|
|
Biomedical Informatics Studies for Knowledge Discovery in Precision Medicine |
Zhang Zhiqiang1(), Fan Shaoping2, Chen Xiujuan1,3 |
1(Chengdu Library and Information Center, Chinese Academy of Sciences, Chengdu 610041, China) 2(Institute of Medical Information & Library, Chinese Academy of Medical Sciences, Beijing 100020, China) 3(University of Chinese Academy of Sciences, Beijing 100049, China) |
|
|
Abstract [Objective] This paper reviews the latest Biomedical Informatics studies and indicates some future directions for data-driven knowledge discovery in precision medicine. [Methods] We summarized the developments of data resources, data analysis platforms and methods, clinical decision-making applications in Biomedical Informatics through literature review and service trials. [Results] Future directions of Biomedical Informatics include building better big data management system, proposing theories and methods for big data analysis, developing new tools and platforms, clinical application of research findings, as well as training senior personnel. [Limitations] More biomedical data resources, methods, and case studies should be added. [Conclusions] This study identifies the future developments of Biomedical Informatics in precision medicine, which utilizes big data analytics to discover more knowledge.
|
Received: 27 December 2017
Published: 05 February 2018
|
|
[1] |
Remarks of President Barack Obama - As Prepared for Delivery State of the Union Address[EB/OL]. [2017-07-25]..
|
[2] |
So What is Precision Medicine? [EB/OL]. [2017-07-25]..
|
[3] |
Embi P J, Kaufman S E, Payne P R.Biomedical Informatics and Outcomes Research: Enabling Knowledge-driven Healthcare[J]. Circulation, 2009, 120(23): 2393-2399.
doi: 10.1161/CIRCULATIONAHA.108.795526
pmid: 2814875
|
[4] |
Sarkar I N.Biomedical Informatics and Translational Medicine[J]. Journal of Translational Medicine, 2010, 8(1): 22.
doi: 10.1186/1479-5876-8-22
pmid: 20187952
|
[5] |
Gonzalez G H, Tahsin T, Goodale B C, et al.Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery[J]. Briefings in Bioinformatics, 2016, 17(1): 33-42.
doi: 10.1093/bib/bbv087
pmid: 4719073
|
[6] |
Barbolosi D, Ciccolini J, Lacarelle B, et al.Computational Oncology - Mathematical Modeling of Drug Regimens for Precision Medicine[J]. Nature Reviews Clinical Oncology, 2016, 13(4): 242-254.
doi: 10.1038/nrclinonc.2015.204
pmid: 26598946
|
[7] |
Chen X, Yan C C, Zhang X, et al.Drug-Target Interaction Prediction: Databases, Web Servers and Computational Models[J]. Briefings in Bioinformatics, 2016, 17(4): 696-712.
doi: 10.1093/bib/bbv066
pmid: 26283676
|
[8] |
Shiono M, Misumi K, Kaieda R, et al.Overview of the BioBank Japan Project: Study Design and Profile[J]. Journal of Epidemiology, 2017, 27(3): S2-S8.
doi: 10.1016/j.je.2016.12.005
pmid: 28189464
|
[9] |
Piñero J, Bravo À, Queraltrosinach N, et al.DisGeNET: A Comprehensive Platform Integrating Information on Human Disease-associated Genes and Variants[J]. Nucleic Acids Research, 2017, 45(Database Issue): D833-D839.
doi: 10.1093/nar/gkw943
pmid: 27924018
|
[10] |
钱庆. 精准医学相关的数据管理与知识服务[J]. 情报工程, 2015, 1(6): 17-22.
|
[10] |
(Qian Qing.Precision Medicine Related Data Management and Knowledge Service[J]. Technology Intelligence Engineering, 2015,1(6): 17-22.)
|
[11] |
Galperin M Y, Fernándezsuárez X M, Rigden D J.The 24th Annual Nucleic Acids Research Database Issue: A Look Back and Upcoming Changes[J]. Nucleic Acids Research, 2017, 45(Database Issue): D1-D11.
doi: 10.1093/nar/gkw1188
pmid: 5210597
|
[12] |
NCBI Resource Coordinators.Database Resources of the National Center for Biotechnology Information[J]. Nucleic Acids Research, 2017, 45(Database Issue): D12-D17.
doi: 10.1109/HAPTIC.2010.5444654
|
[13] |
GenBank and WGS Statistics [EB/OL]. [2017-09-02]..
|
[14] |
DrugBank Statistics [EB/OL]. [2017-09-15]..
|
[15] |
Number of Registered Studies Over Time[EB/OL]. [2017- 09-15]..
|
[16] |
NCBI. Tools [EB/OL].[2017-08-30]. .
