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Elementary approach towards Biological Data Mining

Faiz Hashmi
2017 International Journal of Trend in Scientific Research and Development  
towards solving these challenges: with the goal of supporting human intelligence with machine intelligence.  ...  The application of data mining in the domain of bioinformatics is explained. It also highlights some of the current challenges and opportunities of data mining in bioinformatics.  ...  A tool for analyzing gene expression is microarray.  ... 
doi:10.31142/ijtsrd7198 fatcat:7q7uw6csazc4dolpaz5zenb574

Text Mining in Cancer Gene and Pathway Prioritization

Yuan Luo, Gregory Riedlinger, Peter Szolovits
2014 Cancer Informatics  
This review places existing gene prioritization tools against the backdrop of an integrative Omic hierarchy view toward cancer and focuses on the analysis of their text mining components.  ...  A multitude of gene prioritization tools have been developed, each integrating different data sources covering gene sequences, differential expressions, function annotations, gene regulations, protein  ...  PSZ contributed to the analysis and categorization of text mining methods in gene and pathway prioritization. All authors reviewed and approved of the final manuscript.  ... 
doi:10.4137/cin.s13874 pmid:25392685 pmcid:PMC4216063 fatcat:mtk6jnyvxjbntedeioojlmrq3u

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  
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 managing, storing, and analyzing of this big data have been a great challenge for the researchers, especially when moving towards the goal of generating testable data-driven hypotheses, which has been  ...  A similar approach [87] attempts to support manual curation of links between biological databases such as Gene Expression Omnibus (GEO) and PubMed database.  ... 
doi:10.1155/2017/6213474 pmid:28331849 pmcid:PMC5346376 fatcat:7yhwtsgyqndabcrhpx7uxsx7da

Target discovery from data mining approaches

Yongliang Yang, S. James Adelstein, Amin I. Kassis
2009 Drug Discovery Today  
For instance, Kim et al. [30] have reported the mining of public gene expression data from the CGAP database and GEO database (Box 1) to identify candidate markers for lung cancer.  ...  In the postgenomic era, the explosion of gene expression data requires timely data storage and update of gene databases.  ... 
doi:10.1016/j.drudis.2008.12.005 pmid:19135549 fatcat:plsts2psuvclneuhgd5tlianwi

Target discovery from data mining approaches

Yongliang Yang, S. James Adelstein, Amin I. Kassis
2012 Drug Discovery Today  
For instance, Kim et al. [30] have reported the mining of public gene expression data from the CGAP database and GEO database (Box 1) to identify candidate markers for lung cancer.  ...  In the postgenomic era, the explosion of gene expression data requires timely data storage and update of gene databases.  ... 
doi:10.1016/j.drudis.2011.12.006 pmid:22178890 fatcat:c7k3puzntbhcrmzjlw6uvgxhny

Evaluation of database-derived pathway development for enabling biomarker discovery for hepatotoxicity

Dennie GA Hebels, Marlon JA Jetten, Hugo JW Aerts, Ralf Herwig, Daniël HJ Theunissen, Stan Gaj, Joost H van Delft, Jos CS Kleinjans
2014 Biomarkers in Medicine  
Omics databases that collect 'omics data, such as transcriptomic (mRNA, miRNA and high-throughput sequencing), proteomic and metabolomic data, in some occasions with corresponding metadata.  ...  This is a strong indication that text-mining approaches towards database buildingheavily rely on continuous updating and accurate manual curating of found associations in order to be of value for biomarker  ...  proteins that are associated with hepatotoxic conditions; In this paper we analyzed text-mining and 'omics-based databases to review how gene lists derived from text-mining databases compare with human  ... 
doi:10.2217/bmm.13.154 pmid:24521014 fatcat:mkxr7czhjvbibhypzbw4mekxre

Data Mining in the Molecular Biology Era — A Study Directed to Carbohydrates Biosynthesis and Accumulation in Plants [chapter]

Renato Vicentini, Marcelo Menossi
2009 Data Mining and Knowledge Discovery in Real Life Applications  
To simulate our model we mined literature and databases for kinetic data using the SABIO-RK and Kinetikon databases.  ...  In most DNA array studies, gene expressions are measured on a small number of arrays or samples; however, large collections of arrays are available in several databases.  ...  Data Mining in the Molecular Biology Era -A Study Directed to Carbohydrates Biosynthesis and Accumulation in Plants, Data Mining and Knowledge Discovery in Real Life Applications, Julio Ponce and Adem  ... 
doi:10.5772/6456 fatcat:72r6gtyfhjacbbaootuzl2bzee

Data mining and visualisation of microarray gene expression data

Alan Robinson, Alvis Brazma
1999 Nature Genetics  
Currently, the EBI is assessing the suitability of different data mining algorithms to microarray gene expression data, e.g. neural networks, classification trees, market basket analysis, clustering, classification  ...  expression experiments.  ...  Currently, the EBI is assessing the suitability of different data mining algorithms to microarray gene expression data, e.g. neural networks, classification trees, market basket analysis, clustering, classification  ... 
doi:10.1038/14392 fatcat:cplvxkbzajfnfnigilmmlrtc3y

Article Commentary: The Power of the Web in Cancer Drug Discovery and Clinical Trial Design: Research without a Laboratory?

