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Disease Knowledge Discovery Based on SPO Predications |
Cai Miaozhi,Li Xiaoying,Zhao Jiawei,Feng Fengxiang,Ren Huiling() |
Institute of Medical Information, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100020, China |
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Abstract [Objective] This study tries to discover knowledge from the high-level evidence-based literature on diseases indexed by PubMed, aiming to provide reference for clinical diagnosis, treatment, as well as routine prevention and control of diseases. [Methods] We proposed a diseases knowledge discovery model based on SPO predications with the semantic extraction tool SemRep. Then we selected the diabetes-related literature to evaluate this model, and discovered knowledge based on SPO visualization and clinical knowledge. [Results] We obtained 1 258 SPO predications and 16 semantic relationships, which identified diabetes-related genes, common complications, as well as detection and treatment methods. [Limitations] We only examined our model with publicly accessible literature. More research is needed to include knowledge bases and electronic medical records. [Conclusions] The disease knowledge discovery model based on SPO predication could identify the biomedical knowledge from literature, which provides potential research hypotheses and ideas for biomedical researchers.
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Received: 21 June 2021
Published: 22 February 2022
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Fund:National Key Research and Development Program of China(2019AAA0104901);National Social Science Fund of China(20BTQ062);China-WHO Biennial Collaborative Projects(GJ2-2021-WHOSO-01) |
Corresponding Authors:
Ren Huiling,ORCID:0000-0002-1067-408X
E-mail: wangjd@sic.gov.cn
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[1] |
National Library of Medicine. PubMed Overview[EB/OL].[2021-05-04]. https://pubmed.ncbi.nlm.nih.gov/about/ .
|
[2] |
Pyysalo S, Baker S, Ali I, et al. LION LBD: A Literature-Based Discovery System for Cancer Biology[J]. Bioinformatics, 2019, 35(9):1553-1561.
doi: 10.1093/bioinformatics/bty845
pmid: 30304355
|
[3] |
隗玲, 胡正银, 庞弘燊, 等. 基于“主语-谓语-宾语”三元组的知识发现研究——以诱导多能干细胞领域为例[J]. 数字图书馆论坛, 2017(9):28-34.
|
[3] |
( Wei Ling, Hu Zhengyin, Pang Hongshen, et al. Study on Knowledge Discovery Based on “Subject-Predication-Object” Predications: A Case Study of Induced Pluripotent Stem Cells[J]. Digital Library Forum, 2017(9):28-34.)
|
[4] |
Liu Y, Bill R, Fiszman M, et al. Using SemRep to Label Semantic Relations Extracted from Clinical Text[J]. Proceedings of the AMIA Annual Fall Symposium, 2012: 587-595.
|
[5] |
World Health Organization. Noncommunicable Diseases[EB/OL].(2018-06-1). [2021-05-06]. https://www.who.int/news-room/fact-sheets/detail/noncommunicable-diseases .
|
[6] |
Harding J L, Pavkov M E, Magliano D J, et al. Global Trends in Diabetes Complications: A Review of Current Evidence[J]. Diabetologia, 2019, 62(1):3-16.
doi: 10.1007/s00125-018-4711-2
|
[7] |
国家卫生健康委员会. 健康中国行动(2019—2030年)[EB/OL].(2019-07-15). [2021-05-06]. http://www.gov.cn/xinwen/2019-07/15/content_5409694.htm. .
|
[7] |
(National Health Commission. Healthy China Action(2019-2030)[EB/OL].(2019-07-15). [2021-05-06]. http://www.gov.cn/xinwen/2019-07/15/content_5409694.htm. .
|
[8] |
Gopalakrishnan V, Jha K, Jin W, et al. A Survey on Literature Based Discovery Approaches in Biomedical Domain[J]. Journal of Biomedical Informatics, 2019, 93:103141.
doi: S1532-0464(19)30059-0
pmid: 30857950
|
[9] |
代冰, 胡正银. 基于文献的知识发现新近研究综述[J]. 数据分析与知识发现, 2021, 5(4):1-12.
|
[9] |
( Dai Bing, Hu Zhengyin. Review of Studies on Literature-Based Discovery[J]. Data Analysis and Knowledge Discovery, 2021, 5(4):1-12.)
|
[10] |
Swanson D R, Smalheiser N R. An Interactive System for Finding Complementary Literatures: A Stimulus to Scientific Discovery[J]. Artificial Intelligence, 1997, 91(2):183-203.
doi: 10.1016/S0004-3702(97)00008-8
|
[11] |
Cohen T, Widdows D, Stephan C, et al. Predicting High-throughput Screening Results with Scalable Literature-based Discovery Methods[J]. CPT: Pharmacometrics & Systems Pharmacology, 2014, 3(10):e140.
