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A Survey of Current Work in Medical Text Mining---Data Source Perspective

Li Yanhong
2017 International Journal of Biomedical Science and Engineering  
This paper discusses the application of text mining in medical field at home and abroad based on overview and analysis of current literature data.  ...  In China, text mining based on medical literature data occupies a large part. On the one hand, they can monitor the self disclosure of health information.  ...  Acknowledgements This work was supported partly by the National Science Foundation of China (No.7140106).  ... 
doi:10.11648/j.ijbse.20170503.13 fatcat:qtva3la2rzhyhageo3c7so5eou

A Survey of State of the Art Biomedical Text Mining Techniques for Semantic Analysis

Hong-Jie Dai, Chi-Hsin Huang, Jaimie Yi-Wen Lin, Pei-Hsuan Chou, Richard Tzong-Han Tsai, Wen-Lian Hsu
2008 2008 IEEE International Conference on Sensor Networks, Ubiquitous, and Trustworthy Computing (sutc 2008)  
In recent years, a range of text-mining applications have been developed to improve access to knowledge for biologists and database curators.  ...  This paper surveys text-mining works published from 2006 to 2008, with the emphasis on named entity recognition, biological relation extraction and currently available online biological text mining services  ...  In this paper, we present a survey of recent biomedical text mining works published between the end of 2006 and the beginning of 2008.  ... 
doi:10.1109/sutc.2008.86 dblp:conf/sutc/DaiHLCTH08 fatcat:rro4q63izfesvo7q3mfzhxelwu

Text Mining In Healthcare

2019 VOLUME-8 ISSUE-10, AUGUST 2019, REGULAR ISSUE  
As the scope of the study is limited to text mining classification, state of art in particular to healthcare text mining classification is studied in detail with suggested improvements.  ...  This paper starts with introducing data mining and the healthcare paradigm. This study confers various techniques of data mining in healthcare application domain.  ...  A. Issues and Challenges in Healthcare Text Mining Previous section is detailed study of current state of art in healthcare domain.  ... 
doi:10.35940/ijitee.b1111.1292s19 fatcat:s6rtt3a33ncrfgpxpksnu2hdny

Semantic Mining in Biomedicine (Introduction to the papers selected from the SMBM 2005 Symposium, Hinxton, U.K., April 2005)

U. Hahn, A. Valencia
2006 Bioinformatics  
The NoE has initiated a series of conferences dedicated to these particular challenges of data mining and text mining in the life sciences [for a lifescience-centred survey, cf.  ...  Still, the vast majority of biomedical knowledge captured in texts is not at disposal when biomedical databases are queried.  ... 
doi:10.1093/bioinformatics/btl084 pmid:16527834 fatcat:f434vlsupvffbdaavtjnfak2jm

A Short Survey of Biomedical Relation Extraction Techniques [article]

Elham Shahab
2017 arXiv   pre-print
In the current research, we focus on different aspects of relation extraction techniques in biomedical domain and briefly describe the state-of-the-art for relation extraction between a variety of biological  ...  Biomedical information is growing rapidly in the recent years and retrieving useful data through information extraction system is getting more attention.  ...  In particular, text mining methods have been applied in a variety of biomedical branches and domains such as gene clustering, protein structure prediction, clinical diagnosis, biomedical hypothesis and  ... 
arXiv:1707.05850v3 fatcat:snyvtomcxbbeplkspqaucmpely

NLP and Online Health Reports: What do we say and what do we mean?

Nigel Collier
2016 Proceedings of the Seventh International Workshop on Health Text Mining and Information Analysis  
In this talk I survey the progress made using NLP methods, e.g. for adverse drug reaction profiling, flu surveillance and the study of depressive disorders.  ...  To this end I present state of the art results from our recent work on using deep neural networks to de-conflate word senses as well as 'translating' from social media messages to SNOMED-CT.  ...  He was awarded a Marie Curie fellowship at the European Bioinformatics Institute from 2012 to 2014 where he continued his investigation into biomedical text mining for scientific texts.  ... 
doi:10.18653/v1/w16-6111 dblp:conf/acl-louhi/Collier16 fatcat:uerbdzfgkbgebc5ktu5jgj4rmi

Page 139 of Computational Linguistics Vol. 33, Issue 1 [page]

2007 Computational Linguistics  
Cohen, A. and W. Hersh. 2005. A survey of current work in biomedical text mining. Briefings in Bioinformatics, 6(1):57-71. Friedman, C., P. Kra, H. Yu, M. Krauthammer, and A. Rzhetsky. 2001.  ...  This is a very interesting chapter, which comes closer to the Hearstian notion of text mining than previous chapters, although most of the reviewed techniques treat the text as a bag of words, thus deviating  ... 

