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The next generation of literature analysis: Integration of genomic analysis into text mining

M. Scherf, A. Epple, T. Werner
2005 Briefings in Bioinformatics  
The subsequent sections will illustrate how the principle of data integration in text-mining systems can be extended to genome analysis.  ...  The next section starts with a brief overview of the different tasks and challenges in text mining of biomedical literature.  ... 
doi:10.1093/bib/6.3.287 pmid:16212776 fatcat:bccqazrfmfez5evzv4xbg34kou

Translational web robots for pathogen genome analysis

Vitali Sintchenko, Enrico W Coiera
2011 Microbial Informatics and Experimentation  
The integration of data acquisition from online databases with information retrieval from literature text mining is an important step forward.  ...  Other services include online platforms for comparative genomic analysis of multiple sequences obtained from metagenomic experiments using the 'next generation sequencing platforms' (e.g., CompostBin  ... 
doi:10.1186/2042-5783-1-10 pmid:22587672 pmcid:PMC3372293 fatcat:cdjbw27rv5bjrkxrxvaz5isupe

Integrating Open Data on Cancer in Support to Tumor Growth Analysis [chapter]

Fleur Jeanquartier, Claire Jean-Quartier, Tobias Schreck, David Cemernek, Andreas Holzinger
2016 Lecture Notes in Computer Science  
Furthermore, we describe the integration possibilities into a simulation tool on tumor growth that incorporates the tumor's kinetics.  ...  The general disease group of malignant neoplasms depicts one of the leading and increasing causes for death.  ...  Text mining for literature curation is common for omics data [25] .  ... 
doi:10.1007/978-3-319-43949-5_4 fatcat:6r2lnyiturex7jpdnfdwyaeeee

Knowledge-Based Bioinformatics - From analysis to interpretation. * Edited by Gil Alterovitz and Marco Ramoni

S. Kim
2010 Briefings in Bioinformatics  
requirements for the next-generation KDD.  ...  In addition, the following problems related to the impact of next-generation sequencing (NGS) on genome annotation are discussed: alignment of sequences between multispecies genomes, web-based community  ... 
doi:10.1093/bib/bbq070 fatcat:af44dwyq2ndqrem5rmqwf6eh2y

Applying Lexical Link Analysis to Discover Insights from Public Information on COVID-19 [article]

Ying Zhao, Charles C Zhou
2020 bioRxiv   pre-print
The Next Strain consists of a database of SARS-CoV-2 viral genomes from since 12/3/2019.  ...  We first text-mined the CORD-19. We also data-mined the next strain database. Finally, we linked two databases.  ...  , integrate text and data mining into a single platform to discover the insights that can be visualized, and validated to answer the high-priority questions of genetics, incubation, treatment, symptoms  ... 
doi:10.1101/2020.05.06.079798 fatcat:bck43mcmkrgdneks7gipvnk2hi

What's Hot and What's Not? - Exploring Trends in Bioinformatics Literature Using Topic Modeling and Keyword Analysis [chapter]

Alexander Hahn, Somya D. Mohanty, Prashanti Manda
2017 Lecture Notes in Computer Science  
We found that "big-data", "next generation sequencing", and "cancer" all experienced exponential increase in popularity over the years.  ...  While this approach has been applied on literature in other scientific areas, there has been no formal analysis of bioinformatics literature.  ...  The purple cluster is related to next generation sequencing, gene expression analyses, genomics, transcriptome, and genetics.  ... 
doi:10.1007/978-3-319-59575-7_25 fatcat:j4k5bw3yovfrpivs66klmplfje

Annotating Protein Function through Lexical Analysis

Rajesh Nair, Burkhard Rost
2004 The AI Magazine  
information from different ways (for general discussion, see the literature.  ...  Resources for Text Analysis.  ... 
doi:10.1609/aimag.v25i1.1746 dblp:journals/aim/NairR04 fatcat:eoinvyqphjg4zmk2jvyoiukpfa

Trends in Fetal Medicine: A 10-Year Bibliometric Analysis of Prenatal Diagnosis

Ferdinand Dhombres, Olivier Bodenreider
2017 Studies in Health Technology and Informatics  
The most recent of these terms reflect the new opportunities of next-generation sequencing. Many terms related to cytogenetics exhibit a falling trend.  ...  The objective is to automatically identify trends in Fetal Medicine over the past 10 years through a bibliometric analysis of articles published in Prenatal Diagnosis, using text mining techniques.  ...  More generally, terms denoting new genetic methods (e.g., "next generation sequencing", "whole genome sequencing", "single nucleotide polymorphism" or "microarray analysis") are on the rise.  ... 
pmid:29295220 pmcid:PMC5884683 fatcat:zlxe5gbwm5bwdpwaq6f4ycbndi

Enhancing data integration with text analysis to find proteins implicated in plant stress response

