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Bioinformatics 2008 24(13):i322-i329; doi:10.1093/bioinformatics/btn159
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

GenoQuery: a new querying module for functional annotation in a genomic warehouse

Frédéric Lemoine 1,2, Bernard Labedan 1 and Christine Froidevaux 2,*

1Institut de Génétique et Microbiologie and 2Laboratoire de Recherche en Informatique, Université Paris-Sud XI, 91405 Orsay Cedex, France

*To whom correspondence should be addressed.


  Abstract

Motivation: We have to cope with both a deluge of new genome sequences and a huge amount of data produced by high-throughput approaches used to exploit these genomic features. Crossing and comparing such heterogeneous and disparate data will help improving functional annotation of genomes. This requires designing elaborate integration systems such as warehouses for storing and querying these data.

Results: We have designed a relational genomic warehouse with an original multi-layer architecture made of a databases layer and an entities layer. We describe a new querying module, GenoQuery, which is based on this architecture. We use the entities layer to define mixed queries. These mixed queries allow searching for instances of biological entities and their properties in the different databases, without specifying in which database they should be found. Accordingly, we further introduce the central notion of alternative queries. Such queries have the same meaning as the original mixed queries, while exploiting complementarities yielded by the various integrated databases of the warehouse.

We explain how GenoQuery computes all the alternative queries of a given mixed query. We illustrate how useful this querying module is by means of a thorough example.

Availability: http://www.lri.fr/~lemoine/GenoQuery/

Contact: chris{at}lri.fr, lemoine{at}lri.fr


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