Methods and Trends in Information Retrieval in Big Data Genomic Research

2019 VOLUME-8 ISSUE-10, AUGUST 2019, REGULAR ISSUE  
This paper described information retrieval (IR) and the common methods of finding, extracting, and mining information in genomic research through text mining, and natural language processing (NLP).  ...  in the biomedical and genome research.  ...  A gene-mention finding module LingPipe used in biomedical text mining.  ... 
doi:10.35940/ijitee.i1109.0789s219 fatcat:j2uramagd5a75jusrcor75w7ue

Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II

Z. Lu, L. Hirschman
2012 Database: The Journal of Biological Databases and Curation  
Compared to a survey done in 2009, our 2012 results show that many more databases are now using text mining in parts of their curation workflows.  ...  Despite the continuing advances in biomedical text mining and the pressing needs of biocurators for better tools, few existing text-mining tools have been successfully integrated into production literature  ...  Conflict of interest. None declared.  ... 
doi:10.1093/database/bas043 pmid:23160416 pmcid:PMC3500522 fatcat:tkyl4ik7tfdjflroojq6axjtkq

PubTator: a web-based text mining tool for assisting biocuration

Chih-Hsuan Wei, Hung-Yu Kao, Zhiyong Lu
2013 Nucleic Acids Research  
There is therefore a pressing need to assist biocuration with automated text mining tools. Here, we describe PubTator, a web-based system for assisting biocuration.  ...  PubTator is different from the few existing tools by featuring a PubMed-like interface, which many biocurators find familiar, and being equipped with multiple challenge-winning text mining algorithms to  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkt441 pmid:23703206 pmcid:PMC3692066 fatcat:a4267hraenabjdzggispethbz4

Hairpins in bookstacks: Information retrieval from biomedical text

H. Shatkay
2005 Briefings in Bioinformatics  
She is an active member of the biomedical text-mining community, and one of the first researchers in the area of text mining and information retrieval for bioinformatics.  ...  She works in the area of machine learning and its application to biomedical data.  ...  Acknowledgment Hagit Shatkay's work is partially funded by NSERC Discovery Grant #298292-04.  ... 
doi:10.1093/bib/6.3.222 pmid:16212771 fatcat:2liwpccfq5dhza5mmdw66q7m2m

Text Mining for Finding Functional Community of Related Genes Using TCM Knowledge [chapter]

Zhaohui Wu, Xuezhong Zhou, Baoyan Liu, Junli Chen
2004 Lecture Notes in Computer Science  
It is also a probing research to study the connection of TCM with modern biomedical and post-genomics studies by text mining.  ...  We present a novel text mining approach to uncover the functional gene relationships, maybe, temporal and spatial functional modular interaction networks, from MEDLINE in large scale.  ...  This work is partially supported by National Basic Research Priorities Programme of China Ministry of Science and Technology under grant number 2002DEA30042.  ... 
doi:10.1007/978-3-540-30116-5_42 fatcat:kqonz5bqfjeule52al5bhrj244

Frontiers of biomedical text mining: current progress

P. Zweigenbaum, D. Demner-Fushman, H. Yu, K. B. Cohen
2007 Briefings in Bioinformatics  
In this article we review the current state of the art in biomedical text mining or 'BioNLP' in general, focusing primarily on papers published within the past year.  ...  However, a number of problems at the frontiers of biomedical text mining continue to present interesting challenges and opportunities for great improvements and interesting research.  ...  KBC was supported by NIH grants 'Construction of a Full Text Corpus for Biomedical Text Mining' (#1G08LM009639-01) and 'Technology Development for a Molecular Biology Knowledge-base' (#5R01 LM008111-03  ... 
doi:10.1093/bib/bbm045 pmid:17977867 pmcid:PMC2516302 fatcat:4nfbokb7lfdjbnkijw2v6754qy

Mining the pharmacogenomics literature--a survey of the state of the art

U. Hahn, K. B. Cohen, Y. Garten, N. H. Shah
2012 Briefings in Bioinformatics  
Therefore, publications span the intersection of research in genotypes, phenotypes and pharmacology, a topic that has increasingly become a focus of active research in recent years.This survey covers efforts  ...  This article surveys efforts on text mining of the pharmacogenomics literature, mainly from the period 2008 to 2011.  ...  [2] , for a recent survey). Work in this field builds on and complements research previously carried out in closely related areas such as biomedical text mining (see e.g. Krallinger et al.  ... 
doi:10.1093/bib/bbs018 pmid:22833496 pmcid:PMC3404399 fatcat:por4dnthkrcxjdsir6uc64kdaq

BioC: a minimalist approach to interoperability for biomedical text processing

D. C. Comeau, R. Islamaj Dogan, P. Ciccarese, K. B. Cohen, M. Krallinger, F. Leitner, Z. Lu, Y. Peng, F. Rinaldi, M. Torii, A. Valencia, K. Verspoor (+3 others)
2013 Database: The Journal of Biological Databases and Curation  
Acknowledgement The authors thank the anonymous reviewers for their useful suggestions in improving this manuscript. .................................................................................  ...  Current BioC work Computational biology research is integrally dependent on the accuracy of NLP and text mining tools for purposes of information retrieval and extraction.  ...  information extraction and text mining for biomedical literature.  ... 
doi:10.1093/database/bat064 pmid:24048470 pmcid:PMC3889917 fatcat:m5q3ltrfobg4fgkash3katpkia
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