|
[17] |
EBI. Tools & Databases [EB/OL]. [2017-08-30]. .
|
[18] |
SIB. Databases & Tools [EB/OL].[2017-08-30]. .
|
[19] |
DisGeNET Database Information [EB/OL]. [2017-08-27]. .
|
[20] |
Ingenuity Pathway Analysis [EB/OL]. [2017-08-27]. .
|
[21] |
IPA Features [EB/OL]. [2017-08-27]..
|
[22] |
PharmGKB [EB/OL]. [2017-08-18]..
|
[23] |
CTD (Comparative Toxicogenomics Database) [EB/OL]. [2017-08-27]. .
|
[24] |
UpToDate [EB/OL]. [2017-08-18]. .
|
[25] |
张志强, 范少萍. 论学科信息学的兴起与发展[J]. 情报学报, 2015, 34(10): 1011-1023.
doi: 10.3772/j.issn.1000-0135.2015.010.001
|
[25] |
(Zhang Zhiqiang, Fan Shaoping.On the Emergence and Development of Subject Informatics[J]. Journal of the China Society for Scientific and Technical Information, 2015, 34(10): 1011-1023.)
doi: 10.3772/j.issn.1000-0135.2015.010.001
|
[26] |
Ding J, McConechy M K, Horlings H M, et al. Systematic Analysis of Somatic Mutations Impacting Gene Expression in 12 Tumour Types[J]. Nature Communications, 2015, 6: 8554.
doi: 10.1038/ncomms9554
pmid: 4600750
|
[27] |
李渊, 骆志刚, 管乃洋, 等. 生物医学数据分析中的深度学习方法应用[J]. 生物化学与生物物理进展, 2016, 43(5): 472-483.
|
[27] |
(Li Yuan, Luo Zhigang, Guan Naiyang, et al.Applications of Deep Learning in Biological and Medical Data Analysis[J]. Progress in Biochemistry and Biophysics, 2016, 43(5): 472-483.)
|
[28] |
Fusaro V A, Patil P, Gafni E, et al.Biomedical, Cloud, Computing, with Amazon, Web, Services[J]. PLoS Computational Biology, 2011, 7(8): e1002147.
doi: 10.1371/journal.pcbi.1002147
pmid: 2020202202011202020202020202020202073100214720
|
[29] |
Kang N, Chen T.Big Data for Biomedical Research: Current Status and Prospective[J]. Chinese Science Bulletin, 2015, 60(5-6): 534-546.
doi: 10.1360/N972014-00895
|
[30] |
NCI and the Precision Medicine Initiative® [EB/OL]. [2017- 08-20]..
|
[31] |
Watson Health Perspectives [EB/OL]. [2017-09-20]..
|
[32] |
冯时, 弓孟春, 张抒扬. 中国国家罕见病注册系统及其队列研究: 愿景与实施路线[J]. 中华内分泌代谢杂志, 2016, 32(12): 977-982.
doi: 10.3760/cma.j.issn.1000-6699.2016.12.001
|
[32] |
(Feng Shi, Gong Mengchun, Zhang Shuyang.The National Rare Diseases Registry System of China and the Related Cohorts Studies: Vision and Roadmap[J]. Chinese Journal of Endocrinology and Metabolism, 2016, 32(12): 977-982.)
doi: 10.3760/cma.j.issn.1000-6699.2016.12.001
|
[33] |
Xu R, Wang Q Q.PhenoPredict: A Disease Phenome-wide Drug Repositioning Approach Towards Schizophrenia Drug Discovery[J]. Journal of Biomedical Informatics, 2015, 56(C): 348-355.
doi: 10.1016/j.jbi.2015.06.027
pmid: 26151312
|
[34] |
Shah A D, Langenberg C, Rapsomaniki E, et al.Type 2 Diabetes and Incidence of Cardiovascular Diseases: A Cohort Study in 1.9 Million People[J]. Lancet Diabetes & Endocrinology, 2015, 3(2): 105-113.
doi: 10.1016/S0140-6736(15)60401-9
pmid: 26312908
|
[35] |
焦怡琳, 王吉春, 张群, 等. 中国在精准医学领域面临的机遇与挑战[J]. 中国公共卫生管理, 2015, 31(5): 601-603.
|
[35] |
(Jiao Yilin, Wang Jichun, Zhang Qun, et al.Opportunities and Challenges in Field of Precision Medicine in China[J]. Chinese Journal of Public Health Management, 2015, 31(5): 601-603.)
|
[36] |
付文华, 钱海利, 詹启敏. 中国精准医学发展的需求和任务[J]. 中国生化药物杂志, 2016, 36(4): 1-4.
