactions from the literature using neural networks and narrow instance representation. Database (Oxford) 2019;2019:baz095. [PMID: 31622463 PMCID: PMC6796919 DOI: 10.1093/database/baz095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 06/28/2019] [Accepted: 07/01/2019] [Indexed: 01/21/2023]
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