|
[12] |
贺丹, 姜淼, 郑光, 等. 利用文本挖掘技术探索高血压病症状、证候以及用药规律[J]. 中国实验方剂学杂志, 2014, 20(19):214-216.
|
[12] |
( He Dan, Jiang Miao, Zheng Guang, et al. Exploring Relationship Among Symptom, Pattern and Medication Regularityof Hypertension Based on Text Mining Technology[J]. Chinese Journal of Experimental Traditional Medical Formulae, 2014, 20(19):214-216.)
|
[13] |
胡正银, 刘蕾蕾, 代冰, 等. 基于领域知识图谱的生命医学学科知识发现探析[J]. 数据分析与知识发现, 2020, 4(11):1-14.
|
[13] |
( Hu Zhengyin, Liu Leilei, Dai Bing, et al. Discovering Subject Knowledge in Life and Medical Sciences with Knowledge Graph[J]. Data Analysis and Knowledge Discovery, 2020, 4(11):1-14.)
|
[14] |
Xu B, Shi X, Zhao Z, et al. Leveraging Biomedical Resources in Bi-LSTM for Drug Drug Interaction Extraction[J]. IEEE Access, 2018, 6:33432-33439.
doi: 10.1109/ACCESS.2018.2845840
|
[15] |
李智恒, 桂颖溢, 杨志豪, 等. 基于生物医学文献的化学物质致病关系抽取[J]. 计算机研究与发展, 2018, 55(1):198-206.
|
[15] |
( Li Zhiheng, Gui Yingyi, Yang Zhihao, et al. Chemical-Induced Disease Relation Extraction Based on Biomedical Literature[J]. Journal of Computer Research and Development, 2018, 55(1):198-206.)
|
[16] |
李晓瑛, 李军莲, 李丹亚. 一体化医学语言系统及其在知识发现中的应用研究[J]. 数字图书馆论坛, 2019(9):24-29.
|
[16] |
( Li Xiaoying, Li Junlian, Li Danya. Research on the Unified Medical Language System and Its Application to Knowledge Discovery[J].Digital Library Forum, 2019(9):24-29.)
|
[17] |
Fiszman M, Rindflesch T C, Kilicoglu H. Summarizing Drug Information in Medline Citations[J]. Proceedings of the AMIA Annual Fall Symposium, 2006: 254-258.
|
[18] |
Kilicoglu H, Fiszman M, Rodriguez R, et al. Semantic MEDLINE: A Web Application for Managing the Results of PubMed Searches[C]// Proceedings of the 3rd International Symposium on Semantic Mining in Biomedicine. 2008: 69-76.
|
[19] |
Zhang H, Fiszman M, Shin D, et al. Clustering Cliques for Graph-based Summarization of the Biomedical Research Literature[J]. BMC Bioinformatics, 2013, 14(1):Article No. 182.
doi: 10.1186/1471-2105-14-182
|
[20] |
闫雷, 刘春鹤, 关晶, 等. SemRep处理结果统计挖掘系统的开发[J]. 医学信息学杂志, 2013, 34(4):31-34.
|
[20] |
( Yan Lei, Liu Chunhe, Guan Jing, et al. The Development of Statistics Mining System Based on Result Analysis by Application of SemRep[J]. Journal of Medical Informatics, 2013, 34(4):31-34.)
|
[21] |
王雪, 杨雪梅, 李沛鑫, 等. 基于语义模型的药物矛盾知识发现[J]. 情报杂志, 2020, 39(7):159-165.
|
[21] |
( Wang Xue, Yang Xuemei, Li Peixin, et al. Contradiction Knowledge Discovery of Drugs Based on Semantic Model[J]. Journal of Intelligence, 2020, 39(7):159-165.)
|
[22] |
Fiszman M, Rindflesch T C, Kilicoglu H. Abstraction Summarization for Managing the Biomedical Research Literature[C]// Proceedings of the HLT/NAACL 2004 Workshop on Computational Lexical Semantics. USA: Association for Computational Linguistics, 2004: 76-83.
|
[23] |
Lundkvist P, Pereira MJ, Kamble PG, et al. Glucagon Levels During Short-Term SGLT2 Inhibition are Largely Regulated by Glucose Changes in Patients with Type 2 Diabetes[J]. Journal of Clinical Endocrinology and Metabolism, 2019, 104(1):193-201.
doi: 10.1210/jc.2018-00969
|
[24] |
Stomby A, Otten J, Ryberg M, et al. Diet-induced Weight Loss Alters Hepatic Glucocorticoid Metabolism in Type 2 Diabetes Mellitus[J]. European Journal of Endocrinology, 2020, 182(4):447-457.
