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For: Huang CC, Lu Z. Community challenges in biomedical text mining over 10 years: success, failure and the future. Brief Bioinform 2015;17:132-44. [PMID: 25935162 DOI: 10.1093/bib/bbv024] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
1
Kreuzthaler M, Pfeifer B, Schulz S. Secondary Use of Clinical Problem List Descriptions for Bi-Encoder Based ICD-10 Classification. AMIA ... ANNUAL SYMPOSIUM PROCEEDINGS. AMIA SYMPOSIUM 2025;2024:620-627. [PMID: 40417589 PMCID: PMC12099355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 05/27/2025]
2
Wang Y, Wang F, Liu W, Geng Y, Shi Y, Tian Y, Zhang B, Luo Y, Sun X. New drug discovery and development from natural products: Advances and strategies. Pharmacol Ther 2024;264:108752. [PMID: 39557343 DOI: 10.1016/j.pharmthera.2024.108752] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 11/06/2024] [Accepted: 11/08/2024] [Indexed: 11/20/2024]
3
He X, Tang Y, Yu B, Li S, Ren Y. Joint Extraction of Biomedical Events Based on Dynamic Path Planning Strategy and Hybrid Neural Network. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024;21:2064-2075. [PMID: 39137086 DOI: 10.1109/tcbb.2024.3442199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
4
Zong H, Wu R, Cha J, Feng W, Wu E, Li J, Shao A, Tao L, Li Z, Tang B, Shen B. Advancing Chinese biomedical text mining with community challenges. J Biomed Inform 2024;157:104716. [PMID: 39197732 DOI: 10.1016/j.jbi.2024.104716] [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: 05/06/2024] [Revised: 08/22/2024] [Accepted: 08/25/2024] [Indexed: 09/01/2024]
5
Varela-Vega A, Posada-Reyes AB, Méndez-Cruz CF. Automatic extraction of transcriptional regulatory interactions of bacteria from biomedical literature using a BERT-based approach. Database (Oxford) 2024;2024:baae094. [PMID: 39213391 PMCID: PMC11363960 DOI: 10.1093/database/baae094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 08/09/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024]
6
Jonker RAA, Almeida T, Antunes R, Almeida JR, Matos S. Multi-head CRF classifier for biomedical multi-class named entity recognition on Spanish clinical notes. Database (Oxford) 2024;2024:baae068. [PMID: 39083461 PMCID: PMC11290360 DOI: 10.1093/database/baae068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/15/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024]
7
Taub-Tabib H, Shamay Y, Shlain M, Pinhasov M, Polak M, Tiktinsky A, Rahamimov S, Bareket D, Eyal B, Kassis M, Goldberg Y, Kaminski Rosenberg T, Vulfsons S, Ben Sasson M. Identifying symptom etiologies using syntactic patterns and large language models. Sci Rep 2024;14:16190. [PMID: 39003296 PMCID: PMC11246441 DOI: 10.1038/s41598-024-65645-6] [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: 12/19/2023] [Accepted: 06/21/2024] [Indexed: 07/15/2024]  Open
8
Vlieger R, Austin D, Apthorp D, Daskalaki E, Lensky A, Walton-Sonda D, Suominen H, Lueck CJ. The use of event-related potentials in the investigation of cognitive performance in people with Multiple Sclerosis: Systematic review. Brain Res 2024;1832:148827. [PMID: 38403040 DOI: 10.1016/j.brainres.2024.148827] [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: 09/29/2023] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024]
9
Nachtegael C, De Stefani J, Cnudde A, Lenaerts T. DUVEL: an active-learning annotated biomedical corpus for the recognition of oligogenic combinations. Database (Oxford) 2024;2024:baae039. [PMID: 38805753 PMCID: PMC11131422 DOI: 10.1093/database/baae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/17/2024] [Accepted: 05/13/2024] [Indexed: 05/30/2024]
10
Irrera O, Marchesin S, Silvello G. MetaTron: advancing biomedical annotation empowering relation annotation and collaboration. BMC Bioinformatics 2024;25:112. [PMID: 38486137 PMCID: PMC10941452 DOI: 10.1186/s12859-024-05730-9] [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: 05/26/2023] [Accepted: 03/04/2024] [Indexed: 03/17/2024]  Open
11
Lou Y, Zhu X, Tan K. Dictionary-based matching graph network for biomedical named entity recognition. Sci Rep 2023;13:21667. [PMID: 38066007 PMCID: PMC10709457 DOI: 10.1038/s41598-023-48564-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023]  Open
12
Berge GT, Granmo OC, Tveit TO, Ruthjersen AL, Sharma J. Combining unsupervised, supervised and rule-based learning: the case of detecting patient allergies in electronic health records. BMC Med Inform Decis Mak 2023;23:188. [PMID: 37723446 PMCID: PMC10507898 DOI: 10.1186/s12911-023-02271-8] [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: 07/01/2022] [Accepted: 08/17/2023] [Indexed: 09/20/2023]  Open
