scholarly journals Data Attribution from Download to Publication

2018 ◽  
Vol 2 ◽  
pp. e26060
Author(s):  
Pamela Soltis

Digitized natural history data are enabling a broad range of innovative studies of biodiversity. Large-scale data aggregators such as Global Biodiversity Information facility (GBIF) and Integrated Digitized Biocollections (iDigBio) provide easy, global access to millions of specimen records contributed by thousands of collections. A developing community of eager users of specimen data – whether locality, image, trait, etc. – is perhaps unaware of the effort and resources required to curate specimens, digitize information, capture images, mobilize records, serve the data, and maintain the infrastructure (human and cyber) to support all of these activities. Tracking of specimen information throughout the research process is needed to provide appropriate attribution to the institutions and staff that have supplied and served the records. Such tracking may also allow for annotation and comment on particular records or collections by the global community. Detailed data tracking is also required for open, reproducible science. Despite growing recognition of the value and need for thorough data tracking, both technical and sociological challenges continue to impede progress. In this talk, I will present a brief vision of how application of a DOI to each iteration of a data set in a typical research project could provide attribution to the provider, opportunity for comment and annotation of records, and the foundation for reproducible science based on natural history specimen records. Sociological change – such as journal requirements for data deposition of all iterations of a data set – can be accomplished using community meetings and workshops, along with editorial efforts, as were applied to DNA sequence data two decades ago.

2019 ◽  
Author(s):  
Jeremy R. deWaard ◽  
Sujeevan Ratnasingham ◽  
Evgeny V. Zakharov ◽  
Alex V. Borisenko ◽  
Dirk Steinke ◽  
...  

AbstractThe reliable taxonomic identification of organisms through DNA sequence data requires a well parameterized library of curated reference sequences. However, it is estimated that just 15% of described animal species are represented in public sequence repositories. To begin to address this deficiency, we provide DNA barcodes for 1,500,003 animal specimens collected from 23 terrestrial and aquatic ecozones at sites across Canada, a nation that comprises 7% of the planet’s land surface. In total, 14 phyla, 43 classes, 163 orders, 1123 families, 6186 genera, and 64,264 Barcode Index Numbers (BINs; a proxy for species) are represented. Species-level taxonomy was available for 38% of the specimens, but higher proportions were assigned to a genus (69.5%) and a family (99.9%). Voucher specimens and DNA extracts are archived at the Centre for Biodiversity Genomics where they are available for further research. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, and the Global Genome Biodiversity Network Data Portal.


2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Jeremy R. deWaard ◽  
Sujeevan Ratnasingham ◽  
Evgeny V. Zakharov ◽  
Alex V. Borisenko ◽  
Dirk Steinke ◽  
...  

AbstractThe reliable taxonomic identification of organisms through DNA sequence data requires a well parameterized library of curated reference sequences. However, it is estimated that just 15% of described animal species are represented in public sequence repositories. To begin to address this deficiency, we provide DNA barcodes for 1,500,003 animal specimens collected from 23 terrestrial and aquatic ecozones at sites across Canada, a nation that comprises 7% of the planet’s land surface. In total, 14 phyla, 43 classes, 163 orders, 1123 families, 6186 genera, and 64,264 Barcode Index Numbers (BINs; a proxy for species) are represented. Species-level taxonomy was available for 38% of the specimens, but higher proportions were assigned to a genus (69.5%) and a family (99.9%). Voucher specimens and DNA extracts are archived at the Centre for Biodiversity Genomics where they are available for further research. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, and the Global Genome Biodiversity Network Data Portal.


2009 ◽  
Vol 28 (11) ◽  
pp. 2737-2740
Author(s):  
Xiao ZHANG ◽  
Shan WANG ◽  
Na LIAN

2007 ◽  
Vol 3 ◽  
pp. 193-197 ◽  
Author(s):  
Kou Amano ◽  
Hiroaki Ichikawa ◽  
Hidemitsu Nakamura ◽  
Hisataka Numa ◽  
Kaoru Fukami-Kobayashi ◽  
...  

Author(s):  
Katharine Barker ◽  
Jonas Astrin ◽  
Gabriele Droege ◽  
Jonathan Coddington ◽  
Ole Seberg

Most successful research programs depend on easily accessible and standardized research infrastructures. Until recently, access to tissue or DNA samples with standardized metadata and of a sufficiently high quality, has been a major bottleneck for genomic research. The Global Geonome Biodiversity Network (GGBN) fills this critical gap by offering standardized, legal access to samples. Presently, GGBN’s core activity is enabling access to searchable DNA and tissue collections across natural history museums and botanic gardens. Activities are gradually being expanded to encompass all kinds of biodiversity biobanks such as culture collections, zoological gardens, aquaria, arboreta, and environmental biobanks. Broadly speaking, these collections all provide long-term storage and standardized public access to samples useful for molecular research. GGBN facilitates sample search and discovery for its distributed member collections through a single entry point. It stores standardized information on mostly geo-referenced, vouchered samples, their physical location, availability, quality, and the necessary legal information on over 50,000 species of Earth’s biodiversity, from unicellular to multicellular organisms. The GGBN Data Portal and the GGBN Data Standard are complementary to existing infrastructures such as the Global Biodiversity Information Facility (GBIF) and International Nucleotide Sequence Database (INSDC). Today, many well-known open-source collection management databases such as Arctos, Specify, and Symbiota, are implementing the GGBN data standard. GGBN continues to increase its collections strategically, based on the needs of the research community, adding over 1.3 million online records in 2018 alone, and today two million sample data are available through GGBN. Together with Consortium of European Taxonomic Facilities (CETAF), Society for the Preservation of Natural History Collections (SPNHC), Biodiversity Information Standards (TDWG), and Synthesis of Systematic Resources (SYNTHESYS+), GGBN provides best practices for biorepositories on meeting the requirements of the Nagoya Protocol on Access and Benefit Sharing (ABS). By collaboration with the Biodiversity Heritage Library (BHL), GGBN is exploring options for tagging publications that reference GGBN collections and associated specimens, made searchable through GGBN’s document library. Through its collaborative efforts, standards, and best practices GGBN aims at facilitating trust and transparency in the use of genetic resources.


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