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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.  ...  Another approach [88] combines text mining data with microarray data for discovering disease-gene association by using unsupervised clustering.  ... 
doi:10.1155/2017/6213474 pmid:28331849 pmcid:PMC5346376 fatcat:7yhwtsgyqndabcrhpx7uxsx7da

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 is a way to aid researchers in coping with information overload.  ...  Data mining is seen as an increasingly important tool by modern business to transform data into business intelligence giving an informational advantage.  ...  ACKNOWLEDGMENT This research is supported by the Computer Science and Engineering department, SATI, Vidhisha.  ... 
doi:10.14569/ijacsa.2011.020412 fatcat:cot7somuffdnbikefppbi2aisq

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.  ...  In this survey paper, the researcher identifies and discusses biomedical data (text) mining issues, and recommends a possible technique to cope with possible future growth.  ...  Section III discussed the previous study which is related to text mining, biomedical text mining, biomedical data with feature extraction approach and biomedical data mapping technique.  ... 
doi:10.14569/ijacsa.2017.080804 fatcat:juylimcz4jdbhmifhrz6so7ciq

Mining biomedical images towards valuable information retrieval in biomedical and life sciences

Zeeshan Ahmed, Saman Zeeshan, Thomas Dandekar
2016 Database: The Journal of Biological Databases and Curation  
and analysis of text and content in biomedical images to take advantage in implementing effective information retrieval systems.  ...  In this review, we summarize technologies related to data mining of figures.  ...  as a stable web-based search engine for retrieving the biomedical information by extracting the text from published biomedical literature at PMC (48) .  ... 
doi:10.1093/database/baw118 pmid:27538578 pmcid:PMC4990152 fatcat:dlyhrh5nxjhutlvvw2qkgx3wei

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 Supporting Search for Knowledge Discovery in Diabetes

Sophia Ananiadou, Tomoko Ohta, Martin K. Rutter
2012 Current Cardiovascular Risk Reports  
Text mining methods can support information access for diverse groups such as researchers, clinicians, caregivers, patients and also members of the general public.  ...  Due to increasing specialization, silo effects and literature deluge, researchers are struggling to draw out general truths and to generate testable hypotheses.  ...  Given the rapid growth of the literature, there is an urgent need for text mining tools that improve the accuracy and specificity of information retrieval and at the same time avoid data overload for users  ... 
doi:10.1007/s12170-012-0288-3 fatcat:4hhb4akdgrakbc4sfgmr3f3tcu

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).  ...  This paper presented the recent research trends, survey, reviews, experiments, and concepts in information retrieval applied to text, images and object features in big data genomic research.  ...  Overview of Information Retrieval in Biomedical and Genome Research Information Retrieval (IR) in biomedical and genomic research deals with the text retrieval from many of the published literature in  ... 
doi:10.35940/ijitee.i1109.0789s219 fatcat:j2uramagd5a75jusrcor75w7ue

Text Mining for Translational Bioinformatics

Hong-Jie Dai, Chih-Hsuan Wei, Hung-Yu Kao, Rey-Long Liu, Richard Tzong-Han Tsai, Zhiyong Lu
2015 BioMed Research International  
Wu et al. developed an approach which is able to automatically retrieve disease related knowledge in a summarized form from the large volume of online biomedical literature.  ...  Rapid growth of disease related biomedical literature makes the traditional information retrieval techniques insufficient to fulfill searchers' information needs.  ...  Acknowledgments We would like to express our appreciation to all of the authors for their contributions and the reviewers for their support and constructive critiques in accomplishing this special issue  ... 
doi:10.1155/2015/368264 pmid:26380272 pmcid:PMC4563058 fatcat:mshc5klqsrb2vd7ik7jcauazey

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  
In this review, we introduce the basic concepts underlying text mining and examine some frequently used algorithms, tools, and data sets, as well as assessing how much these algorithms have been utilized  ...  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.  ...  Data sets and tools for biomedical text mining In terms of information retrieval systems, PubMed [64, 65] is one of the best known biomedical databases and it contains more than 20 million citations  ... 
doi:10.1016/j.jbi.2012.10.007 pmid:23159498 fatcat:xd7j77sbwfhklkat6tael64lbq

