RCN4GSC Workshop Report : managing data at the interface of biodiversity and (meta)genomics, March 2011

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Robbins, Robert J.
Amaral-Zettler, Linda A.
Bik, Holly M.
Blum, Stan D.
Edwards, James
Field, Dawn
Garrity, George M.
Gilbert, Jack A.
Kottmann, Renzo
Krishtalka, Leonard
Lapp, Hilmar
Lawrence, Carolyn
Morrison, Norman
O Tuama, Eamonn
Parr, Cynthia Sims
San Gil, Inigo
Schindel, David
Schriml, Lynn M.
Vieglas, David
Wooley, John
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Building on the planning efforts of the RCN4GSC project, a workshop was convened in San Diego to bring together experts from genomics and metagenomics, biodiversity, ecology, and bioinformatics with the charge to identify potential for positive interactions and progress, especially building on successes at establishing data standards by the GSC and by the biodiversity and ecological communities. Until recently, the contribution of microbial life to the biomass and biodiversity of the biosphere was largely overlooked (because it was resistant to systematic study). Now, emerging genomic and metagenomic tools are making investigation possible. Initial research findings suggest that major advances are in the offing. Although different research communities share some overlapping concepts and traditions, they differ significantly in sampling approaches, vocabularies and workflows. Likewise, their definitions of ‘fitness for use’ for data differ significantly, as this concept stems from the specific research questions of most importance in the different fields. Nevertheless, there is little doubt that there is much to be gained from greater coordination and integration. As a first step toward interoperability of the information systems used by the different communities, participants agreed to conduct a case study on two of the leading data standards from the two formerly disparate fields: (a) GSC’s standard checklists for genomics and metagenomics and (b) TDWG’s Darwin Core standard, used primarily in taxonomy and systematic biology.
© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Standards in Genomic Sciences 7 (2012): 159-165, doi:10.4056/sigs.3156511.
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Standards in Genomic Sciences 7 (2012): 159-165
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