WP1 - Scientific Coordination

WP2 - Domain Analysis and Community Relations

This work package is designed to reach out to database users and to database development experts, to formally assess what other key groups are doing that is of relevance to GEN2PHEN and investigate what are the current and future needs of the different actors in the G2P field. Deliverables will include formal documentation of our findings, and these will be focussed in two directions. Firstly, we will establish general trends and needs for G2P databasing, and use this analysis to refine the activities of our project. We do not anticipate this will imply any major changes to our project plan, but we do hope to identify ways to adapt our work so that it brings maximum synergy with the efforts of others. Secondly, we will formalise the data models and the nomenclature systems being utilised by others. This will provide the detailed domain analysis upon which WP3 will build. WP2 will thus constitute a formal ‘requirements analysis’ upon which the rest of our project work will be based. It will also help establish and sustain a spirit of understanding and trust between our project and other G2P domain initiatives, which will encourage others to adopt and use our systems. WP2 will thus be key in initiating a chain-reaction, needed for a long-lasting impact in the field.

WP3 - Standard Data Models and Terminologies

This work package will take the domain analysis documents and priority use cases produced by WP2, and build on these to create reference data models upon which all our subsequent database development and implementation work will be based. Inter-compatible data models will be devised that will support each type of G2P database and data exchange. These data models will also be aligned with genomics data standards being developed in the clinical domain, for example by HL7. The model(s) will be formalized via submission to standards organisation(s). Subsequently, as new scientific issues arise, the models will be enhanced accordingly via a rolling review process. A similar standardisation path will be followed with mutation nomenclatures. However, for the complex field of G2P ontologies, this work package will not undertake direct ontology development work. It will instead devise a plan for precisely incorporating suitable ontologies into G2P databases. WP3 will thus provide mission-critical ‘blue-prints’ upon which all our database development work will be based. By standardising the data models and terminologies from an early stage, and registering these as official global standards, this work package will ensure that the databases and other deliverables from all subsequent work packages are maximally interoperable.

WP4 - Genetics G2P Databases

These two related work packages (WP4 and WP5) will create modular and generic G2P database components, and then use these ‘building blocks’ to construct major demonstration databases for use by the field. All of this work will be based upon the standards developed in WP3. The main distinction between these two work packages is that WP4 will concentrate upon genetics databases (i.e., where the focus is on one or a few genes or diseases, with clinical utility being most important) whereas WP5 will concentrate upon summary level genomics databases (i.e., aggregated datasets, where there is no focus on any particular gene or disease, and with research utility being most important). The two workpackages will implement rather different user interfaces, with WP4 oriented mostly towards the needs of clinical users and WP5 oriented more towards biomedical researchers. WP4 and WP5 are therefore complementary, and will benefit from close co-operation as their respective tools and software solutions are developed. Furthermore, in both cases, the database components and/or complete databases produced will be used as tangible assets around which federated teams of (existing and new) database operators can grow, and this will be actively encouraged by activities in these work packages. WP4 and WP5 involve substantial technology development, and, as such, will be subject to quality assurance measures dictated by WP1. Both work packages will generate operational databases, and these will be used for the data gathering efforts performed in WP7. These databases will also be valuable in their own right, and in that capacity they represent example depositories that will be integrated and made universally searchable by the activities of WP6.

WP5 - Genomics G2P Databases

These two related work packages (WP4 and WP5) will create modular and generic G2P database components, and then use these building blocks to construct major demonstration databases for use by the field. All of this work will be based upon the standards developed in WP3. The main distinction between these two work packages is that WP4 will concentrate upon genetics databases (i.e., where the focus is on one or a few genes or diseases, with clinical utility being most important) whereas WP5 will concentrate upon summary level genomics databases (i.e., aggregated datasets, where there is no focus on any particular gene or disease, and with research utility being most important). The two workpackages will implement rather different user interfaces, with WP4 oriented mostly towards the needs of clinical users and WP5 oriented more towards biomedical researchers. WP4 and WP5 are therefore complementary, and will benefit from close co-operation as their respective tools and software solutions are developed. Furthermore, in both cases, the database components and/or complete databases produced will be used as tangible assets around which federated teams of (existing and new) database operators can grow, and this will be actively encouraged by activities in these work packages. WP4 and WP5 involve substantial technology development, and, as such, will be subject to quality assurance measures dictated by WP1. Both work packages will generate operational databases, and these will be used for the data gathering efforts performed in WP7. These databases will also be valuable in their own right, and in that capacity they represent example depositories that will be integrated and made universally searchable by the activities of WP6.

WP6 - Integration and Data Access Technologies

This work package involves a series of activities designed to variously tackle the core challenges of inter-resource data integration. This involves enabling processes of data exchange between databases, data integration and synchronisation within central databases or warehouses, and holistic searching across databases. It also concerns the question of how to best manage complex G2P queries, and how to represent the results of any and all G2P database searches. This work package will clearly make extensive use of general integration strategies already employed by Ensembl and others, and it will particularly exploit the products of WP4 and WP5. Aspects of the work package will explore using the concepts and capabilities of the GRID to bring ever-greater sophistication to the emerging network of G2P databases. Furthermore, as a core technology work package, WP6 joins WP4 and WP5 in that its software will be subject to quality assurance measures dictated by WP1.

