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GeneX: An Open Source gene expression database and integrated tool set

H. Mangalam, J. Stewart, J. Zhou, K. Schlauch, M. Waugh, G. Chen, A. D. Farmer, G. Colello, J. W. Weller
2001 IBM Systems Journal  
The GeneX TM project is intended to provide an Open Source database and integrated tool set that will allow researchers to store and evaluate their gene expression data and, moreover, such evaluation will  ...  Because gene expression profiles are highly sensitive to sample and processing conditions, it is crucial to accurately represent these conditions along with the numeric data in a way that allows the conditions  ...  Acknowledgments We would like to thank our colleagues at NCGR for helpful comments and coding assistance during the development of GeneX, and in particular Peter Hraber, Andrew Tolopko, and David Bulmore  ... 
doi:10.1147/sj.402.0552 fatcat:hgrexrg7hvdsxkfxdwc7a4bgw4

A comparison of microarray databases

M. Gardiner-Garden
2001 Briefings in Bioinformatics  
Developers of microarray gene-expression databases were asked questions regarding the scope and availability of their database, its system requirements, its future compliance with MGED (GeneX NCGR http  ...  They are the source of information in this article (with the exception of AMAD and NOMAD databases where all information was provided by Paul Spellman, and SMD where some information was supplied by Mike  ...  We are grateful to Andrew Hamilton and Matthew Hobbs for helpful discussions.  ... 
doi:10.1093/bib/2.2.143 pmid:11465732 fatcat:f6sux2jvt5bnvmwu2xukuf5bse

Enabling Semantic Queries Across Federated Bioinformatics Databases [article]

Ana Sima, Tarcisio Mendes de Farias, Erich Zbinden, Maria Anisimova, Manuel Gil, Heinz Stockinger, Kurt Stockinger, Marc Robinson-Rechavi, Christophe Dessimoz
2019 biorxiv/medrxiv   pre-print
To enable federated queries across these sources, we first defined a new semantic model for gene expression called GenEx.  ...  We introduce an ontology-based federated approach for data integration.  ...  Supplementary data Supplementary data are available at Database Online.  ... 
doi:10.1101/686600 fatcat:ajkv2fmvzvbxje3kychiolirxm

Tools for managing and analyzing microarray data

A. Koschmieder, K. Zimmermann, S. Trissl, T. Stoltmann, U. Leser
2011 Briefings in Bioinformatics  
The microarray-based analysis of gene expression has become a workhorse for biomedical research.  ...  It reveals which tasks are covered by mature tools and also shows that important requirements, especially in the area of integrated analysis of different experimental data, are not yet met satisfyingly  ...  Acknowledgements We would like to thank all authors of the tools we reviewed for their generous provision of open source software and documentation.  ... 
doi:10.1093/bib/bbr010 pmid:21422065 fatcat:3dlnv3hlwbdr3p63aksmpy2iuq

Enabling semantic queries across federated bioinformatics databases

2019 Database: The Journal of Biological Databases and Curation  
However, the heterogeneity of the different data sources, both at the syntactic and the semantic level, still poses significant challenges for achieving interoperability among biological databases.  ...  Data integration promises to be one of the main catalysts in enabling new insights to be drawn from the wealth of biological data available publicly.  ...  Supplementary data Supplementary data are available at Database Online.  ... 
doi:10.1093/database/baz106 pmid:31697362 pmcid:PMC6836710 fatcat:o4fk52tkvrajfmf7qcdmgcygvu

Visualization of microarray results to assist interpretation

Irene Papatheodorou, Marek Sergot, Marty Randall, Graham R Stewart, Brian D Robertson
2004 Tuberculosis  
Results of microarray experiments on Mycobacterium tuberculosis were used to develop and evaluate the visualization tool and initiate the development of an inference system for gene interactions based  ...  What is lacking are tools for analysing data sets from different experiments, in order to test and generate hypotheses about the links between regulatory networks.  ...  Acknowledgements This work was funded by the Wellcome Trust (BDR and GRS).  ... 
doi:10.1016/ pmid:15207497 fatcat:tqhybrhwlrh45lizbxd4hf7o6e

StressDB: A Locally Installable Web-Based Relational Microarray Database Designed for Small User Communities

Madhusmita Mitra, Nigam Shah, Lukas Mueller, Scuth Pin, Nina Fedoroff
2002 Comparative and Functional Genomics  
We have built a microarray database, StressDB, for management of microarray data from our studies on stress-modulated genes in Arabidopsis.  ...  The source-code is currently available on request from the authors and will soon be made freely available for downloading from our website at  ...  Scripts will be open source and Figure 2 . A user's experiment folder.  ... 
doi:10.1002/cfg.153 pmid:18628845 pmcid:PMC2447266 fatcat:eyx3uakrmndvpkvox23ujwn3zy

The Longhorn Array Database (LAD): an open-source, MIAME compliant implementation of the Stanford Microarray Database (SMD)