13
Faessler E, Hahn U, Schäuble S. GePI: large-scale text mining, customized retrieval and flexible filtering of gene/protein interactions. Nucleic Acids Res 2023:7177881. [PMID: 37224532 DOI: 10.1093/nar/gkad445] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 05/01/2023] [Accepted: 05/11/2023] [Indexed: 05/26/2023]  Open
14
Valentin S, Decoupes R, Lancelot R, Roche M. Animal disease surveillance: How to represent textual data for classifying epidemiological information. Prev Vet Med 2023;216:105932. [PMID: 37247579 DOI: 10.1016/j.prevetmed.2023.105932] [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: 04/01/2022] [Revised: 04/07/2023] [Accepted: 05/10/2023] [Indexed: 05/31/2023]
15
Kreuzthaler M, Brochhausen M, Zayas C, Blobel B, Schulz S. Linguistic and ontological challenges of multiple domains contributing to transformed health ecosystems. Front Med (Lausanne) 2023;10:1073313. [PMID: 37007792 PMCID: PMC10050682 DOI: 10.3389/fmed.2023.1073313] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 02/13/2023] [Indexed: 03/17/2023]  Open
16
Valentin S, Arsevska E, Vilain A, De Waele V, Lancelot R, Roche M. Elaboration of a new framework for fine-grained epidemiological annotation. Sci Data 2022;9:655. [PMID: 36289243 PMCID: PMC9606314 DOI: 10.1038/s41597-022-01743-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 10/03/2022] [Indexed: 11/09/2022]  Open
17
Hossain MZ, Daskalaki E, Brüstle A, Desborough J, Lueck CJ, Suominen H. The role of machine learning in developing non-magnetic resonance imaging based biomarkers for multiple sclerosis: a systematic review. BMC Med Inform Decis Mak 2022;22:242. [PMID: 36109726 PMCID: PMC9476596 DOI: 10.1186/s12911-022-01985-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 09/02/2022] [Indexed: 11/10/2022]  Open
18
Chen Q, Du J, Allot A, Lu Z. LitMC-BERT: Transformer-Based Multi-Label Classification of Biomedical Literature With An Application on COVID-19 Literature Curation. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:2584-2595. [PMID: 35536809 PMCID: PMC9647722 DOI: 10.1109/tcbb.2022.3173562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 05/20/2023]
19
Chen Q, Allot A, Leaman R, Islamaj R, Du J, Fang L, Wang K, Xu S, Zhang Y, Bagherzadeh P, Bergler S, Bhatnagar A, Bhavsar N, Chang YC, Lin SJ, Tang W, Zhang H, Tavchioski I, Pollak S, Tian S, Zhang J, Otmakhova Y, Yepes AJ, Dong H, Wu H, Dufour R, Labrak Y, Chatterjee N, Tandon K, Laleye FAA, Rakotoson L, Chersoni E, Gu J, Friedrich A, Pujari SC, Chizhikova M, Sivadasan N, Vg S, Lu Z. Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations. Database (Oxford) 2022;2022:baac069. [PMID: 36043400 PMCID: PMC9428574 DOI: 10.1093/database/baac069] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 08/02/2022] [Accepted: 08/13/2022] [Indexed: 05/03/2023]
20
Erdengasileng A, Han Q, Zhao T, Tian S, Sui X, Li K, Wang W, Wang J, Hu T, Pan F, Zhang Y, Zhang J. Pre-trained models, data augmentation, and ensemble learning for biomedical information extraction and document classification. Database (Oxford) 2022;2022:baac066. [PMID: 35962559 PMCID: PMC9375052 DOI: 10.1093/database/baac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/29/2022] [Accepted: 08/09/2022] [Indexed: 11/19/2022]
21
Research on Medical Text Classification Based on Improved Capsule Network. ELECTRONICS 2022. [DOI: 10.3390/electronics11142229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
22
Almeida T, Antunes R, F. Silva J, Almeida JR, Matos S. Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics. Database (Oxford) 2022;2022:6625810. [PMID: 35776534 PMCID: PMC9248917 DOI: 10.1093/database/baac047] [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: 03/01/2022] [Revised: 05/13/2022] [Accepted: 06/06/2022] [Indexed: 11/14/2022]
23
Rodriguez-Esteban R. New reasons for biologists to write with a formal language. Database (Oxford) 2022;2022:6600538. [PMID: 35657112 PMCID: PMC9216469 DOI: 10.1093/database/baac039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/18/2022] [Accepted: 05/17/2022] [Indexed: 12/03/2022]
24
Boosting biomedical document classification through the use of domain entity recognizers and semantic ontologies for document representation: The case of gluten bibliome. Neurocomputing 2022. [DOI: 10.1016/j.neucom.2021.10.100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
