scholarly journals Leveraging the Benefits of Open Data Services for Natural History Collection Management

2018 ◽  
Vol 2 ◽  
pp. e25882
Author(s):  
Maarten Schermer ◽  
Daphne Duin
Keyword(s):  
Natural History ◽  
The Netherlands ◽  
Large Scale ◽  
Open Data ◽  
Collection Management ◽  
Collections Management ◽  
Biodiversity Data ◽  
Data Services ◽  
Natural History Collections ◽  
Digital Collection

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.

scholarly journals Advancing Collections Management with the Netherlands Biodiversity Data Services

2018 ◽  
Vol 2 ◽  
pp. e25746
Author(s):  
Max Caspers ◽  
Maarten Schermer
Keyword(s):  
The Netherlands ◽  
Conservation Status ◽  
Collection Management ◽  
Sources Of Information ◽  
Status Change ◽  
Collections Management ◽  
Biodiversity Data ◽  
Data Services ◽  
Entire Collection ◽  
Important Field

By the summer of 2015 Naturalis Biodiversity Center had come to the end of a five-year digitization programme that aimed at digitally disclosing the entire collection of, at the time, 38 million objects. The result was a vast amount of collections data being made available to researchers, collection managers and the public. In order to utilize these data to their full extent, Naturalis has in the past few years been developing the Netherlands Biodiversity Data Services (NBDS). These services “speak” not only to our digitized collection, but to other sources of information as well and lets us query and use these data in a centralized manner. While the NBDS open up a lot of possibilities for i.e. communication, exhibition, education, policy making, etc., a very important field for its application is collection management. Instead of managing (at this point) 41 million individual objects, the NBDS could provide insight into custom aggregations of data to further professionalize decision making. Not only detailed information about taxonomy, gathering events and collection history can be provided, one can also think about quantifying use, conservation status, change in collection-size over time, etc. Some examples of application for collections management will be given during the presentation and illustrated with a collections dashboard. Even though we have made great progress in digitization, certain parts of our collection are not digitized to specimen-level and to various degrees of completeness, parts of the physical collection are not identified to species level, not all data are consistent or properly validated, etc. But instead of this limiting the applicability of the NBDS, the data service can be used as a tool to pinpoint these areas for improvement and to allow collection management to properly address and prioritize them. This presentation ultimately deals with the potential the NBDSNBA has for managing collections, both physical as digital, and enhancing their quality and value.

scholarly journals The Genomic Resources Collection Policy of the Finnish Museum of Natural History

2021 ◽  
Vol 7 ◽  
Author(s):  
Gunilla Ståhls ◽  
Alexandre Aleixo ◽  
Marko-Tapio Hyvärinen ◽  
Anniina Kuusijärvi ◽  
Leena Myllys ◽  
...  
Keyword(s):  
Natural History ◽  
Biological Diversity ◽  
Animal Tissue ◽  
Collection Management ◽  
Collections Management ◽  
Tissue Samples ◽  
Genomic Resources ◽  
Natural History Collections ◽  
Genome Level ◽  
Research And Education

The Genomic Resources Collection is a separate, independently managed part of the natural history collections of the Finnish Museum of Natural History Luomus specifically intended for consumptive research. The GRC policy deals with the materials that are archived for the very purpose of enabling the study of biological diversity at the genome level, DNA extractions of animal, fungal and plant specimens, and animal tissue samples stored deep-frozen for purposes of future DNA extraction. The GRC policy defines the purpose of the collections, the objectives and content of the procedures and activities related to them, the distribution of responsibilities for collection management and maintenance in Luomus, and the principles of collection accumulation, preservation and accessibility. The aim of the GRC is to store and loan genomic samples for research purposes. In taxonomic coverage the collection overlaps with all the taxonomically delimited specimen collections managed by the Zoology and Botany Units, but is distinguished as being directed to preserve the genomic (DNA) information irrespective of the phenotypic variation that are the focus of specimen collections. The GRC includes both Finnish and foreign samples, all legally and ethically obtained, mostly linked to a specimen voucher in the taxonomic collections. The GRC samples are documented and trackable in Luomus collections management system. In accordance with the Universities Act, the GRC belongs to the national natural science collections of Luomus. For their part, the GRC collection implement the mission of Luomus, which is to be “responsible for the preservation, accumulation and exhibition of the national natural history collections and for research and education relating to them”.

scholarly journals Rapid Creation of a Data Product for the World's Specimens of Horseshoe Bats and Relatives, a Known Reservoir for Coronaviruses

2020 ◽  
Vol 4 ◽  
Author(s):  
Erica Krimmel ◽  
Austin Mast ◽  
Deborah Paul ◽  
Robert Bruhn ◽  
Nelson Rios ◽  
...  
Keyword(s):  
Natural History ◽  
Life Histories ◽  
Lessons Learned ◽  
Reproducible Research ◽  
State University ◽  
Biodiversity Data ◽  
Global Biodiversity Information Facility ◽  
Data Product ◽  
Natural History Collections ◽  
Horseshoe Bats

