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Mining biomarker information in biomedical literature

Erfan Younesi, Luca Toldo, Bernd Müller, Christoph M Friedrich, Natalia Novac, Alexander Scheer, Martin Hofmann-Apitius, Juliane Fluck
2012 BMC Medical Informatics and Decision Making  
In spite of significant advancements in text-and data-mining techniques, the vast knowledge space of biomarkers in biomedical text has remained unexplored.  ...  The evaluation results suggest that this approach enables the automated identification of biomarker information in the literature.  ...  We would like to acknowledge Heinz Theodor Mevissen from Fraunhofer SCAI for ProMiner support, BIOBASE KL for disclosure of details in the article, and Dr.  ... 
doi:10.1186/1472-6947-12-148 pmid:23249606 pmcid:PMC3541249 fatcat:vq3q24g77ve4lhshmviescm7yq

Mining disease associated biomarker networks from PubMed

Zhong Huang
2013 2013 7th International Conference on Systems Biology (ISB)  
We constructed list of human diseases that are most frequently associated with biomarker in literatures by text mining.  ...  With exponential growing of biomedical knowledge deposited in PubMed database, it is now an essential step to mine PubMed for biomarker-disease associations to support the laboratory research and clinical  ...  CONCLUSION In this paper we introduced a context sensitive semantic based information retrieval method to mine disease associated gene biomarker candidates from literature database, as the first step towards  ... 
doi:10.1109/isb.2013.6623786 fatcat:ayjdkiiplve7flgwezljr6aoji

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

A Knowledge-Driven Approach to Extract Disease-Related Biomarkers from the Literature

À. Bravo, M. Cases, N. Queralt-Rosinach, F. Sanz, L. I. Furlong
2014 BioMed Research International  
The biomedical literature represents a rich source of biomarker information.  ...  Text mining approaches have proven to be useful for the exploitation of information contained in the scientific publications.  ...  Amaurosis). 3. 1 . 1 Distribution of Biomarker Information in the Biomedical Literature.  ... 
doi:10.1155/2014/253128 pmid:24839601 pmcid:PMC4009255 fatcat:ez4ocefubncmdofy5erjwas3re

Intelligent Agent System for Bio-medical Literature Mining

Md. Tawhidul Islam, Durgaprasad Bollina, Abhaya Nayak, Shoba Ranganathan
2007 2007 International Conference on Information and Communication Technology  
In Biomarker discovery efforts.  ...  Extraction of scientific information in Over the past few decades there has been remarkbiomedical articles is a central task for supporting able growth in the amount of biomedical data.  ...  Introduction growth of literature in PubMed for "biomarker".  ... 
doi:10.1109/icict.2007.375342 fatcat:otnpjm5k7rc2ngd5sncz6ao6ka

Biomedical Hypothesis Generation by Text Mining and Gene Prioritization

Ingrid Petric, Balazs Ligeti, Balazs Gyorffy, Sandor Pongor
2013 Protein Peptide Letters  
Text mining methods can facilitate the generation of biomedical hypotheses by suggesting novel associations between diseases and genes.  ...  Inform. 42(2): 219-227, 2009) in which hypotheses are formulated on the basis of terms rarely associated with a target domain.  ...  This body of information is constantly broadening in scope, which presents a challenge to text mining researchers seeking to extract information for life scientists [1] .  ... 
doi:10.2174/09298665113209990063 pmid:23855662 fatcat:5dzox2ihgfdxnaalnn3w3txf4e

Text Mining in Biomedical Domain with Emphasis on Document Clustering

Vinaitheerthan Renganathan
2017 Healthcare Informatics Research  
by mining the biomedical literature to reposition drugs.  ...  Biomarkers Text mining techniques are useful for identifying diseaserelated biomarkers and associated genes from the literature [12] .  ... 
doi:10.4258/hir.2017.23.3.141 pmid:28875048 pmcid:PMC5572517 fatcat:ckhjh2i4hbbfhjd2qs6eriibre

BIONDA: A free database for a fast information on published biomarkers

Michael Turewicz, Anika Frericks-Zipper, Markus Stepath, Karin Schork, Spoorti Ramesh, Katrin Marcus, Martin Eisenacher
2021 Bioinformatics Advances  
relevant information from biomedical texts and provide it as structured information to researchers in a user-friendly way.  ...  Summary Because of the steadily increasing and already manually unmanageable total number of biomarker-related articles in biomedical research, there is a need for intelligent systems that extract all  ...  Information acquisition via text mining is performed as follows: (1) Information retrieval: In text mining, information retrieval deals with obtaining or fetching the relevant information from a larger  ... 
doi:10.1093/bioadv/vbab015 fatcat:agx5kgfe4nb5jhsflvxj5m6lpi