25
Bhasuran B. Combining Literature Mining and Machine Learning for Predicting Biomedical Discoveries. Methods Mol Biol 2022;2496:123-140. [PMID: 35713862 DOI: 10.1007/978-1-0716-2305-3_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
26
StaResGRU-CNN with CMedLMs: A stacked residual GRU-CNN with pre-trained biomedical language models for predictive intelligence. Appl Soft Comput 2021. [DOI: 10.1016/j.asoc.2021.107975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
27
Converting Biomedical Text Annotated Resources into FAIR Research Objects with an Open Science Platform. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11209648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
28
Parolo S, Tomasoni D, Bora P, Ramponi A, Kaddi C, Azer K, Domenici E, Neves-Zaph S, Lombardo R. Reconstruction of the Cytokine Signaling in Lysosomal Storage Diseases by Literature Mining and Network Analysis. Front Cell Dev Biol 2021;9:703489. [PMID: 34490253 PMCID: PMC8417786 DOI: 10.3389/fcell.2021.703489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/30/2021] [Indexed: 11/13/2022]  Open
29
Zeng K, Xu Y, Lin G, Liang L, Hao T. Automated classification of clinical trial eligibility criteria text based on ensemble learning and metric learning. BMC Med Inform Decis Mak 2021;21:129. [PMID: 34330259 PMCID: PMC8323220 DOI: 10.1186/s12911-021-01492-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 04/08/2021] [Indexed: 12/02/2022]  Open
30
Queirós P, Novikova P, Wilmes P, May P. Unification of functional annotation descriptions using text mining. Biol Chem 2021;402:983-990. [PMID: 33984880 DOI: 10.1515/hsz-2021-0125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/03/2021] [Indexed: 02/06/2023]
31
Miftahutdinov Z, Kadurin A, Kudrin R, Tutubalina E. Medical Concept Normalization in Clinical Trials with Drug and Disease Representation Learning. Bioinformatics 2021;37:3856-3864. [PMID: 34213526 PMCID: PMC8570806 DOI: 10.1093/bioinformatics/btab474] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/02/2021] [Accepted: 07/01/2021] [Indexed: 11/18/2022]  Open
32
Queirós P, Delogu F, Hickl O, May P, Wilmes P. Mantis: flexible and consensus-driven genome annotation. Gigascience 2021;10:giab042. [PMID: 34076241 PMCID: PMC8170692 DOI: 10.1093/gigascience/giab042] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 03/22/2021] [Accepted: 05/14/2021] [Indexed: 12/22/2022]  Open
33
Islamaj R, Wei CH, Cissel D, Miliaras N, Printseva O, Rodionov O, Sekiya K, Ward J, Lu Z. NLM-Gene, a richly annotated gold standard dataset for gene entities that addresses ambiguity and multi-species gene recognition. J Biomed Inform 2021;118:103779. [PMID: 33839304 PMCID: PMC11037554 DOI: 10.1016/j.jbi.2021.103779] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/14/2021] [Accepted: 04/05/2021] [Indexed: 10/21/2022]
34
Zhao S, Su C, Lu Z, Wang F. Recent advances in biomedical literature mining. Brief Bioinform 2021;22:bbaa057. [PMID: 32422651 PMCID: PMC8138828 DOI: 10.1093/bib/bbaa057] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/22/2020] [Accepted: 03/25/2020] [Indexed: 01/26/2023]  Open
35
Singh G, Papoutsoglou EA, Keijts-Lalleman F, Vencheva B, Rice M, Visser RG, Bachem CW, Finkers R. Extracting knowledge networks from plant scientific literature: potato tuber flesh color as an exemplary trait. BMC PLANT BIOLOGY 2021;21:198. [PMID: 33894758 PMCID: PMC8070292 DOI: 10.1186/s12870-021-02943-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 03/29/2021] [Indexed: 06/12/2023]
36
Turina P, Fariselli P, Capriotti E. ThermoScan: Semi-automatic Identification of Protein Stability Data From PubMed. Front Mol Biosci 2021;8:620475. [PMID: 33842537 PMCID: PMC8027235 DOI: 10.3389/fmolb.2021.620475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/18/2021] [Indexed: 11/13/2022]  Open
37
Wang LL, Lo K. Text mining approaches for dealing with the rapidly expanding literature on COVID-19. Brief Bioinform 2021;22:781-799. [PMID: 33279995 PMCID: PMC7799291 DOI: 10.1093/bib/bbaa296] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/02/2020] [Accepted: 10/07/2020] [Indexed: 12/13/2022]  Open
38
Homeyer A, Lotz J, Schwen LO, Weiss N, Romberg D, Höfener H, Zerbe N, Hufnagl P. Artificial Intelligence in Pathology: From Prototype to Product. J Pathol Inform 2021;12:13. [PMID: 34012717 PMCID: PMC8112352 DOI: 10.4103/jpi.jpi_84_20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/28/2020] [Accepted: 01/18/2021] [Indexed: 12/13/2022]  Open
