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.
  1. The left side panel is the mixed queries editor. It allows the construction of mixed queries
  2. 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

  1. New mixed query: Create a new mixed query
  2. open a mixed query: Import a mixed query from file (SparQL format)
  3. Save mixed query: Save the current mixed query to a file (SparQL format)
  4. Refresh Layout: Refresh the layout of the current mixed query
  5. Dot Format: Display the current mixed query in Graphviz dot format
  6. export as jpg: 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.

The Alternative queries viewer

Functionalitites

  1. previous alternative query: Back to the previous alternative query
  2. Refresh Layout: Refresh the layout of the current alternative query
  3. Execute alternative query: Convert the current alternative query into SQL
  4. next alternative query: Go to the next alternative query
  5. Dot Format: Display the current alternative query in Graphviz dot format
  6. export as jpg: Export the current alternative query as an image file (jpg)
  7. editable image: 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 Previous query image and next query image. To convert the displayed alternative query into SQL, click on the button convert to SQL image.

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 Froidevaux
GenoQuery: a new querying module for functional annotation in a genomic warehouse
Bioinformatics (ISMB 2008), 07, 13, i322-i329, 24, 2008