The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details

Nicole Washington(Ontario Institute for Cancer Research), Eo Stinson(Ontario Institute for Cancer Research), Marc D. Perry(Lawrence Berkeley National Laboratory), Peter Ruzanov(University of Cambridge), Sergio Contrino(Lawrence Berkeley National Laboratory), Richard Smith(Ontario Institute for Cancer Research), Zheng Zha(University of Cambridge), Rachel Lyne(Ontario Institute for Cancer Research), Adrian R. Carr(Ontario Institute for Cancer Research), Paul Lloyd(Ontario Institute for Cancer Research), Ellen Kephart(University of Cambridge), Sheldon McKay(Lawrence Berkeley National Laboratory), Gos Micklem(Ontario Institute for Cancer Research), Lincoln Stein(University of Cambridge), Suzanna Lewis(Lawrence Berkeley National Laboratory)
Database
January 1, 2011
10.1093/database/bar023
Cited by 34Open Access
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Abstract

The model organism Encyclopedia of DNA Elements (modENCODE) project is a National Human Genome Research Institute (NHGRI) initiative designed to characterize the genomes of Drosophila melanogaster and Caenorhabditis elegans. A Data Coordination Center (DCC) was created to collect, store and catalog modENCODE data. An effective DCC must gather, organize and provide all primary, interpreted and analyzed data, and ensure the community is supplied with the knowledge of the experimental conditions, protocols and verification checks used to generate each primary data set. We present here the design principles of the modENCODE DCC, and describe the ramifications of collecting thorough and deep metadata for describing experiments, including the use of a wiki for capturing protocol and reagent information, and the BIR-TAB specification for linking biological samples to experimental results. modENCODE data can be found at http://www.modencode.org.

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