Target discovery from data mining approaches

Yongliang Yang, S. James Adelstein, Amin I. Kassis
2012 Drug Discovery Today  
Iyer for their helpful discussions in this project.  ...  In pace with the growth of biological databases, the flourishing of bioinformatics, especially data mining approaches, to extract or filter valuable targets by combining biological ideas with computer  ...  Text mining Overview of text mining Text mining (TM) can be defined as the computational discovery of new, previously unknown information, by automatically extracting information from different written  ... 
doi:10.1016/j.drudis.2011.12.006 pmid:22178890 fatcat:c7k3puzntbhcrmzjlw6uvgxhny

Target discovery from data mining approaches

Yongliang Yang, S. James Adelstein, Amin I. Kassis
2009 Drug Discovery Today  
Iyer for their helpful discussions in this project.  ...  In pace with the growth of biological databases, the flourishing of bioinformatics, especially data mining approaches, to extract or filter valuable targets by combining biological ideas with computer  ...  Text mining Overview of text mining Text mining (TM) can be defined as the computational discovery of new, previously unknown information, by automatically extracting information from different written  ... 
doi:10.1016/j.drudis.2008.12.005 pmid:19135549 fatcat:plsts2psuvclneuhgd5tlianwi

Combining literature text mining with microarray data: advances for system biology modeling

A. Faro, D. Giordano, C. Spampinato
2011 Briefings in Bioinformatics  
Under this scenario, this article reviews the knowledge discovery systems that fuse information from the literature, gathered by text mining, with microarray data for enriching the lists of down and upregulated  ...  Finally, an easy to use and freely accessible tool, GeneWizard, that exploits text mining and microarray data fusion for supporting researchers in discovering gene^disease relationships is described.  ...  Under this scenario, a first aim of this article is reviewing the knowledge discovery systems that integrate literature information, gathered by text mining, with microarray data.  ... 
doi:10.1093/bib/bbr018 pmid:21677032 fatcat:lvtg7ea74ngb5h6i2ywss6cjru

MBlab: Molecular Biodiversity Laboratory [chapter]

Corrado Loglisci, Annalisa Appice, Michelangelo Ceci, Donato Malerba, Floriana Esposito
2011 Communications in Computer and Information Science  
These integrate sophisticated technologies and innovative approaches of Information Extraction, Data Mining and Machine Learning to perform descriptive tasks of knowledge discovery from biomedical repositories  ...  Technologies in available biomedical repositories do not yet provide adequate mechanisms to support the understanding and analysis of the stored content.  ...  This work is in partial fulfillment of the research objectives of the project MBlab DM19410 "Molecular Biodiversity Laboratory".  ... 
doi:10.1007/978-3-642-27302-5_18 fatcat:semakj3pm5d3xbn43rc672crti

Exploring Molecular Mechanisms Within Biomedical Literature [chapter]

Nicole Glendinning, Christopher Hawthorne, Stephanie Beck, Guillermo Lopez-Campos
2022 Studies in Health Technology and Informatics  
Text mining of the biomedical literature enables vast quantities of information to be extracted and summarised.  ...  Here we describe an updated and improved version of previous methodology for the analysis of gene and protein biomarkers that enables the use of the newer Pubtator Central annotations, based in full text  ...  Biomedical text mining is an incredibly valuable research technique because of its use in deciphering important information and concepts from large amounts of scientific literature.  ... 
doi:10.3233/shti220284 pmid:35673222 fatcat:kx64htcql5gypd3hdr4rrsptvq

Text-mining approaches in molecular biology and biomedicine

M KRALLINGER, R ERHARDT, A VALENCIA
2005 Drug Discovery Today  
To extract relevant information using automatic techniques, text-mining and information-extraction approaches have been developed.  ...  These technologies have a key role in integrating biomedical information through analysis of scientific literature.  ...  Text-mining approaches involve analyzing and extracting information from large collections of free textual data by using automatic or semiautomatic systems.  ... 
doi:10.1016/s1359-6446(05)03376-3 pmid:15808823 fatcat:w5i3ciuq4zhk7oq4kbbv5wqfma
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