Patrick J Killion, Gavin Sherlock, Vishwanath R Iyer
2003 BMC Bioinformatics  
It is a fully open source version of the Stanford Microarray Database (SMD), one of the largest microarray databases.  ...  The Longhorn Array Database (LAD) is a MIAME compliant microarray database that operates on PostgreSQL and Linux.  ...  This work was supported by an NIH INIA Program (Integrative Neuroscience Initiative on Alcoholism) grant AA13518. P.J.K. was supported in part by a pre-doctoral NIAAA-Alcohol Training Grant.  ... 
doi:10.1186/1471-2105-4-32 pmid:12930545 pmcid:PMC194174 fatcat:gijrnimgw5dwrlrejrnzg6jxtm

A metadata framework for interoperating heterogeneous genome data using XML

K H Cheung, A M Deshpande, N Tosches, S Nath, A Agrawal, P Miller, A Kumar, M Snyder
2001 Proceedings. AMIA Symposium  
We illustrate this approach by interoperating two sets of essential yeast genes that are stored in two yeast genome databases (MIPS and YPD).  ...  To answer many of the biologically or medically important questions, researchers often need to integrate data from a number of independent but related genome databases.  ...  Acknowledgements This work was supported in part by NIH grnts G08 LM05583 from the National Library of Medicine, ROI CA77808 and R24 DK58876.  ... 
pmid:11825164 pmcid:PMC2243509 fatcat:6irszwzxurbptd5rrwuthwer6u

Bioinformatics methods for the analysis of expression arrays: data clustering and information extraction

Javier Tamames, Dominic Clark, Javier Herrero, Joaquı́n Dopazo, Christian Blaschke, José M. Fernández, Juan C. Oliveros, Alfonso Valencia
2002 Journal of Biotechnology  
, database storage, gene clustering and information extraction.  ...  Expression arrays facilitate the monitoring of changes in the expression patterns of large collections of genes.  ...  Data gathered from various sources are integrated within a relational database in which genes are indexed according to UNIGENE.  ... 
doi:10.1016/s0168-1656(02)00137-2 pmid:12141992 fatcat:i4jcy5bem5bh7ot76gisiwr5qq

Biomarker Discovery via RT-qPCR and Bioinformatical Validation [chapter]

Christiane Becker, Irmgard Riedmaier, Michael Pfaffl
2013 PCR Technology  
Bioconductor is an open source, open development software project to provide tools for the analysis and comprehension of high-throughput genomic data. 62 There are multiple packages and meta-data packages  ...  of gene expression results from mRNA and miRNA might be an upcoming integrative approach to use for the specific generation of gene-expression patterns as biomarkers for anabolic treatment screening.  ... 
doi:10.1201/b14930-24 fatcat:zc6fxhiyxrcolaklzlc7kprwum

Expression array annotation using the BioMediator biological data integration system and the BioConductor analytic platform

H Mei, P Tarczy-Hornoch, P Mork, A J Rossini, R Shaker, L Donelson
2003 AMIA Annual Symposium Proceedings  
This paper presents the implementation of a model for expression array annotation (EAA) using the BioMediator biological data integration system along with BioConductor, an analytic tools platform.  ...  Annotation provides us with well-curated genomic background knowledge for expression array analysis and interpretation.  ...  ACKNOWLEDGEMENTS We would like to thank Sara Thiebaud for assistance in query testing and paper writing.  ... 
pmid:14728212 pmcid:PMC1479993 fatcat:ye7fxyz2fzdexk6jayjmphxnjq

From access and integration to mining of secure genomic data sets across the Grid

Richard O. Sinnott
2007 Future generations computer systems  
A primary aim of the BRIDGES data Grid is to help control the complexity in access to and integration of a myriad of genomic data sets through simple Grid based tools.  ...  of microarray data sets.  ...  Acknowledgements This work was supported by a grant from the Department of Trade and Industry. The authors would also like to thank members of the BRIDGES and CFG team including Prof.  ... 
doi:10.1016/j.future.2006.07.007 fatcat:m3nbywazozg4pjcaqslnuevxpm

CellMiner: a relational database and query tool for the NCI-60 cancer cell lines

Uma T Shankavaram, Sudhir Varma, David Kane, Margot Sunshine, Krishna K Chary, William C Reinhold, Yves Pommier, John N Weinstein
2009 BMC Genomics  
A Data Intersection tool allows selection of a list of genes (proteins) in common between two or more data sets and outputs the data for those genes (proteins) in the respective sets.  ...  Conclusion: CellMiner is a relational database tool for storing, querying, integrating, and downloading molecular profile data on the NCI-60 and other cancer cell types.  ...  We thank Susan Holbeck, Daniel Zaharevitz, Dominic Scudiero, Anne Monks, and Robert Shoemaker, as well as other DTP staff and contractors for their work on the screen and its data.  ... 
doi:10.1186/1471-2164-10-277 pmid:19549304 pmcid:PMC2709662 fatcat:zjp6anlfnnhhrevl37cqkuaatq
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