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Biomedical Text Mining and Its Applications

Raul Rodriguez-Esteban, Fran Lewitter
2009 PLoS Computational Biology  
Biomedical text mining (henceforth, text mining) is the subfield that deals with text that comes from biology, medicine, and chemistry (henceforth, biomedical text).  ...  This variability means, in practice, that text mining applications are tailored to specific types of text.  ... 
doi:10.1371/journal.pcbi.1000597 pmid:20041219 pmcid:PMC2791166 fatcat:2h3n7vgyurfy5ayfz2utt5t34i

Biomedical text mining and its applications in cancer research

Fei Zhu, Preecha Patumcharoenpol, Cheng Zhang, Yang Yang, Jonathan Chan, Asawin Meechai, Wanwipa Vongsangnak, Bairong Shen
2013 Journal of Biomedical Informatics  
We then discuss the current state-of-the-art text mining applications in cancer research and we also provide some resources for cancer text mining.  ...  Biomedical text mining on cancer research is computationally automatic and high-throughput in nature. However, it is error-prone due to the complexity of natural language processing.  ...  Text mining can help us to mine information and knowledge from a mountain of text and it is now widely applied in biomedical research.  ... 
doi:10.1016/j.jbi.2012.10.007 pmid:23159498 fatcat:xd7j77sbwfhklkat6tael64lbq

Application of Biomedical Text Mining [chapter]

Lejun Gong
2018 Artificial Intelligence - Emerging Trends and Applications  
Then, it describes the biomedical text-mining technology, namely natural language processing, including the several components.  ...  This chapter emphasizes the two aspects in biomedical text mining involving static biomedical information recognization and dynamic biomedical information extraction using instance analysis from our previous  ...  Application of Biomedical Text Mining http://dx.doi.org/10.5772/intechopen.75924 biomedical text mining.  ... 
doi:10.5772/intechopen.75924 fatcat:5o27ptssi5fwzbelnpktkwplby

A Review of Towered Big-Data Service Model for Biomedical Text-Mining Databases

Alshreef Abed, Jingling Yuan, Lin Li
2017 International Journal of Advanced Computer Science and Applications  
Text mining can help us mine information and knowledge from a mountain of text, and is now widely applied in biomedical research.  ...  The applications of text mining are diverse and span to multiple disciplines, ranging from biomedicine to legal, business intelligence and security.  ...  Tan and Lambri [52] suggested a framework for the purpose of selecting a suitable ontology for a specific application for biomedical text mining.  ... 
doi:10.14569/ijacsa.2017.080804 fatcat:juylimcz4jdbhmifhrz6so7ciq

Efficient Retrieval of Text for Biomedical Domain using Data Mining Algorithm

Sumit Vashishta, Dr. Yogendra
2011 International Journal of Advanced Computer Science and Applications  
Biomedical text retrieval refers to text retrieval techniques applied to biomedical resources and literature available of the biomedical and molecular biology domain.  ...  This paper presents a technique for using soft clustering data mining algorithm to increase the accuracy of biomedical text extraction.  ...  ACKNOWLEDGMENT This research is supported by the Computer Science and Engineering department, SATI, Vidhisha.  ... 
doi:10.14569/ijacsa.2011.020412 fatcat:cot7somuffdnbikefppbi2aisq

Adaptation of MelanomaMine and LiMTox to the analysis of paediatric cancers and application to biomedical publications on paediatric cancers

Davide Cirillo, Matteo Manica, Salvador Capella-Gutierrez, Alfonso Valencia, Martin Krallinger, Javier Omar Corvi, José María Fernández, Alejandro Canosa, Elena De La Calle, Joao Pita Costa, Jolanda Modic
2021 Zenodo  
The deliverable reports on the implementation of the iPC text mining workflow and three use cases for extracting biomedical information from large volumes.  ...  The workflow builds on the general framework of two text mining tools, LimTox and MelanomaMine.  ...  MelanomaMine is a text mining application and database dedicated to the processing of melanoma related biomedical literature and knowledge resources.  ... 
doi:10.5281/zenodo.6546342 fatcat:ro3eopiyqbebrpfuk6cxuzujdq

TEXT AND DATA MINING FOR BIOMEDICAL DISCOVERY

GRACIELA GONZALEZ, KEVIN BRETONNEL COHEN, CASEY S. GREENE, UDO HAHN, MARICEL G. KANN, ROBERT LEAMAN, NIGAM SHAH, JIEPING YE
2012 Biocomputing 2013  
The biggest challenge for text and data mining is to truly impact the biomedical discovery process, enabling scientists to generate novel hypothesis to address the most crucial questions.  ...  Among a number of worthy submissions, we have selected six papers that exemplify advances in text and data mining methods that have a demonstrated impact on a wide range of applications.  ...  automatically extending it using text mining.  ... 
doi:10.1142/9789814447973_0036 fatcat:f522y2grifc6xeh7hs245doscy

Overview of the Ninth Annual Meeting of the BioLINK SIG at ISMB: Linking Literature, Information and Knowledge for Biology [chapter]

