Award details

Omics Data Standards: synergy and implementations

Reference	BB/E025080/1
Principal Investigator / Supervisor	Professor Susanna Sansone
Co-Investigators / Co-Supervisors	Dr Alvis Brazma, Dr Dawn Field, Mr Nigel Hardy, Mr Henning Hermjakob, Professor Andrew Jones, Dr Nicolas Le Novere, Dr Norman Morrison, Professor Norman Paton, Dr Philippe Rocca-Serra, Dr Christopher Taylor
Institution	EMBL - European Bioinformatics Institute
Department	Microarray Group
Funding type	Research
Value (£)	103,045
Status	Completed
Type	Research Grant
Start date	01/06/2007
End date	31/05/2010
Duration	36 months

Abstract

This application is guided by the requirements of the RSBI, a working group bringing together several biomedical and environmental communities to tackle the challenges associated with reporting complex investigations employing multiple omics' technologies. RSBI works under the assumption that no one group or community can solve the challenges of developing reporting standards for the functional genomics domain. Although established MGED Society (e.g microarray-based transcriptomics) umbrella, RSBI has always worked in the wider functional genomics context, through extensive liaisons with other standard efforts such as the PSI, the MSI and the GSC. There is a generally accepted view that the need to harmonise and consolidate reporting standards is unarguable. From a technical perspective, it will be necessary to remove redundancies and fill the gaps between the domains covered by checklists, exchange formats and terminologies. These are difficult but not insurmountable tasks and our workshops aim to facilitate synergistic activities, by bringing together the key developers of the grass roots communities to focus on the: - MIcheck project, promoting gradual integration of minimal information checklists - FuGE project, providing a model of common components for exchange format development - OBI project, delivering an set of common terms to support semantic integration Ultimately, data reporting standards create the basis for developing data sharing environments. A crucial outcome of our workshops is set of common practice descriptions and documentation of progress in a clear and understandable manner for the relevant target communities (e.g. developers) so that the standards can be widely used once reaching a mature stage. The development of data standards is an iterative process and gaining community buy-in can be also a long process. We are confident that these workshops will play a crucial role in the developmental phase and in the consensus-building process.

Summary

The marriage of conventional biomedical and environmental research with transcriptomics, proteomics and metabolomics technologies has created not only opportunities, but also new informatics challenges to biologists and bioinformaticians. We require new approaches to describe, store and exchange these - information intensive investigations, so that the datasets can be properly analyzed, compared and integrated. We need reporting standards agreed upon by a community for describing the way to report, for publication and dissemination, the results of a particular investigation and for making the research more accessible for the benefit of the wider scientific community. Data reporting standards, the basic pillar of data sharing, include: - Checklists, outlining the minimal requirements that should be reported - Syntax, defining the transmission formats that facilitate the exchange of the information - Semantics, adding the interpretive layer to the information. Given the high value of functional genomics and system biology information, standardization activities have moved from the fringes to centre-stage. Several grass roots, community-driven, international data standardization activities are underway to define standard reporting structure for one particular omics technologies (e.g. transcriptomics, proteomics). Discipline-specific initiatives, however, remain within each given discipline and as a consequence of this the overall standardization effort fragments, resulting in unnecessary duplication of effort, and the development of different semantics and syntaxes thereby limiting the potential for data exchange. Fortunately, there is a generally accepted view that concerted efforts are required throughout the functional genomics and reaching out to the system biology. Synergistic activities have begun already to remove redundancy and foster harmonisation and consolidation of reporting standards. By contrast, the sociological barriers can be quite challenging, mandating extensive liaison amongst communities. Also the time invested in these activities is often severely limited due to lack of resources. Face-to-face developers' workshops are critical to create consensus. Unfortunately it is very difficult to hold such workshops when no central fund exits to support the projects and when developers participate on a volunteer base, paying their own travel and accommodation expenses from wherever they can find the funds. In this proposal we are seeking funding to organize a series of hands-on workshops to ensure the coordinated development of data reporting standards. We propose to focus on the three thematic projects and with several environmental communities - both from the UK and around the globe - create the basis for developing data sharing environments, with the use cases from several biomedical and environmental communities.

Committee	Closed Committee - Engineering & Biological Systems (EBS)
Research Topics	Technology and Methods Development
Research Priority	X – Research Priority information not available
Research Initiative	Tools and Resources Development Fund (TRDF) [2006-2015]
Funding Scheme	X – not Funded via a specific Funding Scheme

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