Meeting Report: Hackathon-Workshop on Darwin Core and MIxS Standards Alignment (February 2012)

Éamonn Ó Tuama,Hiroshi Mori,Peter Sterk,John Wieczorek,Norman Morrison,Linhuan Wu,Juncai Ma,Dawn Field,Hideaki Sugawara,Pelin Yilmaz,Markus Döring,Gabriel Dröge,Renzo Kottmann,John Deck

doi:10.4056/sigs.3166513

Abstract

The Global Biodiversity Information Facility and the Genomic Standards Consortium convened a joint workshop at the University of Oxford, 27-29 February 2012, with a small group of experts from Europe, USA, China and Japan, to continue the alignment of the Darwin Core with the MIxS and related genomics standards. Several reference mappings were produced as well as test expressions of MIxS in RDF. The use and management of controlled vocabulary terms was considered in relation to both GBIF and the GSC, and tools for working with terms were reviewed. Extensions for publishing genomic biodiversity data to the GBIF network via a Darwin Core Archive were prototyped and work begun on preparing translations of the Darwin Core to Japanese and Chinese. Five genomic repositories were identified for engagement to begin the process of testing the publishing of genomic data to the GBIF network commencing with the SILVA rRNA database.

Highlights

The Global Biodiversity Information Facility [1] (GBIF) Strategic Plan 2012-2016 [2] highlights the need to address the coming challenge and opportunity of making accessible information regarding the estimated 90% of the planet's biodiversity that is still to be discovered and shared, the currency of which will primarily be genomic biodiversity data
The goals of the workshop were to continue the process of aligning the Darwin Core [6] with the MIxS [7] and related genomic standards (e.g. ABCDDNA [8] and WFCC [9]), advance issues on vocabulary/ontology management including multilingual aspects, develop a DwC-A extension for serving genomic data, and identify suitable genomic data repositories with which to engage on connecting to the GBIF network
The alignment of the DwC and GSC MIxS checklists which had begun in previous workshops was completed, and an Resource Description Framework (RDF) expression of the MIxS terms was prepared

Summary

Background

The Global Biodiversity Information Facility [1] (GBIF) Strategic Plan 2012-2016 [2] highlights the need to address the coming challenge and opportunity of making accessible information regarding the estimated 90% of the planet's biodiversity that is still to be discovered and shared, the currency of which will primarily be genomic biodiversity data. To this end, GBIF is collaborating with the Genomic Standards Consortium [3] (GSC) Biodiversity Working Group (GBWG) on common issues, principally around the alignment of standards. Hosted at the Oxford e-Research Centre [5], the workshop brought together a small group of experts from Europe, USA, China and Japan

Purposes of the Meeting

Participants

Vocabulary and Ontology Management

Vocabulary Translation

Genomic repositories