doi: 10.3969/j.issn.1005-1678.2016.04.01
|
[36] |
(Fu Wenhua, Qian Haili, Zhan Qimin.Precision Medicine in China[J]. Chinese Journal of Biochemical Pharmaceutics, 2016, 36(4): 1-4.)
doi: 10.3969/j.issn.1005-1678.2016.04.01
|
[37] |
Field D, Garrity G, Gray T, et al.The Minimum Information about a Genome Sequence (MIGS) Specification[J]. Nature Biotechnology, 2008, 26(5): 541-547.
doi: 10.1038/nbt1360
pmid: 18464787
|
[38] |
Yilmaz P, Kottmann R, Field D, et al.Minimum Information about a Marker Gene Sequence (MIMARKS) and Minimum Information about Any (x) Sequence (MIxS) Specifications[J]. Nature Biotechnology, 2011, 29(5): 415-420.
doi: 10.1038/nbt.1823
pmid: 3367316
|
[39] |
Harvey A, Brand A, Holgate S T, et al.The Future of Technologies for Personalised Medicine[J]. New Biotechnology, 2012, 29(6): 625-633.
doi: 10.1016/j.nbt.2012.03.009
pmid: 23091837
|
[40] |
向俊, 刘朦. 基于大数据分析法的精准医疗前景[J]. 中国医疗设备, 2017, 32(8):112-115, 124.
|
[40] |
(Xiang Jun, Liu Meng.Prospects of Precision Medical Based on Big Data Analysis[J]. China Medical Devices, 2017, 32(8): 112-115, 124.)
|
[41] |
Miñarrogiménez J A, Marínalonso O, Samwald M.Applying Deep Learning Techniques on Medical Corpora from the World Wide Web: A Prototypical System and Evaluation [OL]. arXiv Preprint. arXiv: 1502.03682.
|
[42] |
Lv X, Guan Y, Yang J, et al.Clinical Relation Extraction with Deep Learning[J]. International Journal of Hybrid Information Technology, 2016, 9(7): 237-248.
doi: 10.14257/ijhit.2016.9.7.22
|
[43] |
Shen D, Wu G, Suk H I.Deep Learning in Medical Image Analysis[J]. Annual Review of Biomedical Engineering, 2017, 19: 221-248.
doi: 10.1146/annurev-bioeng-071516-044442
pmid: 28301734
|
[44] |
Vougas K, Krochmal M, Jackson T, et al.Deep Learning and Association Rule Mining for Predicting Drug Response in Cancer. A Personalised Medicine Approach [OL].[2017-09- 25]. .
|
[45] |
Dong X, Qian L, Guan Y, et al.A Multiclass Classification Method Based on Deep Learning for Named Entity Recognition in Electronic Medical Records[C]//Proceedings of Scientific Data Summit. IEEE, 2016:1-10.
|
[46] |
高汉松, 肖凌, 许德玮, 等. 基于云计算的医疗大数据挖掘平台[J]. 医学信息学杂志, 2013, 34(5): 32-38.
doi: 10.3969/j.issn.1673-6036.2013.05.002
|
[46] |
(Gao Hansong, Xiao Ling, Xu Dewei, et al.Medical Data Mining Platform Based on Cloud Computing[J]. Journal of Medical Intelligence, 2013, 34(5): 32-38.)
doi: 10.3969/j.issn.1673-6036.2013.05.002
|
[47] |
Hintzsche J, Kim J, Yadav V, et al.IMPACT: A Whole- exome Sequencing Analysis Pipeline for Integrating Molecular Profiles with Actionable Therapeutics in Clinical Samples[J]. Journal of the American Medical Informatics Association Jamia, 2016, 23(4): 721-730.
doi: 10.1093/jamia/ocw022
pmid: 27026619
|
[48] |
任思冲, 周海琴, 彭萍. 大数据挖掘促进精准医学发展[J]. 国际检验医学杂志, 2015, 36(23): 3499-3501.
|
[48] |
(Ren Sichong, Zhou Haiqin, Peng Ping.Big Data Mining Promotes the Development of Precision Medicine[J]. International Journal of Laboratory Medicine, 2015, 36(23): 3499-3501.)
|
[49] |
Canadian Bioinformatics and Computational Biology Strategic Framework [EB/OL]. [2017-09-09]..
|
[50] |
Committee on Key Challenge Areas for Convergence and Health, Studies E L, Council N. Convergence: Facilitating Transdisciplinary Integration of Life Sciences, Physical Sciences, Engineering, and Beyond[M]. National Academies Press (US), 2014.
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
|
Shared |
|
|
|
|
|
Discussed |
|
|
|
|