ZooKeys 209: No specimen left behind: mass digitization of natural history collections
Centuries of exploration and discovery have documented the diversity of life on Earth. Records of this biodiversity are, for the most part, distributed across varied and distinct natural history collections worldwide. This makes the task of extracting and mobilising the information within these collections an immense challenge.
In this special issue of ZooKeys, 18 papers by 81 authors examine progress and prospects for mass digitising entire natural history collections. These papers provide a snapshot of activity, in what is a fast moving field that is seeing ever-increasing degrees of collaboration across disciplines and between collection-based institutions. Examples of research covered by these articles include a description to efforts digitise 30 million plant, invertebrate and vertebrate specimens at NCB Naturalis in the Netherlands; new scanning and telemicroscopy solutions to digitise the millions of pinned insect specimens held in the Australian National Insect Collection and its European and North American counterparts; citizen science projects being used to crowdsource the transcription of thousands of specimen labels and field notebooks; and new data portals providing central access to millions of biological specimens across Europe.
Many of these projects deal with the unique challenges associated with major collections that have built up over several centuries, with different communities of practices and different user communities. Despite many differences, standards for collection acquisition, preservation and documentation are broadly consistent, meaning that there is sufficient common ground to bring together the enormous amounts of data that are being exposed through mass digitisation efforts. These data will become the new frontier for natural history collection management and research in the next decade.
- Bringing collections out of the dark (Vincent Smith, Vladimir Blagoderov) Pages: 1-6
- Mass digitization of scientific collections: New opportunities to transform the use of biological specimens and underwrite biodiversity science (Reed Beaman, Nico Cellinese) Pages: 7-17
- Five task clusters that enable efficient and effective digitization of biological collections (Gil Nelson, Deborah Paul, Greg Riccardi, Austin Mast) Pages: 19-45
- OpenUp! Creating a cross-domain pipeline for natural history data (Walter Berendsohn, Anton Güntsch) Pages: 47-54
- The US Virtual Herbarium: working with individual herbaria to build a national resource (Mary Barkworth, Zack Murrell) Pages: 55-73
- The development of a digitising service centre for natural history collections (Riitta Tegelberg, Jaana Haapala, Tero Mononen, Mika Pajari, Hannu Saarenmaa) Pages: 75-86
- 'From Pilot to production': Large Scale Digitisation project at Naturalis Biodiversity Center (Jon Peter Oever, Marc Gofferjé) Pages: 87-92
- Developing integrated workflows for the digitisation of herbarium specimens using a modular and scalable approach (Elspeth Haston, Robert Cubey, Martin Pullan, Hannah Atkins, David Harris) Pages: 93-102
- Increasing the efficiency of digitization workflows for herbarium specimens (Melissa Tulig, Nicole Tarnowsky, Michael Bevans, Anthony Kirchgessner, Barbara Thiers) Pages: 103-113
- Results and insights from the NCSU Insect Museum GigaPan project (Matthew Bertone, Robert Blinn, Tanner Stanfield, Kelly Dew, Katja Seltmann, Andrew Deans) Pages: 115-132
- No specimen left behind: industrial scale digitization of natural history collections (Vladimir Blagoderov, Ian Kitching, Laurence Livermore, Thomas Simonsen, Vincent Smith) Pages: 133-146
- Whole-drawer imaging for digital management and curation of a large entomological collection (Beth Mantle, John LaSalle, Nicole Fisher) Pages: 147-163
- InvertNet: a new paradigm for digital access to invertebrate collections (Chris Dietrich, John Hart, David Raila, Umberto Ravaioli, Nahil Sobh, Omar Sobh, Chris Taylor) Pages: 165-181
- DScan – a high-performance digital scanning system for entomological collections (Stefan Schmidt, Michael Balke, Stefan Lafogler) Pages: 183-191
- Nomenclatural benchmarking: the roles of digital typification and telemicroscopy (Quentin Wheeler, Thierry Bourgoin, Jonathan Coddington, Timothy Gostony, Andrew Hamilton, Roy Larimer, Andrew Polaszek, Michael Schauff, Alma Solis) Pages: 193-202
- Image based Digitisation of Entomology Collections: Leveraging volunteers to increase digitization capacity (Paul Flemons, Penny Berents) Pages: 203-217
- The notes from nature tool for unlocking biodiversity records from museum records through citizen science (Andrew Hill, Robert Guralnick, Arfon Smith, Andrew Sallans, Rosemary Gillespie, Michael Denslow, Joyce Gross, Zack Murrell, Tim Conyers, Peter Oboyski, Joan Ball, Andrea Thomer, Robert Prys-Jones, Javier de la Torre, Patrick Kociolek, Lucy Fortson) Pages: 219-233
- From documents to datasets: A MediaWiki-based method of annotating and extracting species observations in century-old field notebooks (Andrea Thomer, Gaurav Vaidya, Robert Guralnick, David Bloom, Laura Russell) Pages: 235-253
- Integrating specimen databases and revisionary systematics (Randall Schuh) Pages: 255-267
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