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News from the open access movement

Monday, June 18, 2007

OS tool for sharing OA data

Charles G. Howes and Leonard J. Foster, PrestOMIC, an open source application for dissemination of proteomic datasets by individual laboratories, Proteome Science, June 6, 2007.  Abstract:

Background.  Technological advances in mass spectrometry and other detection methods are leading to larger and larger proteomics datasets. However, when papers describing such information are published the enormous volume of data can typically only be provided as supplementary data in a tabular form through the journal website. Several journals in the proteomics field, together with the Human Proteome Organization's (HUPO) Proteomics Standards Initiative and institutions such as the Institute for Systems Biology are working towards standardizing the reporting of proteomics data, but just defining standards is only a means towards an end for sharing data. Data repositories such as and the Open Proteomics Database allow for public access to proteomics data but provide little, if any, interpretation.

Results & conclusion.  Here we describe PrestOMIC, an open source application for storing mass spectrometry-based proteomic data in a relational database and for providing a user-friendly, searchable and customizable browser interface to share one's data with the scientific community. The underlying database and all associated applications are built on other existing open source tools, allowing PrestOMIC to be modified as the data standards evolve. We then use PrestOMIC to present a recently published dataset from our group through our website.