scholarly journals Digitization and the Future of Natural History Collections

BioScience ◽  
2020 ◽  
Vol 70 (3) ◽  
pp. 243-251 ◽  
Author(s):  
Brandon P Hedrick ◽  
J Mason Heberling ◽  
Emily K Meineke ◽  
Kathryn G Turner ◽  
Christopher J Grassa ◽  
...  

Abstract Natural history collections (NHCs) are the foundation of historical baselines for assessing anthropogenic impacts on biodiversity. Along these lines, the online mobilization of specimens via digitization—the conversion of specimen data into accessible digital content—has greatly expanded the use of NHC collections across a diversity of disciplines. We broaden the current vision of digitization (Digitization 1.0)—whereby specimens are digitized within NHCs—to include new approaches that rely on digitized products rather than the physical specimen (Digitization 2.0). Digitization 2.0 builds on the data, workflows, and infrastructure produced by Digitization 1.0 to create digital-only workflows that facilitate digitization, curation, and data links, thus returning value to physical specimens by creating new layers of annotation, empowering a global community, and developing automated approaches to advance biodiversity discovery and conservation. These efforts will transform large-scale biodiversity assessments to address fundamental questions including those pertaining to critical issues of global change.

2019 ◽  
Author(s):  
Brandon Hedrick ◽  
Mason Heberling ◽  
Emily Meineke ◽  
Kathryn Turner ◽  
Christopher Grassa ◽  
...  

Natural history collections (NHCs) are the foundation of historical baselines for assessing anthropogenic impacts on biodiversity. Along these lines, the online mobilization of specimens via digitization–the conversion of specimen data into accessible digital content–has greatly expanded the use of NHC collections across a diversity of disciplines. We broaden the current vision of digitization (Digitization 1.0)–whereby specimens are digitized within NHCs–to include new approaches that rely on digitized products rather than the physical specimen (Digitization 2.0). Digitization 2.0 builds upon the data, workflows, and infrastructure produced by Digitization 1.0 to create digital-only workflows that facilitate digitization, curation, and data linkages, thus returning value to physical specimens by creating new layers of annotation, empowering a global community, and developing automated approaches to advance biodiversity discovery and conservation. These efforts will transform large-scale biodiversity assessments to address fundamental questions including those pertaining to critical modern issues of global change.


Author(s):  
Brandon Hedrick ◽  
Mason Heberling ◽  
Emily Meineke ◽  
Kathryn Turner ◽  
Christopher Grassa ◽  
...  

Natural history collections (NHCs) are the foundation of historical baselines for assessing anthropogenic impacts on biodiversity. Along these lines, the online mobilization of specimens via digitization–the conversion of specimen data into accessible digital content–has greatly expanded the use of NHC collections across a diversity of disciplines. We broaden the current vision of digitization (Digitization 1.0)–whereby specimens are digitized within NHCs–to include new approaches that rely on digitized products rather than the physical specimen (Digitization 2.0). Digitization 2.0 builds upon the data, workflows, and infrastructure produced by Digitization 1.0 to create digital-only workflows that facilitate digitization, curation, and data linkages, thus returning value to physical specimens by creating new layers of annotation, empowering a global community, and developing automated approaches to advance biodiversity discovery and conservation. These efforts will transform large-scale biodiversity assessments to address fundamental questions including those pertaining to critical modern issues of global change.


2018 ◽  
Vol 374 (1763) ◽  
pp. 20170405 ◽  
Author(s):  
Heather M. Kharouba ◽  
Jayme M. M. Lewthwaite ◽  
Rob Guralnick ◽  
Jeremy T. Kerr ◽  
Mark Vellend

Over the past two decades, natural history collections (NHCs) have played an increasingly prominent role in global change research, but they have still greater potential, especially for the most diverse group of animals on Earth: insects. Here, we review the role of NHCs in advancing our understanding of the ecological and evolutionary responses of insects to recent global changes. Insect NHCs have helped document changes in insects' geographical distributions, phenology, phenotypic and genotypic traits over time periods up to a century. Recent work demonstrates the enormous potential of NHCs data for examining insect responses at multiple temporal, spatial and phylogenetic scales. Moving forward, insect NHCs offer unique opportunities to examine the morphological, chemical and genomic information in each specimen, thus advancing our understanding of the processes underlying species’ ecological and evolutionary responses to rapid, widespread global changes. This article is part of the theme issue ‘Biological collections for understanding biodiversity in the anthropocene’.


2021 ◽  
Author(s):  
DA S Park ◽  
Xiao Feng ◽  
Shinobu Akiyama ◽  
Marlina Ardiyani ◽  
Neida Avendano ◽  
...  

