title: The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details.
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.
authors.affiliation: Lawrence Berkeley National Laboratory, Genomics Division, 1 Cyclotron Road MS64-121, Berkeley, CA 94720, USA.
authors.forename: Nicole L
authors.initials: NL
authors.lastname: Washington
authors.forename: E O
authors.initials: EO
authors.lastname: Stinson
authors.forename: Marc D
authors.initials: MD
authors.lastname: Perry
authors.forename: Peter
authors.initials: P
authors.lastname: Ruzanov
authors.forename: Sergio
authors.initials: S
authors.lastname: Contrino
authors.forename: Richard
authors.initials: R
authors.lastname: Smith
authors.forename: Zheng
authors.initials: Z
authors.lastname: Zha
authors.forename: Rachel
authors.initials: R
authors.lastname: Lyne
authors.forename: Adrian
authors.initials: A
authors.lastname: Carr
authors.forename: Paul
authors.initials: P
authors.lastname: Lloyd
authors.forename: Ellen
authors.initials: E
authors.lastname: Kephart
authors.forename: Sheldon J
authors.initials: SJ
authors.lastname: McKay
authors.forename: Gos
authors.initials: G
authors.lastname: Micklem
authors.forename: Lincoln D
authors.initials: LD
authors.lastname: Stein
authors.forename: Suzanna E
authors.initials: SE
authors.lastname: Lewis
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics; D004247:DNA / Q000235:genetics; D030541:Databases, Genetic; D004331:Drosophila melanogaster / Q000235:genetics; D016678:Genome; D023281:Genomics / Q000379:methods*; D006801:Humans; D020407:Internet; D012984:Software
chemical_list: D004247:DNA