The Darwin Core extension for genebanks opens up new opportunities for sharing genebank datasets

Abstract

Abstract. -Darwin Core (DwC) defines a standard set of terms to describe the primary biodiversity data. Primary biodiversity data are data records derived from direct observation of species occurrences in nature or describing specimens in biological collections. The Darwin Core terms can be seen as an extension to the standard Dublin Core metadata terms. The new Darwin Core extension for genebanks declares the additional terms required for describing genebank data sets, and is based on established standards from the plant genetic resources community. The Global Biodiversity Information Facility (GBIF) provides an information infrastructure for biodiversity data including a suite of software tools for data publishing, distributed data access, and the capture of biodiversity data. The Darwin Core extension for genebanks is a key component that provides access for the genebanks and the plant genetic resources community to the GBIF informatics infrastructure including the new toolkits for data exchange. This paper provides one of the first examples and guidelines for how to create extensions to the Darwin Core standard.Keywords. -Darwin Core; Darwin Core extension; GBIF; genebank collections; germplasm; plant genetic resources.There are more than 1750 genebanks distributed all around the world, with more than 130 large and medium-size genebank collections holding more than 10,000 accessions each (FAO, 2010). Each of these genebanks maintains living material of plant genetic resources. New accessions are added to the genebank collections from collecting expeditions and from old cultivars obsolete to the commercial seed trade. The genebank documentation systems are continuously being extended with new accessions and with updated information on existing accessions.The International Treaty on Plant Genetic Resources for Food and Agriculture 1 (ITPGRFA; FAO, 2009, page 29, Article 17.1) calls for building a global information system on plant genetic resources for food and agriculture. Such a system needs to be frequently refreshed with new and updated information from each genebank collection (and other information sources such as inventories of crop wild relatives). With modern information technology, a distributed information system can be designed to allow extracting a snapshot of the decentralized genebank data sets at any time. Moreover, a distributed germplasm information system will make updated germplasm information * Corresponding author; email: dag.endresen@gmail.com. 1 http://www.planttreaty.org/.more easily accessible to plant breeders, crop scientists and other users, thus providing better access also to the plant material. The lack of easy access to germplasm information remains an important bottleneck for utilization of plant genetic resources material . The Global Biodiversity Information Facility (GBIF) 2 has developed a software toolkit for publishing decentralized biodiversity data sets, known as the "Integrated Publishing Toolkit" (GBIF IPT) 3 . It provides a successful example of a software tool ...

Darwin Core: An Evolving Community-Developed Biodiversity Data Standard

“…A careful review was made of Darwin Core and a set of additional terms that did not overlap or conflict with existing Darwin Core terms was proposed to meet the community's needs. The new terms, modeled directly from FAO/IPGRI Multi-Crop Passport Descriptors [45] (2001) and the proposed EPGRIS3 trait data standard for characterization and evaluation data [46] , were expressed and published openly in an XML schema for germplasm data (DwC-germplasm, http://code.google.com/p/darwincore-germplasm/ ) [47] , resulting in the first successfully deployed extension to the Darwin Core Standard.…”

GBIS: the information system of the German Genebank

“…In its present state, GBIS is already an important source of information for various external systems, such as the European search catalogue for plant genetic resources, EURISCO (European Search Catalogue for Plant Genetic Resources of the European Cooperative Programme for Plant Genetic Resources, http://eurisco.ecpgr.org/ , as of 2014-10-14) ( 26 ), the Global Biodiversity Information Facility, GBIF ( http://www.gbif.org/ , as of 2014-10-14) ( 27 ), Mansfeld’s World Database of Agricultural and Horticultural Crops ( http://mansfeld.ipk-gatersleben.de/ , as of 2014-10-14) ( 28 ), the Garlic and Shallot Core Collection (GSCC) ( 29 ), or the Life Science search engine LAILAPS ( 30 ). Access to GBIS data is provided in several ways, e.g.…”

Document or Lose It—On the Importance of Information Management for Genetic Resources Conservation in Genebanks

“…Aggregating platforms and databases for a cross-genebank search for suitable accessions have also been and are being developed. MCPD and Darwin Core [ 51 , 52 ] have been established for the exchange of passport data between genebanks and these platforms. It is only through such standards that it is possible to feed and operate international information systems such as the World Information and Early Warning System on Plant Genetic Resources for Food and Agriculture (WIEWS, ), EURISCO ( ), Genesys ( ) or the Global Biodiversity Information Facility (GBIF, ), which combine the information as homogeneously as possible and make it available beyond the boundaries of the individual genebank collection.…”