The Vision and Objectives of ACGT
ACGT (Advancing Clinico-Genomic Trials on cancer: Open Grid Services for improving Medical Knowledge Discovery) is an Integrated Project (IP) funded in the 6th Framework Program of the European Commission under the Action Line "Integrated biomedical information for better health".
ACGT aims to develop methods and systems for improved medical knowledge discovery and understanding through the integration of biomedical information and the use of modeling, visualization, data mining and grid technologies. Biomedical data and information include not only clinical information relating to tissues, organs or personal health-related information but also information at the level of molecules and cells that is produced by genomics and proteomics research.
The project will design, develop and validate an integrated Grid-enabled technological platform in support of post-genomic, multi-centric Clinical Trials with an initial focus in the domain of Cancer. The driving motivation behind the project is our committed belief that the breadth and depth of information already available in the research community at large, present an enormous opportunity for improving our ability to reduce mortality from cancer, improve therapies and meet the increasing demand for personalized health care.
The problem with data integration
In addition to its shear volume, data collected for use in clinical trials and other analyses related with the provision of healthcare services is often published without the background information (method of capture, sample preparation, statistical techniques applied) that is needed to reproduce results. Even within a single laboratory, researchers have difficulty integrating data from different sources not only because of a lack of common standards but also because of other technological, medical, legal and even ethical issues. As a result, very few cross-site studies and clinical trials are performed and in most cases it isn't possible to seamlessly integrate multi-level data. The benefit of such multi-centric trials is hence never realized.
Apart from problems in sharing and re-using data, what is even more critical is the fact that clinical researchers or molecular biologists often find it hard to exploit each others' expertise due to the absence of a cooperative environment which enables the sharing of resources and tools, as well as a uniform platform that supports the seamless integration and analysis of disease-related data at all levels.
With this in mind ACGT aims to develop a European Knowledge Grid infrastructure offering high-level tools and techniques for the distributed mining and extraction of knowledge from data repositories available on the Grid, leveraging semantic descriptions of components and data and offering knowledge discovery services in the domain of Cancer research. Special emphasis will be given to the trust mechanisms that need to be embedded in the platform as well as the relevant ethical issues, thus creating conditions that promote service uptake.
ACGT technologies and approach - an overview
ACGT is a 4 year project run by a 25 member international consortium and represents a significant undertaking by any measure. To meet its objectives, the project is developing solutions in a multitude of technological areas, the main ones of which are:
Focusing on the semantic integration of data but also on the discovery, integration, and management of sharable data assets (i.e. data and tools operating on such data). As a result the issue of metadata becomes of paramount importance for the successful achievement of the project objectives. The project is developing standards and metadata specifications describing and exposing web services (semantics), scientific services, and the properties of data sources, datasets, scientific objects, and data elements;
Developing new, domain-specific ontologies, built on established theoretical foundations and taking into account current initiatives, existing standard data representation models and reference ontologies; The ACGT Master Ontology on Cancer plays a pivotal role in enabling (a) semantic information integration and (b) ontology based implementation of end-user applications;
Developing innovative and powerful data exploitation tools, for example multi-scale modeling and simulation, considering and integrating from the molecular to the systems biology level, and from the organ to the living organism level, as well as technologies for interactive visualization on the grid;
- Developing an open biomedical GRID infrastructure offering seamless mediation services for sharing data and data-processing methods and tools; Set up cross-disciplinary task forces to propose guidelines concerning issues related to sharing legal, regulatory, and ethical data. ACGT is also developing advanced security tools (including anonymisation and pseudonymisation of personal data) for data protection in a web (grid) services environment in accordance with existing European legal and ethical regulations;.
- Developing an ontology based Trial Builder for helping to easily set up new clinico-genomic trials, to collect clinical, research and administrative data, and to put researchers in the position to perform cross trial (meta) analysis;
- Developing data-mining services in order to support and improve complex knowledge discovery processes;
- Creating an easy to use workflow environment, so that biomedical researchers can easily design their "discovery workflows" and execute them securely on the grid.
The ACGT consortium is currently focusing on the development of this core set of tools and components up to a stage where they can effectively support in silico investigations. Later stage developments will subsequently allow the consortium to improve and refine the capabilities of the services offered via the ACGT infrastructure.
To introduce the project to its intended target groups, a range of demonstrators, are currently under development. First prototypes are expected early in 2008 enabling the consortium members to begin evaluation and at the same time gather additional and more concrete requirements to guide future refinements and work.
ACGT opts for Open Source
The project promotes the principles of open source and open access, and has conceived an overall architecture for an integrated biomedical sciences platform. The infrastructure being developed enables efficient management of Virtual Organizations crated in the context of multi-centric, post-genomic clinical trials and uses a common set of services and service registrations for the entire clinical-trials-in-cancer community.
ACGT and the Community
ACGT is an infrastructure and related services project and as such its success ultimately hinges on its adoption by the intended user communities. Demonstration and awareness activities have already begun and will continue for the duration of the project. One of the planned highlights will be the ACGT competition, expected to take place in the middle of 2009. Open to everybody, it will bring together representatives from the healthcare, life sciences and IT communities rewarding entries that most convincingly demonstrate the use of the ACGT infrastructure and offer true value to the end users.
For more information on ACGT visit: www.eu-acgt.org