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A standard MIGS/MIMS compliant XML schema: Toward the development of the Genomic Contextual Data Markup Language (GCDML)

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Kottmann,  R.
Microbial Genomics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Lombardot,  T.
Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Gloeckner,  F. O.
Microbial Genomics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Kottmann8.pdf
(Publisher version), 155KB

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Citation

Kottmann, R., Gray, T., Murphy, S., Kagan, L., Kravitz, S., Lombardot, T., et al. (2008). A standard MIGS/MIMS compliant XML schema: Toward the development of the Genomic Contextual Data Markup Language (GCDML). OMICS: A Journal of Integrative Biology, 12(2), 115-121.


Cite as: http://hdl.handle.net/21.11116/0000-0001-CD6C-0
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).