Christine Galustian, Angus G. Dalgleish
2010 Cancer Informatics  
A growing number of papers highlight the use of data mining tools to determine associations between drugs, genes or protein targets, and possible mechanism of actions or therapeutic efficacy which could  ...  Epstein, which illustrates the potential of text mining using Boolean parameters in cancer drug discovery, and other studies which use alternative data mining approaches to aid cancer research.  ...  Acknowledgement Commentary and opinion on "Unblocking Blockbusters: Using Boolean Text-Mining to Optimise Clinical Trial Design and Timeline for Novel Anticancer Drugs" Cancer Informatics 2009 7, 231-8  ... 
doi:10.4137/cin.s3191 pmid:20234771 pmcid:PMC2834378 fatcat:svyarddfcvgmtpqvl5334fpoky

yMGV: a cross-species expression data mining tool

G. Lelandais
2004 Nucleic Acids Research  
data sets published in 82 different articles. yMGV couples data mining tools with a user-friendly web interface so that, with a few mouse clicks, one can identify the conditions that affect the expression  ...  of a gene or list of genes regulated in a set of experiments.  ...  The yeast Microarray Global Viewer (yMGV) is a data mining tool coupled to a multi-organism database that currently houses Saccharomyces cerevisiae and Schizosaccharomyces pombe expression data.  ... 
doi:10.1093/nar/gkh135 pmid:14681424 pmcid:PMC308869 fatcat:akyorkkwnfgpthhel3dprfda54

The Cancer Genome Anatomy Project: new resources for reading the molecular signatures of cancer

Robert L. Strausberg
2001 Journal of Pathology  
These efforts have sought to (a) identify new genes, (b) identify genes that overexpressed in various cancers, and (c) to build microarrays toward the comprehensive study of gene expression patterns in  ...  Examples of successful data mining from the CGAP gene catalog The utility of data mining of the CGAP gene catalog has been reported in several recent communications.  ... 
doi:10.1002/1096-9896(200109)195:1<31::aid-path920>3.0.co;2-w pmid:11568889 fatcat:hw7lzt7nkbf4ncsnn3grusvq5y

Defining the pathogenesis of inflammatory and immune diseases through database mining

Fan Yang
2012 Frontiers in Bioscience (Elite Edition)  
search in a given field is required to initiate a database mining project; 2) Scope: Database mining scope in terms of gene numbers are far more extensive than that examined using experimental methods  ...  We also found that 21 out of the 33 inflammatory genes (64%) are targets of highly expressed microRNAs, while the remaining 12 genes (36%) are targeted by normally expressed microRNAs.  ... 
doi:10.2741/e555 pmid:22652650 fatcat:bdizuvyku5fdlcctz2xmgvu3wu

The Pancreatic Expression Database: 2018 update

Jacek Marzec, Abu Z. Dayem Ullah, Stefano Pirrò, Emanuela Gadaleta, Tatjana Crnogorac-Jurcevic, Nicholas R. Lemoine, Hemant M. Kocher, Claude Chelala
2017 Nucleic Acids Research  
The Pancreatic Expression Database (PED, http:// www.pancreasexpression.org) continues to be a major resource for mining pancreatic -omics data a decade after its initial release.  ...  A new analytical module has been implemented to run in parallel with the existing literature mining functions.  ...  We also thank our colleagues who contributed data for previous versions of the database, especially Professor Stephan A Hahn.  ... 
doi:10.1093/nar/gkx955 pmid:29059374 pmcid:PMC5753364 fatcat:iqpxown4jrf6ho76cydzaemnka

DRASTIC--INSIGHTS: querying information in a plant gene expression database

D. K. Button
2006 Nucleic Acids Research  
DRASTIC is a relational database of plant expressed sequence tags and genes up-or down-regulated in response to various pathogens, chemical exposure or other treatments such as drought, salt and low temperature  ...  The INSIGHTS (INference of cell SIGnaling HypoTheseS) suite of web-based tools allows intelligent data mining and extraction of information from the DRASTIC database.  ...  Some mining tools use AGI numbers where expression data correctly identify a specific member of a gene family.  ... 
doi:10.1093/nar/gkj136 pmid:16381965 pmcid:PMC1347498 fatcat:i3upi7ohefhzzaaza5mnmi4g5q

GeneKeyDB: a lightweight, gene-centric, relational database to support data mining environments

S A Kirov, X Peng, E Baker, D Schmoyer, B Zhang, J Snoddy
2005 BMC Bioinformatics  
Such database should be sufficiently versatile to allow easy system integration. GeneKeyDB is a gene-centered relational database developed to enhance data mining in biological data sets.  ...  The analysis of biological data is greatly enhanced by existing or emerging databases.  ...  Define a set of candidate genes, based on the genome localization and tissue expression pattern [15] 2. Get all genes expressed in a specific tissue that share a conserved protein domain[16].  ... 
doi:10.1186/1471-2105-6-72 pmid:15790402 pmcid:PMC1274265 fatcat:brghnebad5aehivpuomfyhto2u
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