GenoQuery:
a new querying module for functional annotation in a genomic
warehouse
Introduction
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
databases.
Documentation
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 alternative queries
The mixed queries editor
Functionalitites
:
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.
To 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 displayed.
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 second entity.
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.
To 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 displayed.
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 second entity.
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
Functionalitites
:
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
The alternative queries viewer displays only one query at the same time. To browse the different queries, click the buttons
and .
To convert the displayed alternative query into SQL, click
on the button .
Other functionalities
Computing alternative queries
To compute the alternative queries from the mixed query, click on the menu "Query" and "Compute alternative queries".Examples
Both examples from the article are accessible via the "Example" menu. You can run the examples using GenoQuery via Java Web Start here.Download
To run GenoQuery, use this Java web start link: run.Publication
Frederic Lemoine, Bernard Labedan, Christine FroidevauxGenoQuery: a new querying module for functional annotation in a genomic warehouse
Bioinformatics (ISMB 2008), 07, 13, i322-i329, 24, 2008