GEN2PHEN

Genotype-To-Phenotype Databases: A Holistic Solution

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 Obiettivo del progetto (Objective)

'The GEN2PHEN project aims to unify human and model organism genetic variation databases towards increasingly holistic views into Genotype-To-Phenotype (G2P) data, and to link this system into other biomedical knowledge sources via genome browser functionality. The project will establish the technological building-blocks needed for the evolution of today’s diverse G2P databases into a future seamless G2P biomedical knowledge environment. The project will then utilise these elements to construct an operational first-version of that knowledge environment, by the projects end. This will consist of a European-centred but globally-networked hierarchy of bioinformatics GRID-linked databases, tools and standards, all tied into the Ensembl genome browser. The project has the following specific objectives: 1) To analyse the G2P field and thus determine emerging needs and practices; 2) To develop key standards for the G2P database field; 3) To create generic database components, services, and integration infrastructures for the G2P database domain; 4) To create search modalities and data presentation solutions for G2P knowledge; 5) To facilitate the process of populating G2P databases; 6) To build a major G2P internet portal; 7) To deploy GEN2PHEN solutions to the community; 8) To address system durability and long-term financing; 9) To undertake a whole-system utility and validation pilot study GEN2PHEN Consortium members have been selected from a talented pool of European research groups and companies that are interested in the G2P database challenge. Additionally, a few non-EU participants have been included to bring extra capabilities to the initiative. The final constellation is characterised by broad and proven competence, a network of established working relationships, and high-level roles/connections within other significant projects in this domain.'

Introduzione (Teaser)

Over five years, an EU-funded project examined the genotype-phenotype (G2P) data field and enhanced it towards a unified, data-rich, multi-purpose knowledge ecosystem.

Descrizione progetto (Article)

The phenotype lies at the heart of genomic research. The 'Genotype-to-phenotype databases: A holistic solution' (http://www.gen2phen.org (GEN2PHEN)) project has established all the technology necessary better integration, storage and access of G2P data from all independent sources in a holistic way. Additionally, efforts were linked to other biomedical knowledge domains via genome central database and browser functionality.

Underlying the success of the project was the in-depth continual analysis of the field's needs and subsequent alignment of direction. Standards and policy developments covered a wide range of issues. These included ethical principles, data models, exchange formats and gene mutation nomenclature.

The consortium has created modular and interoperable database and data management components, tools and services. Altogether several thousand new gene/disease specific databases and comprehensive genome wide association study databases have been created as well as several commercial systems and tools. Researchers and healthcare users can access the databases as a result of integration through web services with new data aggregation and discovery approaches.

Community resources to facilitate and extend the use of the G2P system included training and support services and initiatives. This ensured platform effectiveness and system sustainability. One core result is a two-way internet-based exchange of information that is accessible at the web portal, http://www.gen2phen.org (G2P Knowledge Centre). Users can upload and download information, data and opinions. GEN2PHEN launched the 'OneSearch' system to allow users to search across the complete G2P public data domain. The recently upgraded site has more than 500 visitors a week and has successfully deployed GEN2PHEN solutions to the community.

In summary, GEN2PHEN organised and innovatively enhanced the G2P data domain using a consolidation of community level efforts. The resulting system can further evolve and develop as new data and inputs become available. The project has effectively merged IT, research and healthcare to produce data that can be applied in the clinic. All key players will benefit including researchers and patients with genetic diseases, particularly those with rare disorders where data is difficult to collate.