Public deliverables
- D2.1: Use requirements and specification of the ACGT internal clinical trials
- D5.1: Consolidated requirements and specifications for data access
- D6.1: Consolidated Requirement Analysis for Data Mining, Analysis and the Visualization Environment
- D7.1: Consolidated Requirements on ontological approaches for integration of multi-level biomedical information
- D8.1: Consolidated requirements (including information flows) of the in silico simulation models
- D10.1: Production of informed-consent form in compliance with the clinical trials, post-genomic research and genetic data handling requirements
- D10.2: The ACGT ethical and legal requirements
- D13.1 :Evaluation criteria and verification procedures of the ACGT platform
D2.1: Use requirements and specification of the ACGT internal clinical trials
The present deliverable presents the rational of the project, in a more explicit and detailed manner, as well as its specific objectives. It elaborates the adopted requirements engineering methodology adopted by the project and shortly present details of the Clinical Studies designed for the evaluation of the results of the project.
Explicit scenarios, presenting both user-driven stories expressing user-needs, as they are documented by representative users, as well as technology-driven description of requirements of the system under design, representing indicative functionality of the system, as understood by experienced technological experts, have been developed and are described. The various future user groups and stakeholders of the project's results are presented and analyzed. Initial user requirements and functional requirements of the ACGT platform are elaborated. These requirements will be further elicited in the various WPs of the project, as foreseen in the DoW.
With the initial requirements of the project in mind, a large number of data sources, tools, standards and technology are available for the different aspects of the intended system and significant R&D results are available in a number of related scientific domains.
PART 2 of the deliverable provides a detailed state-of-the-art review in all of the scientific areas relevant to the project.
D5.1: Consolidated requirements and specifications for data access
This report comprises the first deliverable of WP5 of the ACGT project. A main goal of this work package is to provide seamless and interoperable data access to the distributed data sources that are relevant to each of the ACGT clinical trials by developing a set of compatible software modules and services based on web services. The main objective of this deliverable is to consolidate the user requirements defined in WP2 with respect to distributed data access. For this purpose we use the CAFCR architecting framework. This deliverable contains a chapter for each of the five CAFCR views: the Customer View, the Application View, the Functional View, the Conceptual View, and the Realization View.
Using this structure, we not only document the requirements for data access in more detail, but also make first steps towards a solution. This deliverable documents what has been done so far in WP5, and concludes by outlining what is next.
D6.1: Consolidated Requirement Analysis for Data Mining, Analysis and the Visualization Environment
The present document provides an overview of the contributions of individual partners in ACGT WP6. The contributions are as follows: SIB provides datasets based on actual clinical-trial for testing, FhG addresses data mining tools and use of R in a grid environment, LundU addresses database developments and analysis tools based on pathway information, Biovista proposes a literature-based analysis tool, INRIA develops new clustering algorithms, UPM addresses the use of ontologies in the clinical data analysis, and UvA proposes a framework for interactive visualization.
D7.1: Consolidated Requirements on ontological approaches for integration of multi-level biomedical information
This deliverable presents an analysis of the requirements needed in Work Package (WP) 7: Ontologies and Semantic Mediation Tools. It has been extended to provide a vision of the state of the art in some of the focused issues within WP7. A description of the approaches adopted, at the time of writing this document, has been included, as well as a complete requirements specification of the methods and tools to be investigated and developed during the next phases of the ACGT project.
The partners involved in WP7 have adopted a standard-based methodology for gathering requirements. It is based on specific scenarios provided by both technicians and end users. Such requirements can evolve during the entire project. They can be modified to follow up the evolution of the state of the art in the involved areas.
This document includes the ACGT Master Ontology on Cancer. This important objective for ACGT is described here to facilitate its understanding and use as a core resource for semantic mediation and interoperability.
D8.1: Consolidated requirements (including information flows) of the in silico simulation models
The present deliverable outlines the requirements of the in silico oncology simulation models to be developed within the frame of workpackage WP8 of ACGT. An introduction to the notion of the "Oncosimulator" along with a number of high-level information flow diagrams and a brief description of the corresponding clinical trials constitute the core of the document.
