Publications

The following publications are related to the COnQueSt system:

Alejandra González-Beltrán, Ben Tagger, Anthony Finkelstein Federated Ontology-based Queries over Cancer Data BMC Bioinformatics Volume 13 Supplement 1, Semantic Web Applications and Tools for Life Sciences (SWAT4LS) 2010.
Alejandra González-Beltrán, Ben Tagger, Anthony Finkelstein “Ontology-based Queries over Cancer Data” BEST PAPER AWARD In proceedings Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2010) Berlin, Germany. December 10, 2010.
Alejandra González-Beltrán, Anthony Finkelstein, J Max Wilkinson, Jeff Kramer “Domain Concept-Based Queries for Cancer Research Data Sources ” In the proceedings of the 22nd IEEE International Symposium on Computer-Based Medical Systems 2009 (CBMS 2009) Special track on HealthGrid Computing - Applications to Biomedical Research and Healthcare August 3-4 2009, Albuquerque, New Mexico, USA

For more details, please see the publications page.

Graphical User Interface

The following flash movies show the functionalities available through the ConQueSt interface:

This demo shows the Browser functionality, which allows to inspect the registered projects, or information models. Currently, the information models presented are the ones from the caGrid infrastructure. It is possible to search projects by their name, inspect the concepts used to annotate the project and view their definition and link to the NCI thesaurus browser.
This demo shows the Concept Search facility. When searching for a concept, the result shown includes the projects (or information models) with matching concepts as well as the concepts themselves. While the "search" button considers all the concepts containing the search criteria, the "I'm feeling lucky" button retrieves the concept that matches exactly the search criteria.
This demo shows how to use the Query Builder tab to find the Genetic Markers associated with the Gene whose Gene Symbol is TGFB1.
This demo shows how to use the Query Builder tab to find the Genetic Markers associated with the Gene whose Gene Symbol is TGFB1. The Services frame shows which available caGrid services contain all or some of the concepts used in the query, listed in the Query Concepts frame.
This demo shows how to use the Query Builder tab to find the Single Nucleotide Polymorphisms associated with the Gene whose Gene Symbol is TGFB1.
Finally, this demo shows the use of all the tabs. The query built is the one that finds all the Genes whose symbol starts with BRCA.

OWL Generator Service

The OWLGenService can be accessed through the caGrid portal.

The current location of the OWLGenService is: http://94.175.234.231:9600/wsrf/services/cagrid/OwlgenService

OWL Generator code (module and service)

The code for the OWL generator business logic and service can be browsed at this repository. And you can download it using the following svn command:

svn co http://mafalda.cs.ucl.ac.uk/svn/owlgen/
The code is distributed under the CPAL license, and attribution should be given referring to this page and citing the BMC Bioinformatics paper.

Performance Evaluation

Contents

Publications

Graphical User Interface

OWL Generator Service

OWL Generator code (module and service)

Performance Evaluation