by Alexander Hoppe and Manolis Tsiknakis

ACGT (Advancing Clinico-Genomic clinical Trials on cancer: open grid services for improving medical knowledge discovery) is an Integrated Project funded by the 6th Framework Programme of the European Commission, under the action line ‘Integrated biomedical information for better health’. The overall vision of the project is to become a pan-European voluntary network or grid connecting individuals and institutions, which will enable the sharing of data and tools. This will create a European Wide Web of cancer clinical research with the goal of speeding the delivery of innovative approaches for the prevention and treatment of cancer.

Life sciences are currently at the centre of an information revolution. The development of new techniques and tools is making possible the collection and organization of biological information at an unprecedented level of detail and in extremely large quantities. With respect to cancer research, the use of high-throughput technology has resulted in an explosion of information and knowledge about cancers and their treatment.. However, the lack of an open and shared information infrastructure is preventing clinical research institutions from being able to mine and analyse disparate data sources. Our inability to share technology and data that have been developed by different organizations is severely hampering the research process. As a result, very few cross-site studies and multicentre clinical trials are being performed.

The ultimate objective of ACGT is therefore the development of a semantic grid infrastructure facilitating a common platform for researchers, clinicians, biostatisticians and software developers that will (i) facilitate seamless and secure access to heterogeneous, distributed multilevel databases; (ii) provide a range of semantically rich reusable, open tools for the analysis of such integrated, multilevel clinico-genomic data in the context of discovery-driven (eScience) workflows; (iii) support the creation and management of dynamic virtual organizations (VOs); and (iv) do so in full compliance with existing ethical and legal regulations.

To achieve this high-level goal, the project is delivering a Master Ontology on Cancer – soon to be submitted for membership in the Open Biomedical Ontologies (OBO) foundry, and an innovative software mediation tool, the ACGT Mediator, used for hiding the complexity of query translation and data integration. One fundamental component is the implementation of a clinical trial management system, called ObTiMA, based on an ontology-driven software development process, providing uniform access to heterogeneous clinical trial, genetic and public biological databases. Another is the implementation of a range of tools for bioinformatics and biomedical data analysis and visualization, and grid-enabled knowledge discovery. The gridified version of the R package (GridR) enables the use of the complete ACGT platform and services by choosing the (familiar) R language.

The main outcome of the work to date is the development of a generic integration framework using semantic Web technology, standards and tools, which enables the integration of not only ACGT compliant services but also of other third-party bioinformatics services like BioMOBY.

The status of the two pilot trials is being continuously monitored. Clinical, imaging and genetic data are used for the evaluation and defining codes for the Oncosimulator in order to simulate tumour growth and response to treatment. A range of new clinico-genomic trials and scenarios were defined to use the ACGT platform. Keeping end-users in line with ethical and legal requirements demands special consideration. To address these needs, the CDP (Center for Data Protection) promoted at European level by the consortium was established on the legal side, and several security mechanisms were implemented (eg an innovative data anonymization and privacy enhancing tool) on the technical side.

Two large scenarios were developed and used to test the logical and execution architecture in general as well as separate tools and services. A consequent user-developer loop led to experiences gathered in building and demonstrating these end-to-end demonstrations. Training-evaluation sessions with end users were conducted to further increase robustness, reduce technical complexities in using the systems/services and improve the usability of the whole platform. As the ontology-based clinical trial management system for ACGT (ObTiMA) plays a crucial role from a clinical perspective the main focus was to steadily improve the functionality of ObTiMA including a user-friendly integration of the Master Ontology.

In 2009 ACGT established a formal collaboration with the European Organisation for Research and Treatment of Cancer (EORTC). EORTC's experience is an invaluable asset in achieving the project goals. ACGT was also made visible to end-user communities by being presented to important organizations in the field of oncology, such as the Breast International Group (BIG), and the International Society of Paediatric Oncology (SIOP) and by inviting external experts (such as an the European Clinical Research Infrastructures Network (ECRIN) representative) to an advisory board meeting, where highly positive feedback was received.

Mature demonstrations of all the technological components functioning as a whole are now running, and since the project has been extended to July 2010 we believe that by the end of the project we will deliver a solid platform for end-user communities.

The ACGT project is managed by ERCIM.

Link:
http://www.eu-acgt.org/

Please contact:
Manolis Tskinakis
FORTH, Greece
E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

Next issue: January 2020
Special theme:
Educational Technology
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