doi: 10.1530/EJE-19-0901
|
[25] |
Furuhashi M, Hiramitsu S, Mita T, et al. Reduction of Serum FABP4 Level by Sitagliptin, a DPP-4 Inhibitor, in Patients with Type 2 Diabetes Mellitus[J]. Journal of Lipid Research, 2015, 56(12):2372-2380.
doi: 10.1194/jlr.M059469
pmid: 26467280
|
[26] |
殷雨晨. 糖尿病并发症(Ⅰ)[J]. 中国伤残医学, 2020, 28(23):I0003.
|
[26] |
(Yin Yuchen. Diabetes Complications (Ⅰ)[J]. Chinese Journal of Trauma and Disability Medicine, 2020, 28(23):I0003.)
|
[27] |
Henriksen M M, Andersen H U, Thorsteinsson B, et al. Asymptomatic Hypoglycaemia in Type 1 Diabetes: Incidence and Risk Factors[J]. Diabetic Medicine, 2019, 36(1):62-69.
doi: 10.1111/dme.13848
|
[28] |
中华医学会糖尿病学分会. 2020年2型糖尿病防治指南[EB/OL].[2021-05-15].https://max.book118.com/html/2021/0412/5134100120003220.shtm .
|
[28] |
(Chinese Diabetes Society. 2020 Type 2 Diabetes Prevention Guidelines[EB/OL].[2021-05-15].https://max.book118.com/html/2021/0412/5134100120003220.shtm .)
|
[29] |
王永胜, 杨丽霞, 程涛, 等. 糖尿病肾病的炎症致病机制与中药防治[J]. 中国实验方剂学杂志, 2018, 24(2):200-207.
|
[29] |
( Wang Yongsheng, Yang Lixia, Cheng Tao, et al. Pathogenic Mechanism of Inflammation and TCM Intervention of Diabetic Nephropathy[J]. Chinese Journal of Experimental Traditional Medical Formulae, 2018, 24(2):200-207.)
|
[30] |
Weng J P, Bi Y. Epidemiological Status of Chronic Diabetic Complications in China[J]. Chinese Medical Journal, 2015, 128(24):3267-3269.
doi: 10.4103/0366-6999.171350
|
[31] |
科普中国. 口服葡萄糖耐量试验[EB/OL]. [2021-05-15].https://baike.baidu.com/item/口服葡萄糖耐量试验/10729512?fr=aladdin .
|
[31] |
(China Science Communication. Oral Glucose Tolerance Test[EB/OL].[2021-05-15].https://baike.baidu.com/item/口服葡萄糖耐量试验/10729512?fr=aladdin .)
|
[32] |
王超. 中国成人超重和肥胖及主要危险因素对糖尿病发病的影响[D]. 北京: 北京协和医学院, 2014.
|
[32] |
( Wang Chao. The Influence of Overweight, Obesity and Main Risk Factors on the Incidence of Diabetes in Chinese Adults[D]. Beijing: Peking Union Medical College, 2014.)
|
[33] |
Sanchez-Rangel E, Inzucchi S E. Metformin: Clinical Use in Type 2 Diabetes[J]. Diabetologia, 2017, 60(9):1586-1593.
doi: 10.1007/s00125-017-4336-x
pmid: 28770321
|
[34] |
Fullerton B, Siebenhofer A, Jeitler K, et al. Short-acting Insulin Analogues Versus Regular Human Insulin for Adult, Non-pregnant Persons with Type 2 Diabetes Mellitus[J]. The Cochrane Database of Systematic Reviews, 2018, 12: CD013228.
|
[35] |
Defronzo R A, Inzucchi S, Abdul-Ghani M, et al. Pioglitazone: The Forgotten, Cost-effective Cardioprotective Drug for Type 2 Diabetes[J]. Diabetes & Vascular Disease Research, 2019, 16(2):133-143.
|
[36] |
Lee I M, Shiroma E J, Lobelo F, et al. Effect of Physical Inactivity on Major Non-Communicable Diseases Worldwide: An Analysis of Burden of Disease and Life Expectancy[J]. The Lancet, 2012, 380(9838):219-229.
doi: 10.1016/S0140-6736(12)61031-9
|
[37] |
科普中国. 糖尿病[EB/OL]. [2021-05-15].https://baike.baidu.com/item/糖尿病/100969?fr=aladdin .
|
[37] |
(China Science Communication. Diabetes Mellitus[EB/OL]. [2021-05-15].https://baike.baidu.com/item/糖尿病/100969?fr=aladdin .)
|
[38] |
Kilicoglu H, Shin D, Fiszman M, et al. SemMedDB: A PubMed-scale Repository of Biomedical Semantic Predications[J]. Bioinformatics, 2012, 28(23):3158-3160.
doi: 10.1093/bioinformatics/bts591
pmid: 23044550
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