39
Wei Q, Ji Z, Li Z, Du J, Wang J, Xu J, Xiang Y, Tiryaki F, Wu S, Zhang Y, Tao C, Xu H. A study of deep learning approaches for medication and adverse drug event extraction from clinical text. J Am Med Inform Assoc 2021;27:13-21. [PMID: 31135882 DOI: 10.1093/jamia/ocz063] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/23/2019] [Accepted: 04/17/2019] [Indexed: 11/13/2022]  Open
40
Incorporating bidirectional interactive information and regional features for relational facts extraction. AI OPEN 2021. [DOI: 10.1016/j.aiopen.2021.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
41
Harris DR, Eisinger C, Wang Y, Delcher C. Challenges and Barriers in Applying Natural Language Processing to Medical Examiner Notes from Fatal Opioid Poisoning Cases. PROCEEDINGS : ... IEEE INTERNATIONAL CONFERENCE ON BIG DATA. IEEE INTERNATIONAL CONFERENCE ON BIG DATA 2020;2020:3727-3736. [PMID: 35282306 PMCID: PMC8910776 DOI: 10.1109/bigdata50022.2020.9378443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
42
Qu J, Steppi A, Zhong D, Hao J, Wang J, Lung PY, Zhao T, He Z, Zhang J. Triage of documents containing protein interactions affected by mutations using an NLP based machine learning approach. BMC Genomics 2020;21:773. [PMID: 33167858 PMCID: PMC7654050 DOI: 10.1186/s12864-020-07185-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 10/26/2020] [Indexed: 11/17/2022]  Open
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Wang J, Li M, Diao Q, Lin H, Yang Z, Zhang Y. Biomedical document triage using a hierarchical attention-based capsule network. BMC Bioinformatics 2020;21:380. [PMID: 32938366 PMCID: PMC7495737 DOI: 10.1186/s12859-020-03673-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
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Luong NDM, Coroller L, Zagorec M, Membré JM, Guillou S. Spoilage of Chilled Fresh Meat Products during Storage: A Quantitative Analysis of Literature Data. Microorganisms 2020;8:E1198. [PMID: 32781668 PMCID: PMC7465036 DOI: 10.3390/microorganisms8081198] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 08/03/2020] [Indexed: 01/21/2023]  Open
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Zeng K, Pan Z, Xu Y, Qu Y. An Ensemble Learning Strategy for Eligibility Criteria Text Classification for Clinical Trial Recruitment: Algorithm Development and Validation. JMIR Med Inform 2020;8:e17832. [PMID: 32609092 PMCID: PMC7367522 DOI: 10.2196/17832] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/09/2020] [Accepted: 03/14/2020] [Indexed: 01/09/2023]  Open
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Leaman R, Wei CH, Allot A, Lu Z. Ten tips for a text-mining-ready article: How to improve automated discoverability and interpretability. PLoS Biol 2020;18:e3000716. [PMID: 32479517 PMCID: PMC7289435 DOI: 10.1371/journal.pbio.3000716] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/11/2020] [Indexed: 12/22/2022]  Open
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Extracting chemical reactions from text using Snorkel. BMC Bioinformatics 2020;21:217. [PMID: 32460703 PMCID: PMC7251675 DOI: 10.1186/s12859-020-03542-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 05/11/2020] [Indexed: 11/19/2022]  Open
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Liu C, Peres Kury FS, Li Z, Ta C, Wang K, Weng C. Doc2Hpo: a web application for efficient and accurate HPO concept curation. Nucleic Acids Res 2020;47:W566-W570. [PMID: 31106327 PMCID: PMC6602487 DOI: 10.1093/nar/gkz386] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 01/18/2023]  Open
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Eicher T, Kinnebrew G, Patt A, Spencer K, Ying K, Ma Q, Machiraju R, Mathé EA. Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources. Metabolites 2020;10:E202. [PMID: 32429287 PMCID: PMC7281435 DOI: 10.3390/metabo10050202] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/07/2020] [Accepted: 05/13/2020] [Indexed: 02/06/2023]  Open
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Wang X, Zhang Y, Ren X, Zhang Y, Zitnik M, Shang J, Langlotz C, Han J. Cross-type biomedical named entity recognition with deep multi-task learning. Bioinformatics 2020;35:1745-1752. [PMID: 30307536 DOI: 10.1093/bioinformatics/bty869] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 10/03/2018] [Accepted: 10/09/2018] [Indexed: 12/13/2022]  Open
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