Herbarium collections shape our understanding of the world's flora and are crucial for addressing global change and biodiversity conservation. The formation of such natural history collections, however, are not free from sociopolitical issues of immediate relevance. Despite increasing efforts addressing issues of representation and colonialism in natural history collections, herbaria have received comparatively less attention. While it has been noted that the majority of plant specimens are housed in the global North, the extent of this disparity has not been rigorously quantified to date. Here, by analyzing over 85 million specimen records and surveying herbaria across the globe, we assess the colonial legacy of botanical collections and how we may move towards a more inclusive future. We demonstrate that colonial exploitation has contributed to an inverse relationship between where plant biodiversity exists in nature and where it is housed in herbaria. Such disparities persist in herbaria across physical and digital realms despite overt colonialism having ended over half a century ago, suggesting ongoing digitization and decolonization efforts have yet to alleviate colonial-era discrepancies. We emphasize the need for acknowledging the inconvenient history of herbarium collections and the implementation of a more equitable, global paradigm for their collection, curation, and use.


2015 ◽  
Vol 12 (13) ◽  
pp. 4085-4098 ◽  
Author(s):  
R. Aguilera ◽  
R. Marcé ◽  
S. Sabater

Abstract. Attributing changes in river water quality to specific factors is challenging because multiple factors act at different temporal and spatial scales, and it often requires examining long-term series of continuous data. Data consistency is sometimes hindered by the lack of observations of relevant water quality variables and the low and uneven sampling frequency that characterizes many water quality monitoring schemes. Nitrate and dissolved phosphate concentration time series (1980–2011) from 50 sampling stations across a large Mediterranean river basin were analyzed to disentangle the role of hydrology, land-use practices, and global climatic phenomena on the observed nutrient patterns, with the final aim of understanding how the different aspects of global change affected nutrient dynamics in the basin. Dynamic factor analysis (DFA) provided the methodological framework to extract underlying common patterns in nutrient time series with missing observations. Using complementary methods such as frequency and trend analyses, we sought to further characterize the common patterns and identify the drivers behind their variability across time and space. Seasonal and other cyclic patterns were identified as well as trends of increase or decrease of nutrient concentration in particular areas of the basin. Overall, the impact of global change, which includes both climate change and anthropogenic impacts, on the dynamics of nitrate concentration across the study basin was found to be a multifaceted process including regional and global factors, such as climatic oscillations and agricultural irrigation practices, whereas impacts on phosphate concentration seemed to depend more on local impacts, such as urban and industrial activities, and less on large-scale factors.


ZooKeys ◽  
2012 ◽  
Vol 209 ◽  
pp. 75-86 ◽  
Author(s):  
Riitta Tegelberg ◽  
Jaana Haapala ◽  
Tero Mononen ◽  
Mika Pajari ◽  
Hannu Saarenmaa

Digitarium is a joint initiative of the Finnish Museum of Natural History and the University of Eastern Finland. It was established in 2010 as a dedicated shop for the large-scale digitisation of natural history collections. Digitarium offers service packages based on the digitisation process, including tagging, imaging, data entry, georeferencing, filtering, and validation. During the process, all specimens are imaged, and distance workers take care of the data entry from the images. The customer receives the data in Darwin Core Archive format, as well as images of the specimens and their labels. Digitarium also offers the option of publishing images through Morphbank, sharing data through GBIF, and archiving data for long-term storage. Service packages can also be designed on demand to respond to the specific needs of the customer. The paper also discusses logistics, costs, and intellectual property rights (IPR) issues related to the work that Digitarium undertakes.


2019 ◽  
Vol 100 (5) ◽  
pp. 1678-1689 ◽  
Author(s):  
Robert C Lonsinger ◽  
David Daniel ◽  
Jennifer R Adams ◽  
Lisette P Waits

AbstractSpecimens from natural history collections (NHCs) are increasingly being used for genetic studies and can provide information on extinct populations, facilitate comparisons of historical and contemporary populations, produce baseline data before environmental changes, and elucidate patterns of change. Destructive sampling for DNA may be in disagreement with NHC goals of long-term care and maintenance. Differentiating quality among sample sources can direct destructive sampling to the source predicted to yield the highest quality DNA and most reliable data, potentially reducing damage to specimens, laboratory costs, and genotyping errors. We used the kit fox (Vulpes macrotis) as a model species and evaluated the quality and reliability of genetic data obtained from carnivoran specimens via three different sample sources: cranial bones, nasal bones, and toepads. We quantified variation in microsatellite amplification success and genotyping error rates and assessed the reliability of source-specific genic data. Toepads had the highest amplification success rates and lowest genotyping error rates. Shorter loci had higher amplification success and lower allelic dropout rates than longer loci. There were substantial differences in the reliability of resulting multilocus genotypes. Toepads produced the most reliable data, required the fewest replicates, and therefore, had the lowest costs to achieve reliable data. Our results demonstrate that the quality of DNA obtained from specimens varies by sample source and can inform NHCs when evaluating requests for destructive sampling. Our results suggest that prior to large-scale specimen sampling, researchers should conduct pilot studies to differentiate among source-specific data reliability, identify high performing loci, reduce costs of analyses, and minimize destructive sampling.