Keywan Hassani-Pak, Roxane Legaie, Catherine Canevet, Hugo A van den Berg, Jonathan D Moore, Christopher J Rawlings
2010 Journal of Integrative Bioinformatics  
In conclusion, we show that the additional text mining features are able to highlight proteins using the scientific literature that would not have been seen using data integration alone.  ...  High throughput genomic studies can identify large numbers of potential candidate genes, which must be interpreted and filtered by investigators to select the best ones for further analysis.  ...  Acknowledgements The authors gratefully acknowledge their thanks to the Ondex team for developing the data integration framework and to the PRESTA team for sharing their time and data.  ... 
doi:10.2390/biecoll-jib-2010-121 pmid:20375451 fatcat:ezu4oifqmvezng3oi6wgm7szwu

Enhancing Data Integration with Text Analysis to Find Proteins Implicated in Plant Stress Response

Keywan Hassani-Pak, Roxane Legaie, Catherine Canevet, Hugo A. van den Berg, Jonathan D. Moore, Christopher J. Rawlings
2010 Journal of Integrative Bioinformatics  
In conclusion, we show that the additional text mining features are able to highlight proteins using the scientific literature that would not have been seen using data integration alone.  ...  SummaryHigh throughput genomic studies can identify large numbers of potential candidate genes, which must be interpreted and filtered by investigators to select the best ones for further analysis.  ...  Acknowledgements The authors gratefully acknowledge their thanks to the Ondex team for developing the data integration framework and to the PRESTA team for sharing their time and data.  ... 
doi:10.1515/jib-2010-121 fatcat:hlzcj4e3rfhl3prentnzs2m7ka

Data Mining Based Collaborative Analysis of Microarray Data

G. Tsiliki, S. Kossida, N. Friesen, S. Rueping, M. Tzagarakis, N. Karacapilidis
2012 2012 IEEE 24th International Conference on Tools with Artificial Intelligence  
set up new iterations of the data mining algorithm by defining other descriptive attributes or integrating other relevant data.  ...  We present an application of a data-mining algorithm to gene-expression data in a collaborative decision-making support environment, as a typical example of how multidisciplinary researchers can collaborate  ...  This publication reflects only the authors views and the Community is not liable for any use that may be made of the information contained therein.  ... 
doi:10.1109/ictai.2012.97 dblp:conf/ictai/TsilikiKFRTK12 fatcat:fznfaap7irf2dod4eu4lbvnpua

BioPubMiner: Machine Learning Component-Based Biomedical Information Analysis Platform [chapter]

Jae-Hong Eom, Byoung-Tak Zhang
2004 Lecture Notes in Computer Science  
literature.  ...  The evaluation of inference proceeded using the protein interaction data of S.cerevisiae (bakers yeast) from MIPS and SGD.  ...  Acknowledgements This research was supported by the Korean Ministry of Science and Technology under the NRL Program and the Systems Biology Program.  ... 
doi:10.1007/978-3-540-30561-3_2 fatcat:bfcztxddrjb6xlisdb5zqhrk7q

Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis

Guocai Chen, Juan Camilo Ramírez, Nan Deng, Xing Qiu, Canglin Wu, W Jim Zheng, Hulin Wu
2019 Database: The Journal of Biological Databases and Curation  
Gene Expression Omnibus (GEO) and other publicly available data store their metadata in the format of unstructured English text, which is very difficult for automated reuse.  ...  Conflict of interest: None declared.  ...  Funding National Institute of Health (7R01AI087135 to H.W.), Cancer Prevention and Research Institute of Texas (RP170668 to W.J.Z.) and National Institute of Health (HHSN272201700019C to C.W.).  ... 
doi:10.1093/database/bay145 pmid:30649296 pmcid:PMC6333964 fatcat:p27cu7utwzdsjcjdaijkscpvu4

Topic Evolution Analysis for Omics Data Integration in Cancers

Li Ning, He Huixin
2021 Frontiers in Cell and Developmental Biology  
Omics data integration plays a crucial role in the mining of biomarkers in the human condition.  ...  The topic extraction results indicate that, with the rapid development of omics data integration research, multi-omics analysis (Topic 11) and genomics of colorectal cancer (Topic 10) have more studies  ...  Despite the rapid development of omics data integration toward mining biomarkers in the academic medical world, few studies explored statistical relationships between literature text terms and their time-series  ... 
doi:10.3389/fcell.2021.631011 pmid:33898421 pmcid:PMC8058380 fatcat:inytqh6ywfarjh2neryg7jpu5m

Graph-based analysis and visualization of experimental results with ONDEX

J. Kohler, J. Baumbach, J. Taubert, M. Specht, A. Skusa, A. Ruegg, C. Rawlings, P. Verrier, S. Philippi
2006 Bioinformatics  
ONDEX is a database system that combines the features of semantic database integration and text mining with methods for graph-based analysis.  ...  The challenge is to bring these genes together with biological information distributed across hundreds of databases or buried in the scientific literature (millions of articles).  ...  Rothamsted Research Graph analysis of experimental results with ONDEX  ... 
doi:10.1093/bioinformatics/btl081 pmid:16533819 fatcat:u36k6sbn2nbqzm3rbaw4h34iqm
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