Christian Blaschke, Lynette Hirschman, Hagit Shatkay, Alfonso Valencia
2010 Lecture Notes in Computer Science  
from biomedical text.  ...  The broad area of biomedical text mining is concerned with using methods from natural language processing, information extraction, information retrieval and summarization to automate knowledge discovery  ...  These meetings focus on the development and the application of resources and tools for biomedical text mining.  ... 
doi:10.1007/978-3-642-13131-8_1 fatcat:42nm5vxcdnafjkogcz4wcoasoa

A Review of Recent Advancement in Integrating Omics Data with Literature Mining towards Biomedical Discoveries

Kalpana Raja, Matthew Patrick, Yilin Gao, Desmond Madu, Yuyang Yang, Lam C. Tsoi
2017 International Journal of Genomics  
In this review paper, we discuss the recent advancement in approaches that integrate results from omics data and information generated from text mining approaches to uncover novel biomedical information  ...  Text mining (also known as literature mining) is one of the commonly used approaches for automated generation of biological knowledge from the huge number of published articles.  ...  The authors acknowledge the support from the Undergraduate Research Opportunity Program (UROP) from the University of Michigan, the Dermatology Foundation, the Arthritis National Research Foundation, and  ... 
doi:10.1155/2017/6213474 pmid:28331849 pmcid:PMC5346376 fatcat:7yhwtsgyqndabcrhpx7uxsx7da

Text and data mining for biomedical discovery

Graciela Gonzalez, Kevin Bretonnel Cohen, Casey S Greene, Udo Hahn, Maricel G Kann, Robert Leaman, Nigam Shah, Jieping Ye
2013 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
Among a number of worthy submissions, we have selected six papers that exemplify advances in text and data mining methods that have a demonstrated impact on a wide range of applications.  ...  The biggest challenge for text and data mining is to truly impact the biomedical discovery process, enabling scientists to generate novel hypothesis to address the most crucial questions.  ...  automatically extending it using text mining.  ... 
pmid:23424141 pmcid:PMC6230431 fatcat:3on3xcf3wvgsfm66e4xns4ycdy

Highlights of the BioTM 2010 workshop on advances in bio text mining

Thomas Abeel, Sofie Van Landeghem, Roser Morante, Vincent Van Asch, Yves Van de Peer, Walter Daelemans, Yvan Saeys
2010 BMC Bioinformatics  
It featured a tutorial aimed towards a broad audience of (computational) biologists, (computational) linguists and researchers working purely on text mining.  ...  This meeting report gives an overview of the keynote lectures, the panel discussion and a selection of the contributed presentations. The workshop was held in Gent, Belgium on May 10-11.  ...  and its Applications" and "Computational Linguistics in Flanders".  ... 
doi:10.1186/1471-2105-11-s5-i1 pmcid:PMC2956387 fatcat:uxijwmf4djerjcoh5hg72s6i4m

Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges

Ayush Singhal, Robert Leaman, Natalie Catlett, Thomas Lemberger, Johanna McEntyre, Shawn Polson, Ioannis Xenarios, Cecilia Arighi, Zhiyong Lu
2016 Database: The Journal of Biological Databases and Curation  
Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges.  ...  Abstract Text mining in the biomedical sciences is rapidly transitioning from small-scale evaluation to large-scale application.  ...  Finally, we summarize the opportunities for text mining in such applications and the multiple challenges that hamper its immediate adoption in these applications.  ... 
doi:10.1093/database/baw161 pmid:28025348 pmcid:PMC5199160 fatcat:q22gw7owfjejznsrom3c4xnlem

TRANSLATING BIOLOGY: TEXT MINING TOOLS THAT WORK

K Bretonnel Cohen, Hong Yu, Philip E Bourne, Lynette Hirschman
2008 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
• How usable are biomedical text mining applications?  ...  • How robust and reliable are biomedical text mining applications? What are the best ways to assess robustness and reliability?  ... 
pmid:20827444 pmcid:PMC2934913 fatcat:pnqyyxcrs5fgnn4gourjbebwri

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  ...  of offering high quality biological and biomedical text mining services.  ... 
doi:10.1109/sutc.2008.86 dblp:conf/sutc/DaiHLCTH08 fatcat:rro4q63izfesvo7q3mfzhxelwu

A COMPARATIVE APPROACH OFTEXT MINING: CLASSIFICATION, CLUSTERING ANDEXTRACTION TECHNIQUES

Surya Bhupal Rao
2020 JOURNAL OF MECHANICS OF CONTINUA AND MATHEMATICAL SCIENCES  
We also explain briefly text mining in the fields of biomedicine and health care.  ...  In this paper, we discuss several of the most basic tasks and techniques of text mining, including pre-processing, classification, and clustering.  ...  Biomedical Text Mining Biomedical text mining refers to text mining activities in the fields of biomedical sciences.  ... 
doi:10.26782/jmcms.spl.5/2020.01.00010 fatcat:r7wxb3eyrrd75bownfhzosqzci
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