Author(s):  
Ian Owens ◽  
Kirk Johnson

The world's natural history collections represent a vast repository of information on the natural and cultural world, collected over 250 years of human exploration, and distributed across institutions on six continents. These collections provide a unique tool for answering fundamental questions about biological, geological and cultural diversity and how they interact to shape our changing planet. Recent advances in digital and genomic technologies promise to transform how natural history collections are used, especially with respect to addressing scientific and socio-economic challenges ranging from biodiversity loss, invasive species and food security, to climate change, scarce minerals, and emerging tropical diseases. It is not clear, however, how ready these collections are to meet this challenge because relatively little is known about their size, composition or geographical distribution. Similarly, relatively little is known about the extent, expertise or demography of their curatorial workforce. To address these questions, a large collaborative team of directors and scientists have collated a global database on natural history collections that comprises more than 70 of the world's largest institutions, including museums, botanic gardens, research institutes and universities. The institutions represented in the database span Africa, Asia, Australasia, Europe, and North and South America, with approximately one third of institutions from each of the Global South, Europe and North America. The database includes information on the number of specimens and experts with respect to both geographic regions and collection categories and geographic regions. Geographic regions include both the terrestrial and marine realms, and collection categories span anthropology, botany, entomology, geology, paleobiology, and vertebrate and invertebrate zoology. Analyses of this new database reveal that the global natural history collection represents one of the most extensive distributed scientific infrastructures in the world, comprising more than 1 billion specimens that are curated by a workforce of more than 7,000 individuals. The analyses also indicate, however, that a major change in approach is required for these collections to realize their potential to inform future decision making and stimulate the basic research that underpins future questions and knowledge. For instance, at a global scale the collection and expertise does indeed exist to map change in key groups and regions - but this requires large-scale coordination across institutions and countries. Similarly, cross-institution collaboration is required to fill strategic gaps in the collection, particularly for tropical, marine and polar regions. And finally, there is an urgent need for coordinated investment in digital and genomic technologies to make collections available to the global research community and link them with other sources of information. The vast majority of collection information currently exists as 'dark data'. We conclude that the global natueral history collection comprises one of the most extensive distributed scientific infrastructures in the world, but a major change in approach is required for them to realize their potential to inform future decision making. In particular, natural history collections need to work more effectively together to develop a global strategy, create a common data platform, accelerate the availability and use of specimen data and pursue major new collecting programs.


2018 ◽  
Vol 2 ◽  
pp. e25882
Author(s):  
Maarten Schermer ◽  
Daphne Duin

The value of data present in natural history collections for research and collection management cannot be overstated. Naturalis Biodiversity Center, home to one of the largest natural history collections in the world, completed a large-scale digitisation project resulting in the registration of more than 38 million objects, many of them annotated with descriptive metadata, such as geographic coordinates and multimedia content. While digitisation is ongoing, we are now also looking for ways to leverage our digital collection, both for the benefit of collection management and that of networking with other natural history collections. To this end, we developed the Netherlands Biodiversity Data Services, providing centralized access to our collection data via state of the art, open access interfaces. Full, centralized access to the digital collection allows us to combine the data with other sources, such as collection scans focusing on the physical condition and accessibility of the collection. But also with data from external sources, such as the collection information of sister institutions, allowing for combining and comparing data, and exploring areas where collections can reinforce each other. Focusing on availability and accessibility, the services were deliberately designed as a versatile, low-level API to allow the use of our data with a broad variety of applications and services. These applications range from scientific research and remote mobile access to collection information, to “mash ups” with other data sources, apps and application in our own museum. We will demonstrate this range of applications through several examples, including the embedding of data in websites (example, Dutch Caribbean Species Register: http://www.dutchcaribbeanspecies.org/linnaeus_ng/app/views/species/nsr_taxon.php?id=177968&cat=165), use in the development of deep learning models, thematic portals (example, Naturalis meteorite collection: http://bioportal.naturalis.nl/result?theme=meteorites&language=en) and the development of Java- and R-clients. This presentation ties in with Max Caspers' presentation “Advancing collections management with the Netherlands Biodiversity Data Services“, in which he will demonstratie the potential of the services described in this presentation for the area of collections management, specifically.


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