Byte Size Biology » genomics - 1 views
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etadata is the “data about the data”: all the habitat data, SOPs and abiotic data that is in dire need of the standardization Kyrpides writes about.
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Metadata is the “data about the data”: all the habitat data, SOPs and abiotic data that is in dire need of the standardization Kyrpides writes about.
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In 2005 the Genomics Standards Consortium was formed to address this problem. Renzo Kottman from the Max-Planck Institute for Marine Microbiology in Bremen, Germany talked about software development within the GSC, and specifically about his own project: the Genomic Contextual Data Markup Language, or GCDML. GCDML is an XML-based standard for describing everything associated with a genomic or a metagenomic sample: where it was taken from , under what conditions, which protocols were used to extract, sequence, assemble, finish and analyze the metagenome.
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Standards organizations are community desktops waiting to happen. More specifically, not reference to "protocols" with a five step process similar to our technology transfer framework. If we could get a copy of this protocol we could develop a diagram and a community site around the four "research cycle" stages: extract, sequence, assemble, finish and analyze. What we need is a similar structure for the tissue sourcing process. Scott, can you think of who might have such a protocol documented?
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Excerpt from further down the article that Steve sent via email. Note the embedded presentation on "Software development by the Genomics Standards Consortium."
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wow.. this page is a tour de force for bio science info issues ... and I very much like where you are going with the extract, sequence, assemble, finish and analyze.. pattern.. similar to the NIST model we are using at NERC.... hopefully