WP7 - Data Flows

This work package is primarily concerned with the gathering of data to populate the databases constructed by the GEN2PHEN project. The undertaking will span various types of G2P data gathered from many different sources, including receiving direct submissions from the community. To accomplish its goals, the work package will utilise tools and systems built by WP4, WP5, and WP6 as appropriate. These tools will provide the mechanics of the process, but there must also be an engine to drive the data flow, and this will come from the community involvement activities of WP2 and the community federation activities of WP4 and WP5. As GEN2PHEN databases consequently become increasingly populated by WP7 efforts, they will exponentially increase in their utility - exemplifying the main purpose of the GEN2PHEN project.

WP8 - GEN2PHEN Knowledge Centre

This work package is designed to concomitantly endow the GEN2PHEN project with maximal visibility, whilst also providing great added-value utility. The intention is to build a strategic internet portal that is named after our project, providing a virtual ‘Centre of Excellence’ for G2P science. This ‘GEN2PHEN Knowledge Centre’ will encompass many functions. It will act as the project website and present a diary of our events, thereby assisting with dissemination activities of WP9. It will also carry useful expert knowledge for the G2P community (some emerging from various GEN2PHEN work packages, and some originating outside our project), provide a G2P meeting calendar, host G2P chat pages, and make available for download all the public-domain outputs from GEN2PHEN – thus enabling the community involvement work of WP2 and WP9, and the tool deployment work of WP4, WP5, and WP6. Centralised search functions created by WP6 will also be possible to launch directly from this site, and by a related modality it will be possible to deposit comment or updates pertaining to any aspect of the field, even individual database records. We thus intend that the GEN2PHEN Knowledge Centre, via the efforts of this work package, will become a highly popular website that will significantly assist the G2P community and thereby place the GEN2PHEN project centre-stage in that scientific domain.

The GEN2PHEN Knowledge Centre will also constitute the central component of a broader knowledge management strategy. This will encompass both ‘internal’ training for partners (so that expertise and knowledge is effectively shared within the Consortium for maximum efficiency in the development of the work) and ‘external’ training for prospective users of the GEN2PHEN results (to support deployment and adoption of the solutions devised by the project). Both types of training are therefore included in WP8.

WP9 - Dissemination, Use and Future Sustainability

This work package is designed to reinforce and complete the tasks undertaken under WP2 and WP8, thereby helping the project create good relations with, and have a durable impact on, the G2P community. To this end, activities in WP9 encompass both ‘dissemination’ and ‘exploitation’ tasks. The former will focus on publicising the project and its results, according to a well-designed communication plan and ad-hoc developed tools. This will involve synergistic interaction with the GEN2PHEN Knowledge Center developed under WP8, for mutual benefit.

The ‘exploitation’ side of WP9 will involve studying incentive, reward, and business issues, as well as other socio-economic aspects that currently hamper progress in the G2P field and limit recurrent funding. This activity is predicated on the view that technical and scientific developments can provide only part of the solution to current problems; there is also a need to discuss and develop sustainability models that accommodate isolated academic and industrial perspectives into a bigger, inclusive framework. The ideal scenario would harmonise a) the need to quickly and openly translate the scientific and healthcare benefits of G2P activities to the targeted communities and citizens in general, with b) the need to continuously be able to gather sufficient resources to undertake the huge task of creating, developing and maintaining G2P data systems. As such, WP9 will be an ‘end-point’ of the other work packages, and a key component in helping GEN2PHEN achieve its ultimate goal of having a widespread and durable effect on the G2P database domain.

WP10 - Management

While strong scientific leadership can be sufficient to run smaller, individual grants, additional expertise is required in the supervision and monitoring of large-scale, complex projects. Specifically, complementary professional project management is required in such undertakings so that the amount of resources and number of participants are orchestrated along the extended schedule towards the appropriate fulfilment of objectives. Traditional project management standards have in these cases to be flexibly adapted and selected to match the specifics of EC-funded projects, not least because; i) trade-offs between scope, quality, time and cost cannot always be readily solved; ii) there are contractual obligations that limit what can be done and how; iii) there are specific financial and administrative procedures that have the potential to create an excessive overhead; iv) there is a need to create a working team out of independent, geographically scattered institutions. This implies the need for generating adequate work and communication dynamics that support the role of the scientific co-ordination in commanding the project and underpinning the whole work plan, without prejudice of the co-ordinator retaining legal responsibility on specific issues as indicated in the Grant Agreement. It also requires strong financial and legal management that effectively deals with the added flexibility that European projects represent, and the evolving circumstances that a 5-year endeavour will have to face. All of these activities, deeply interrelated with WP1, will be developed under WP10.