ENS microarray platform: A global evaluation of microarray data warehouses

This evaluation was realised mainly in 2002 and directed by Olivier Alibert, on the CEA/Genopole microarray platform (directed by Xavier Gidrol).
We aimed at installing a database on the platform to cover the microarray production, their use and their analysis. We decided not to developp our own system but to use an exitant one. So, I made a global evaluation of the existing databases. Regarding the microarray domain dynamism, it does not have the pretention to be an exhaustive evaluation. These information have been updated so they are mainly still « significant ».
Among 23 databases, 4 where evaluated more precisely (BASE, GeneTraffic, MaxD, RAD ). We wanted to be sure not to miss any important point of the MGED standards. To achieve this, we based ourselves on the developpement of ArrayExpress, an implementation of the MAGE project.
We also followed demos of Resolver, Luminator and Acuity.

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 :

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.

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.

BASE	GeneTraffic	Resolver and Luminator	SMD
ArrayDB	ARGUS	Acuity	AMAD
NOMAD	GeNet	ArrayExpress	GeneX Lite
Maxd	READ	HugeIndex	RAD
MAPS	GEO	Mchips	ExpressDB
LIMas	Partisan Array LIMS	Genedirector2