TITLE

A software framework for microarray and gene expression object model (MAGE-OM) array design annotation

AUTHOR(S)
Qureshi, Matloob; Ivens, Alasdair
PUB. DATE
January 2008
SOURCE
BMC Genomics;2008, Vol. 9, Special section p1
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: The MIAME and MAGE-OM standards defined by the MGED society provide a specification and implementation of a software infrastructure to facilitate the submission and sharing of data from microarray studies via public repositories. However, although the MAGE object model is flexible enough to support different annotation strategies, the annotation of array descriptions can be complex. Results: We have developed a graphical Java-based application (Adamant) to assist with submission of Microarray designs to public repositories. Output of the application is fully compliant with the standards prescribed by the various public data repositories. Conclusion: Adamant will allow researchers to annotate and submit their own array designs to public repositories without requiring programming expertise, knowledge of the MAGE-OM or XML. The application has been used to submit a number of ArrayDesigns to the Array Express database.
ACCESSION #
38122704

 

Related Articles

  • IDUX: INTERNATIONALIZATION OF DATA USING XML. Benoit, Darcy G.; Müldner, Tomasz // Proceedings of the IADIS International Conference on WWW/Interne;Nov2004, p469 

    Interest is rapidly growing in internationalized software that can be localized to various languages. This paper describes IDUX, an XML-based system designed to support the process of internationalizing data. A specific application of IDUX is to create internationalized websites, allowing the...

  • QuickBase builds solid apps. Caton, Michael // eWeek;12/15/2003, Vol. 20 Issue 50, p53 

    Intuit Inc.'s Quickbase does a good job of combining ease of use with robust customization options, thus giving corporations a quick and easy way to build database applications. QuickBase did particularly well in "eWEEK" magazine's labs' tests at providing the tools necessary for a workgroup to...

  • Language Bindings to XML. Simeoni, Fabio; Lievens, David; Connor, Richard; Manghi, Paolo // IEEE Internet Computing;Jan/Feb2003, Vol. 7 Issue 1, p19 

    Discusses the applications of XML language bindings. Background on the XML language; Function of the SAX programmer in XML document; Information on the Java Architecture for XML Binding.

  • Processing XML with Java -- A Performance Benchmark. Oliveira, Bruno; Santos, Vasco; Belo, Orlando // International Journal of New Computer Architectures & their Appl;2013, Vol. 3 Issue 1, p72 

    Over time, XML markup language has acquired a considerable importance in applications development, standards definition and in the representation of large volumes of data, such as databases. Today, processing XML documents in a short period of time is a critical activity in a large range of...

  • Sonic Loads the Bus for SOA. Borck, James R. // InfoWorld;3/28/2005, Vol. 27 Issue 13, p22 

    This article features the Sonic service oriented architectures (SOA) Suite 6.1 computer software introduced by Sonic Software in 2005. This software delivers a Java-based server infrastructure and toolset for connecting applications, Web services, data sources and orchestrating interactions...

  • Create Advanced XML Data-Integration Applications.  // SQL Server Magazine;Oct2005, Vol. 7 Issue 10, p41 

    The article states that DataDirect Technologies Inc. introduced Stylus Studio 6 XML Enterprise Edition, a tool for advanced XML data-integration projects. The software includes tools for XML mapping, XML data modeling, Web services development, and legacy data integration. The new release...

  • Ontology-Based Query in Heterogeneous & Distributed Data Sources. Al-Ghamdi, Najood; Saleh, Mostafa; Eassa, Fathy // International Journal of Electrical & Computer Sciences;Dec2010, Vol. 10 Issue 6, p94 

    Information sharing, exchanging and retrieving from heterogeneous data sources not only needs complete data accessibility, but also it needs solving data heterogeneity between these data sources. To solve this rising problems of heterogeneity, a lot of recent work has been done towards solving...

  • Generating Text Search Applications for Databases. Alonso, Omar // IEEE Software;May/Jun2003, Vol. 20 Issue 3, p98 

    Focuses on the production of software products from reusable components. Importance of the ability to connect the output of a domain analysis tool to a program generator; Combination of XML document markup language and Java computer program language as alternative to classical parser generation...

  • ToolBox: Working With XML.  // Inter@ctive Week;06/05/2000, Vol. 7 Issue 22, p96 

    Presents information on some software for dealing with eXtensible Markup Language coding. MSXML Parser from Microsoft Corp.; Allora from HiT Software; Java Document Object Model from JDOM open source project.

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics