A global evaluation of microarray data warehouses
Contact:Sophie Lemoine ( firstname.lastname@example.org)
This evaluation was realised mainly in 2002 and directed by Olivier Alibert, on the CEA/Genopole
microarray platform (directed by Xavier Gidrol).
I-The need of criteria
To choose a database among these, you have to determine criteria depending on your lab, on the people you work with, on your goals... You first have to ask you the good questions. Here are the criteria we chose, just as an example :
II-A summary of the evaluation : the main points
Academic and commercial databases both exist. The academic databases are uselly free for a non profit use, what is a positive point ! The disadvantage is that you have to install it on your own, what can be discouraging if you have nobody to help. Commercial products can be very expensive (Resolver and Luminator), some are more reasonnable. It can be a good choice if you do not have anybody to take care of the database in you lab.
Both windows and linux databases exist : it depends on your equipements...
What kind of arrays do you use or plan to use ? Most of the databases can deal with cDNA arrays or affymetrix arrays. Some even deal with SAGE data.
Some databases are both local systems and public repositories. It can be an advantage if you want to export your data before publication. If your database is only a local installation, it may not be a problem for the exchange : it exists an exchange format, the MAGE-ML format, dedicated to the large-scale expression technologies that is becomming a standard. This format is the implementation of the MAGE project (MicroArray Gene Expression), supported by the MGED group. MAGE is an extended formalisation of the MIAME standard (Minimal Information About Microarray Experiment). Many databases adopt these new standards because the public repository and MIAME compliance are imposed by editors before publication, to ensure the validity of the experiment and the avaibility of the whole protocols and data.
III- The database home links and the complete evaluation table
Database home links :
The complete evaluation table (pdf file) :
Contact: Sophie Lemoine (email@example.com )
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