a new querying module for functional annotation in a genomic
GenoQuery is a module
for querying a relational genomic warehouse,
which is based on an original multi-layer architecture of the
warehouse, made of two layers, the entities layer and the databases
layer. We have further distinguished two levels in the
entities layer: abstract entities that are extracted from the databases
and concrete entities that are views of these abstract entities in the
The application frame is divided in two Panels.
- The left side panel is the mixed queries editor.
It allows the construction of mixed queries
- The right side panel is the Alternative queries viewer.
It allows the visualization and the execution of the resulting
The mixed queries editor
Create a new mixed query
- : Import a mixed query from file (SparQL format)
Save the current mixed query to a file (SparQL format)
Refresh the layout of the current mixed query
- : Display the current mixed query in Graphviz dot format
Export the mixed query as an image file (jpg)
Building a mixed query
The mixed queries editor allows to add abstract entities and concrete
entities, by right clicking on the mixed queries editor. A menu appear,
which displays the list of abstract and concrete entities.
make a link between two entities of the mixed queries
editor, middle-click with the mouse on the first entity, and
release the button over the
second entity. Then a list of possible links between both entities is
The other way to make a link is to right click on an
entity. A list of possible links from this entity is displayed. Once a
link is clicked, the editor adds it to the mixed query and add the
To add a property on an entity, right click on the entity, and choose
the property to add.
You can Zoom in and out in the editor by using the mouse wheel.
The Alternative queries viewer
Back to the previous alternative query
Refresh the layout of the current alternative query
Convert the current alternative query into SQL
Go to the next alternative query
- : Display the current alternative query in Graphviz dot format
Export the current alternative query as an image file (jpg)
- : Make the alternative query graph editable or not (to move the vertices independently of each other)
Browsing the alternative queries
alternative queries viewer displays only one query at the same time. To browse
the different queries, click the buttons
To convert the displayed alternative query into SQL, click
on the button
Computing alternative queries
To compute the alternative queries from the mixed query, click on the menu "Query" and "Compute alternative queries".
Both examples from the article are accessible via
menu. You can run the examples using GenoQuery via Java Web Start here
To run GenoQuery, use this Java web start link: run
Frederic Lemoine, Bernard Labedan, Christine Froidevaux
GenoQuery: a new querying module for functional annotation in a genomic warehouse
Bioinformatics (ISMB 2008), 07, 13, i322-i329, 24, 2008