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The main objectives of SysMO-DB are to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. We aim to devise a progressive and scalable solution to the data management needs of the SysMO initiative, that:
- maximises the ‘shelf life’ and utility of data generated by SysMO;
- provides an integrated platform for the dissemination ...
Programme: Dummy programme
Public web page: http://www.sysmo-db.org/
Organisms: Lactic Acid Bacteria, Agapornis
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Abstract (Expand)
The torrent of data emerging from the application of new technologies to functional genomics and systems biology can no longer be contained within the traditional modes of data sharing and publication … with the consequence that data is being deposited in, distributed across and disseminated through an increasing number of databases. The resulting fragmentation poses serious problems for the model organism community which increasingly rely on data mining and computational approaches that require gathering of data from a range of sources. In the light of these problems, the European Commission has funded a coordination action, CASIMIR (coordination and sustainability of international mouse informatics resources), with a remit to assess the technical and social aspects of database interoperability that currently prevent the full realization of the potential of data integration in mouse functional genomics. In this article, we assess the current problems with interoperability, with particular reference to mouse functional genomics, and critically review the technologies that can be deployed to overcome them. We describe a typical use-case where an investigator wishes to gather data on variation, genomic context and metabolic pathway involvement for genes discovered in a genome-wide screen. We go on to develop an automated approach involving an in silico experimental workflow tool, Taverna, using web services, BioMart and MOLGENIS technologies for data retrieval. Finally, we focus on the current impediments to adopting such an approach in a wider context, and strategies to overcome them.
Authors: Damian Smedley, Morris A Swertz, Firstname Lastname, Glenn Proctor, Michael Zouberakis, Jonathan Bard, John M Hancock, Paul Schofield
Date Published: 30th Dec 2008
Publication Type: Not specified
PubMed ID: 19112082
Citation:
Created: 5th Jul 2010 at 14:04, Last updated: 24th Mar 2022 at 10:39
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Created: 31st Aug 2011 at 15:14, Last updated: 4th Oct 2011 at 15:24