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  
Rapid growth of disease related biomedical literature makes the traditional information retrieval techniques insufficient to fulfill searchers' information needs.  ...  In their work entitled "Supervised Learning Based Hypothesis Generation from Biomedical Literature," S.  ...  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

Completing the Metabolome

Peter L. Elkin
2012 Journal of Postgenomics: Drug & Biomarker Development  
With the advent of high performance computing and advances in Ontology and data mining we are now able to ask questions of large datasets such as the biomedical literature.  ...  There are approximately 6,000 articles published every month in the biomedical literature. There are >19,000,000 citations in MedLine Figure 1 : 1 KEGG map of Metabolic Pathways.  ... 
doi:10.4172/2153-0769.1000e115 fatcat:kp6ut4bbxvfxhfwecap7hvjkqi

Automated extraction of potential migraine biomarkers using a semantic graph

Wytze J. Vlietstra, Ronald Zielman, Robin M. van Dongen, Erik A. Schultes, Floris Wiesman, Rein Vos, Erik M. van Mulligen, Jan A. Kors
2017 Journal of Biomedical Informatics  
Problem: Biomedical literature and databases contain important clues for the identification of potential disease biomarkers.  ...  Discussion: Semantic knowledge graphs composed of information integrated from multiple and varying sources can assist researchers in identifying potential disease biomarkers.  ...  For biomedical literature, the most important knowledge reservoir, potential biomarkers could be extracted with several literature mining techniques such as: (a) co-occurrences, where non-specific cooccurrences  ... 
doi:10.1016/j.jbi.2017.05.018 pmid:28579531 fatcat:xs6gqcgsindhdebmq2ttxrzo7q

Detection Of Cancer Biomarker

M. Bagyarani, A. Kunthavai, V. Vidhyashree, A. Sumathi, C. Kalaivani
2017 Zenodo  
Biomarker the indicator of disease plays a vital role in diagnosing of the presence of disease. The presence of cancer disease can be detected using the measurable indicator called cancer biomarker.  ...  New methods or techniques are necessary to extract useful information from the raw data collected in repositories.  ...  Biomedical Text Analysis: Extracting useful health information from warehouse underlies numerous advances in the biomedical research called biomedical text mining.  ... 
doi:10.5281/zenodo.574593 fatcat:m5x4m4n2hjhxvbsa2lhpiu5b2i

Text Mining for Building Biomedical Networks Using Cancer as a Case Study

Sofia I. R. Conceição, Francisco M. Couto
2021 Biomolecules  
This review will focus on different approaches of automatic information extraction from biomedical text that can be used to enhance existing networks or create new ones, such as deep learning state-of-the-art  ...  One of the most important tasks in text mining for biological network building is relation extraction, which identifies relations between the entities of interest.  ...  This is one of the most challenging tasks of text mining in biomedical literature due to the complexity that may be found in the sentences, and, in recent years, numerous efforts went into optimizing this  ... 
doi:10.3390/biom11101430 pmid:34680062 pmcid:PMC8533101 fatcat:pfoi74nq5fewrgg3mchguwlbsa

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.  ...  Finally, we explain the recent methods to integrate omics and biomedical literature mining data in order to uncover novel biomedical information.  ... 
doi:10.1155/2017/6213474 pmid:28331849 pmcid:PMC5346376 fatcat:7yhwtsgyqndabcrhpx7uxsx7da

Scientific Discovery by Machine Intelligence: A New Avenue for Drug Research [article]

Carlo A. Trugenberger
2015 arXiv   pre-print
text mine large repositories of biomedical research papers, a technique pioneered by Merck with the InfoCodex software.  ...  The ultimate goal of semantic artificial intelligence is to devise software that can understand the meaning of free text, at least in the practical sense of providing new, actionable information condensed  ...  The present paper is about machine knowledge discovery in the biomedical and pharmacogenomics literature.  ... 
arXiv:1506.07116v1 fatcat:ciuab5j5xbhknpdplkkg7cji7e
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