A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2004; you can also visit the original URL.
The file type is application/pdf.
Filters
GeneX: An Open Source gene expression database and integrated tool set
2001
IBM Systems Journal
Preserved Fulltext
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
2001
Briefings in Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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]
2019
biorxiv/medrxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2011
Briefings in Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2004
Tuberculosis
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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/j.tube.2003.12.012
pmid:15207497
fatcat:tqhybrhwlrh45lizbxd4hf7o6e
Open Bioinformatics
2003
Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
For example, microarray gene expression analysis often identifies hundreds of interesting genes. ...
The Open Source initiative makes the original source code available to other developers via a license that allows for free redistribution and derived works while preserving the integrity of the author's ...
doi:10.1093/bioinformatics/btg214
pmid:12691978
fatcat:er26ndsebje5nltbynacnz5bo4
StressDB: A Locally Installable Web-Based Relational Microarray Database Designed for Small User Communities
2002
Comparative and Functional Genomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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 athttp://arastressdb.cac.psu.edu. ...
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)
2003
BMC Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2001
Proceedings. AMIA Symposium
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2002
Journal of Biotechnology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
, 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]
2013
PCR Technology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2003
AMIA Annual Symposium Proceedings
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2007
Future generations computer systems
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2009
BMC Genomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
« Previous
Showing results 1 — 15 out of 159 results