The Global Genome Biodiversity Network (GGBN) Data Standard specification

Abstract

Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs to be concise and consistent in today’s ever-increasing bioinformatic era, for complementary data aggregators to easily map databases to one another. In order to facilitate exchange of information on genomic samples and their derived data, the Global Genome Biodiversity Network (GGBN) Data Standard is intended to provide a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way. The new data standard presented here build upon existing standards commonly used within the community extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard will reveal and democratize the hidden contents of biodiversity biobanks, for the convenience of everyone in the wider biobanking community. Technical tools exist for data providers to easily map their databases to the standard.Database URL: http://terms.tdwg.org/wiki/GGBN_Data_Standard

Taxonomy and phylogeny of mud owls (Annelida: Sternaspidae), including a new synonymy and new records from the Southern Ocean, North East Atlantic Ocean and Pacific Ocean: challenges in morphological delimitation

“…Darwin Core (Wieczorek et al 2012) and the GGBN data standard (Droege et al 2016) were used in the management and transfer of specimen and derived sample data between the central museum collections database, a molecular collections database and external repositories (e.g. GenBank, WoRMS, OBIS, GBIF, GGBN, ZooBank).…”

The Expectations and Challenges of Wildlife Disease Research in the Era of Genomics: Forecasting with a Horizon Scan-like Exercise

“…org, Williams 2004), pathological specimens from diseased and also healthy wildlife are less common (although see González et al 2017 for a good example in fish). These resources, along with sufficient metadata (Droege et al 2016), are critical for the comparison of future samples with current specimens to evaluate pathogen prevalence and association with disease. Likewise, storage of various types of genomic data, such as sequence and expression data, in public databases (Duke and Porter 2013) could encourage and facilitate replication, follow-up studies, and development of results into application.…”

A reference library for the identification of Canadian invertebrates: 1.5 million DNA barcodes, voucher specimens, and genomic samples

“…The DNA extracts derived from the 1,500,003 barcoded specimens are held in the DNA Archive at the CBG, either within -80°C freezers or dried in a trehalose-based preservative and held in -20°C freezers. The specimen data and DNA storage information were submitted to the Global Genome Biodiversity Network (GGBN) Data Portal [65] following the GGBN Data Standard [66]. The upload of CBG's DNA extract data added 566 families and 4,287 genera to GGBN, increasing the number of families and genera by 22% and 30%, respectively (based on an API download of Animalia records from GGBN in May 2019).…”