Genomic evidence suggests that the causative virus of COVID-19 (SARS-CoV-2) was introduced to humans from horseshoe bats (family Rhinolophidae) (Andersen et al. 2020) and that species in this family as well as in the closely related Hipposideridae and Rhinonycteridae families are reservoirs of several SARS-like coronaviruses (Gouilh et al. 2011). Specimens collected over the past 400 years and curated by natural history collections around the world provide an essential reference as we work to understand the distributions, life histories, and evolutionary relationships of these bats and their viruses. While the importance of biodiversity specimens to emerging infectious disease research is clear, empowering disease researchers with specimen data is a relatively new goal for the collections community (DiEuliis et al. 2016). Recognizing this, a team from Florida State University is collaborating with partners at GEOLocate, Bionomia, University of Florida, the American Museum of Natural History, and Arizona State University to produce a deduplicated, georeferenced, vetted, and versioned data product of the world's specimens of horseshoe bats and relatives for researchers studying COVID-19. The project will serve as a model for future rapid data product deployments about biodiversity specimens. The project underscores the value of biodiversity data aggregators iDigBio and the Global Biodiversity Information Facility (GBIF), which are sources for 58,617 and 79,862 records, respectively, as of July 2020, of horseshoe bat and relative specimens held by over one hundred natural history collections. Although much of the specimen-based biodiversity data served by iDigBio and GBIF is high quality, it can be considered raw data and therefore often requires additional wrangling, standardizing, and enhancement to be fit for specific applications. The project will create efficiencies for the coronavirus research community by producing an enhanced, research-ready data product, which will be versioned and published through Zenodo, an open-access repository (see doi.org/10.5281/zenodo.3974999). In this talk, we highlight lessons learned from the initial phases of the project, including deduplicating specimen records, standardizing country information, and enhancing taxonomic information. We also report on our progress to date, related to enhancing information about agents (e.g., collectors or determiners) associated with these specimens, and to georeferencing specimen localities. We seek also to explore how much we can use the added agent information (i.e., ORCID iDs and Wikidata Q identifiers) to inform our georeferencing efforts and to support crediting those collecting and doing identifications. The project will georeference approximately one third of our specimen records, based on those lacking geospatial coordinates but containing textual locality descriptions. We furthermore provide an overview of our holistic approach to enhancing specimen records, which we hope will maximize the value of the bat specimens at the center of what has been recently termed the "extended specimen network" (Lendemer et al. 2020). The centrality of the physical specimen in the network reinforces the importance of archived materials for reproducible research. Recognizing this, we view the collections providing data to iDigBio and GBIF as essential partners, as we expect that they will be responsible for the long-term management of enhanced data associated with the physical specimens they curate. We hope that this project can provide a model for better facilitating the reintegration of enhanced data back into local specimen data management systems.

scholarly journals Closing Gaps But Increasing Bias In North American Butterfly Inventory Completeness

2020 ◽  
Author(s):  
Vaughn Shirey ◽  
Michael W. Belitz ◽  
Vijay Barve ◽  
Robert Guralnick
Keyword(s):  
Climate Change ◽  
Natural History ◽  
Data Sources ◽  
Museum Specimens ◽  
Biodiversity Data ◽  
Human Footprint ◽  
Natural History Collections ◽  
Global Change Research ◽  
Under Sampling ◽  
Community Science

AbstractAggregate biodiversity data from museum specimens and community observations have promise for macroscale ecological analyses. Despite this, many groups are under-sampled, and sampling is not homogeneous across space. Here we used butterflies, the best documented group of insects, to examine inventory completeness across North America. We separated digitally accessible butterfly records into those from natural history collections and burgeoning community science observations to determine if these data sources have differential spatio-taxonomic biases. When we combined all data, we found startling under-sampling in regions with the most dramatic trajectories of climate change and across biomes. We also found support for the hypothesis that community science observations are filling more gaps in sampling but are more biased towards areas with the highest human footprint. Finally, we found that both types of occurrences have familial-level taxonomic completeness biases, in contrast to the hypothesis of less taxonomic bias in natural history collections data. These results suggest that higher inventory completeness, driven by rapid growth of community science observations, is partially offset by higher spatio-taxonomic biases. We use the findings here to provide recommendations on how to alleviate some of these gaps in the context of prioritizing global change research.

