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A standard MIGS/MIMS compliant XML Schema: toward the development of the Genomic Contextual Data markup Language (GCDML)

By Renzo Kottmann, Tanya Gray, Sean Murphy, Leonid Kagan, Saul Kravitz, Thierry Lombardot, Dawn Field and Frank Oliver Glockner

Abstract

The Genomic Contextual Data Markup Language (GCDML) is a core project of the Genomic Standards Consortium (GSC) that implements the “Minimum Information about a Genome Sequence” (MIGS) specification and its extension, the “Minimum Information about a Metagenome Sequence” (MIMS). GCDML is an XML Schema for generating MIGS/MIMS compliant reports for data entry, exchange, and storage. When mature, this sample-centric, strongly-typed schema will provide a diverse set of descriptors for describing the exact origin and processing of a biological sample, from sampling to sequencing, and subsequent analysis. Here we describe the need for such a project, outline design principles required to support the project, and make an open call for participation in defining the future content of GCDML. GCDML is freely available, and can be downloaded, along with documentation, from the GSC Web site (http://gensc.org).\ud \u

Topics: Biology and Microbiology, Data and Information
Year: 2008
DOI identifier: 10.1089/omi.2008.0A10
OAI identifier: oai:nora.nerc.ac.uk:5543
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