RCN4GSC Workshop Report: Modeling a Testbed for Managing Data at the Interface of Biodiversity and (Meta)Genomics, April 2011

Éamonn Ó Tuama,Neil Davies,Robert J. Robbins,Inigo San Gil,Guy Cochrane,Norman Morrison,Peter Dawyndt,Renzo Kottmann,John Wooley,Leonard (Kris) Krishtalka

doi:10.4056/sigs.3146509

Abstract

At the GSC11 meeting (4-6 April 2011, Hinxton, England, the GSC’s genomic biodiversity working group (GBWG) developed an initial model for a data management testbed at the interface of biodiversity with genomics and metagenomics. With representatives of the Global Biodiversity Information Facility (GBIF) participating, it was agreed that the most useful course of action would be for GBIF to collaborate with the GSC in its ongoing GBWG workshops to achieve common goals around interoperability/data integration across (meta)-genomic and species level data. It was determined that a quick comparison should be made of the contents of the Darwin Core (DwC) and the GSC data checklists, with a goal of determining their degree of overlap and compatibility. An ad-hoc task group lead by Renzo Kottman and Peter Dawyndt undertook an initial comparison between the Darwin Core (DwC) standard used by the Global Biodiversity Information Facility (GBIF) and the MIxS checklists put forward by the Genomic Standards Consortium (GSC). A term-by-term comparison showed that DwC and GSC concepts complement each other far more than they compete with each other. Because the preliminary analysis done at this meeting was based on expertise with GSC standards, but not with DwC standards, the group recommended that a joint meeting of DwC and GSC experts be convened as soon as possible to continue this joint assessment and to propose additional work going forward.

Highlights

In March of 2011, a planning meeting on managing data at the interface between biodiversity andgenomics was held at the University of California at San Diego [1]
The Global Biodiversity Information Facility (GBIF) call for a white paper on genomic level biodiversity observational data was again discussed and it was agreed that the most useful course of action would be for GBIF to collaborate with the Genomic Standards Consortium (GSC) in its ongoing Genomic Biodiversity Working Group (GBWG) workshops to achieve common goals around interoperability/data integration across-genomic and species level data
An ad-hoc task group lead by Renzo Kottman and Peter Dawyndt undertook an initial comparison between the Darwin Core (DwC) standard used by the Global Biodiversity Information Facility (GBIF) and the MIxS checklists put forward by the Genomic Standards Consortium (GSC) and implemented in GCDML

Summary

Background

In March of 2011, a planning meeting on managing data at the interface between biodiversity and (meta)genomics was held at the University of California at San Diego [1]. The recommendations were presented in plenary session of the full GSC meeting, discussed at length in breakout sessions of the GSC Genomic Biodiversity Working Group (GBWG). RCN4GSC Workshop Report paper on the publishing and discovery of, and access to, primary biodiversity data in the form of genomic level observations” [2] with a submission date in March; this request was later withdrawn. The purposes of the meeting were to present the GBWG planning-meeting recommendations to the full GSC plenary session for input, and to hold GBWG breakout sessions to consider the recommendations in depth and form task groups as necessary

Participants

Conclusions