The basic actions to be implemented are the following:
1. Development of the "Oncosimulator".
The constituent simulation models will be based on the novel, essentially "top-down" modeling approach developed by the In Silico Oncolog Group, ICCS, National Technical University of Athens.
2. Provision of pertinent clinical data for the two cases to be addressed, namely nephroblastoma (Wilm's tumour) and breast cancer. The in silico oncology trial will be based on the two clinical trials (nephroblastoma SIOP 2001/GPOH and breast cancer TOP trial) following their considerable enhancement in terms of data collection. It is pointed out that the design and
implementation of clinical trials in order to validate, adapt and optimize tumour behaviour models is a worldwide novelty.
3. Technical requirements (data handling, parallelization and grid
architecture usage, image processing, visualization).
Indicative references delineating the basis of the overall modeling philosophy to be adopted are also provided.
D10.1: Production of informed-consent form in compliance with the clinical trials, post-genomic research and genetic data handling requirements
This deliverable contains in the first part an analysis of the relevant ethical and legal requirements for informed-consent forms within ACGT. Special issues such as the scope of the consent with special regard to future research, informed consents of minors and relatives are discussed.
The second part contains the general terms of ACGT, that have to be accepted by every participant, as well as different consent forms and agreements, that have to be concluded between the different participants.
D10.2: The ACGT ethical and legal requirements
This deliverable contains an analysis of the relevant ethical and legal requirements for ACGT.
The first part of this document analyzes the ethical requirements regarding clinico-genomic research within the ACGT architecture, especially with regard to informed consent and disclosure of research results. In order to protect patients' autonomy and their right to self-determination - the most basic principles to be respected in the context of medical research involving patients - the informed consent for participation in ACGT has to react in an appropriate manner to these challenges. In ethical terms, a tiered consent offering to donors the possibility to authorize a broader or more restricted range of research to be done with their samples and data and time frame they may be used for research would be preferable. However, this model is difficult to handle in practice.
Therefore, a model of consent referring to a purpose of intermediate scope (clinico-genomic research on cancer) in the context of a specific structure or project (ACGT) is proposed, which is within the limits of ethical as well as legal considerations. Concerning the disclosure of research results, it is widely agreed that general research results must accessible for research subjects regardless of the inalienable right of the patients to access his or her personal data. Since clinico-genomic research may also yield individually relevant results, it is additionally recommended that ACGT provides the technical and organizational means for individual feedback processes of such results.
The second part analyzes the legal requirements, particularly with regard to data protection and privacy. The goal to be achieved is to establish a structure where the competing aims of modern genetic research and the data protection needs of the participating patients can be met. Genetic data is very sensitive data which differs from ?normal? data in a crucial point: it cannot be anonymized completely and therefore falls under special requirements for data processing. In order to get as many data protection operations within ACGT outside the scope of the Data Protection Directive as possible, it is recommended to establish a Data Protection Architecture within the ACGT framework, which comprises a double pseudonymization procedure, the establishment of an ACGT Data Protection Board as central data controller and a Trusted Third Party.
Furthermore we analyze the impact of the Directive 2000/31/EC on E - commerce on ACGT. This analyzsis concerns the relationship between ACGT / physicians and researchers, dealing with service provider, users, contract by electronic means, etc. in the context of ACGT.
D13.1 :Evaluation criteria and verification procedures of the ACGT platform
The present document provides a list of evaluation and validation procedures for the ACGT infrastructure. It is subdivided into two major parts. The first part provides recommendations for the development of quality procedures to ensure the quality of software in each technical work package. The actual QA procedures for the ACGT software components can be found on the BSCW document server. The access to software management tools made available is the context of ACGT is also described in the present document.
The second part provides evaluation criteria from the perspective of the end-user. The latter is focused on the ability of users to utilize the ACGT infrastructure to solve practical scenarios. The scenarios are tightly bound to the data architecture currently accepted they may and will evolve with the architecture of the system.