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Data Specifications
This section contains computer-based tools
used to manage microarray experiments data. It
permits individuals to browse existing tools
or to add new tools they have developed
The purpose of this section is both to permit the
exchange of tools and to facilitate discussion of
their use. As such, each tool contains a link at
the bottom through which you can add information
related to your experience.
NHGRI ArrayDB 2.1
Sybase database schema to
manage a wide variety of data. This relational database
stores information including image data, experiment data
(printing arrays, probes), and clones (IMAGE Clone ID,
title, UniGene cluster). A commercial middleware product,
Websql, is utilized to provide real-time interactive queries
of the database through a convenient and widely
accessible Web interface. The Web interface is provided
as both standard HTML Web pages and, where a greater
degree of interaction is needed, Java applets have been
implemented.
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AMAD: Another Microarray Database
a simple yet very effective flat file database
designed specifically for microarray data. It will run
on any web server that supports PERL.
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Gene Expression Markup Language (GEML)
Gene Expression Markup Language developed by Rosetta Inpharmatics
is a file format for storing DNA microarray and gene expression data.
GEML is an open-standard XML format which enables exchange of data between
gene expression databases and analysis systems. GEML stores which data
collection methodology was used, without making assumptions about the
meaning of a measurement.
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Microarray Markup Language (MAML)
Microarray Markup Language is a data format for describing information about DNA-array
based experiments. MAML is based on the Extensible Markup Language (XML). MAML provides a
framework for describing experiments done on all types of DNA-arrays, including spotted and
synthesized arrays, and oligo-nucleotide and cDNA arrays.
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Minimum Information About a Microarray Experiment (MIAME)
The goal of the MIAME is to specify the minimum information that must be
reported about an array based gene expression monitoring experiment in order to
ensure the interpretability of the results, as well as potential verification by third
parties. This is to facilitate establishing repositories and a data exchange format
for array based gene expression data.
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GeneX: a Collaborative Internet Database and Toolset for Gene Expression Data
The GeneX project began with a the idea of a massively distributed gene expression database,
something along the idea of a 'Napster' for gene expression. The underlying communication channel
would be a mechanism that would allow the complex annotations and protocols to be transmitted along
with the numeric data in a way that would not require the explicit association of many files and certainly
not by hand-editing different formats into a coherent whole.
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ArrayExpress
ArrayExpress is a database schema and object model developed by EBI for representing microarray data. The ArrayExpress project supports the MIAME standard (Minimum Information About a Microarray Experiment).
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