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 ◽  
...  
Keyword(s):  
Natural History ◽  
Global Change ◽  
Large Scale ◽  
Anthropogenic Impacts ◽  
Digital Content ◽  
Global Community ◽  
New Approaches ◽  
Natural History Collections ◽  
Data Links ◽  
Critical Issues

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.

scholarly journals The development of a digitising service centre for natural history collections

ZooKeys ◽  
2012 ◽  
Vol 209 ◽  
pp. 75-86 ◽  
Author(s):  
Riitta Tegelberg ◽  
Jaana Haapala ◽  
Tero Mononen ◽  
Mika Pajari ◽  
Hannu Saarenmaa
Keyword(s):  
Natural History ◽  
Large Scale ◽  
Data Entry ◽  
Imaging Data ◽  
Long Term Storage ◽  
Service Centre ◽  
Natural History Collections ◽  
Darwin Core ◽  
The University

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.

scholarly journals Digitization and the future of natural history collections

2019 ◽  
Author(s):  
Brandon Hedrick ◽  
Mason Heberling ◽  
Emily Meineke ◽  
Kathryn Turner ◽  
Christopher Grassa ◽  
...  
Keyword(s):  
Natural History ◽  
Global Change ◽  
Large Scale ◽  
Anthropogenic Impacts ◽  
Digital Content ◽  
Global Community ◽  
New Approaches ◽  
Natural History Collections ◽  
The Future ◽  
Data Linkages

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.

scholarly journals FinBIF: An all-embracing, integrated, cross-sectoral biodiversity data infrastructure

2019 ◽  
Vol 3 ◽  
Author(s):  
Leif Schulman ◽  
Aino Juslén ◽  
Kari Lahti
Keyword(s):  
Natural History ◽  
Data Management ◽  
Species Identification ◽  
Large Scale ◽  
Dna Barcode ◽  
National Research Council ◽  
Observation Data ◽  
Biodiversity Data ◽  
Research Infrastructures ◽  
Biodiversity Information

The service model of the Global Biodiversity Information Facility (GBIF) is being implemented in an increasing number of national biodiversity (BD) data services. While GBIF already shares >109 data points, national initiatives are an essential component: increase in GBIF-mediated data relies on national data mobilisation and GBIF is not optimised to support local use. The Finnish Biodiversity Information Facility (FinBIF), initiated in 2012 and operational since late 2016, is one of the more recent examples of national BD research infrastructures (RIs) – and arguably among the most comprehensive. Here, we describe FinBIF’s development and service integration, and provide a model approach for the construction of all-inclusive national BD RIs. FinBIF integrates a wide array of BD RI approaches under the same umbrella. These include large-scale and multi-technology digitisation of natural history collections; building a national DNA barcode reference library and linking it to species occurrence data; citizen science platforms enabling recording, managing and sharing of observation data; management and sharing of restricted data among authorities; community-driven species identification support; an e-learning environment for species identification; and IUCN Red Listing (Fig. 1). FinBIF’s aims are to accelerate digitisation, mobilisation, and distribution of biodiversity data and to boost their use in research and education, environmental administration, and the private sector. The core functionalities of FinBIF were built in a 3.5-year project (01/2015–06/2018) by a consortium of four university-based natural history collection facilities led by the Finnish Museum of Natural History Luomus. Close to 30% of the total funding was granted through the Finnish Research Infrastructures programme (FIRI) governed by the national research council and based on scientific excellence. Government funds for productivity enhancement in state administration covered c.40 % of the development and the rest was self-financed by the implementing consortium of organisations that have both a research and an education mission. The cross-sectoral scope of FinBIF has led to rapid uptake and a broad user base of its functionalities and services. Not only researchers but also administrative authorities, various enterprises and a large number of private citizens show a significant interest in the RI (Table 1). FinBIF is now in its second construction cycle (2019–2022), funded through the FIRI programme and, thus, focused on researcher services. The work programme includes integration of tools for data management in ecological restoration and e-Lab tools for spatial analyses, morphometric analysis of 3D images, species identification from sound recordings, and metagenomics analyses.

scholarly journals Assessment of North American arthropod collections: prospects and challenges for addressing biodiversity research

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8086 ◽  
Author(s):  
Neil S. Cobb ◽  
Lawrence F. Gall ◽  
Jennifer M. Zaspel ◽  
Nicolas J. Dowdy ◽  
Lindsie M. McCabe ◽  
...  
Keyword(s):  
United States ◽  
Natural History ◽  
North American ◽  
The United States ◽  
Biodiversity Data ◽  
Biodiversity Crisis ◽  
Biodiversity Research ◽  
Natural History Collections ◽  
Rate Of Increase ◽  
Crucial Information

Over 300 million arthropod specimens are housed in North American natural history collections. These collections represent a “vast hidden treasure trove” of biodiversity −95% of the specimen label data have yet to be transcribed for research, and less than 2% of the specimens have been imaged. Specimen labels contain crucial information to determine species distributions over time and are essential for understanding patterns of ecology and evolution, which will help assess the growing biodiversity crisis driven by global change impacts. Specimen images offer indispensable insight and data for analyses of traits, and ecological and phylogenetic patterns of biodiversity. Here, we review North American arthropod collections using two key metrics, specimen holdings and digitization efforts, to assess the potential for collections to provide needed biodiversity data. We include data from 223 arthropod collections in North America, with an emphasis on the United States. Our specific findings are as follows: (1) The majority of North American natural history collections (88%) and specimens (89%) are located in the United States. Canada has comparable holdings to the United States relative to its estimated biodiversity. Mexico has made the furthest progress in terms of digitization, but its specimen holdings should be increased to reflect the estimated higher Mexican arthropod diversity. The proportion of North American collections that has been digitized, and the number of digital records available per species, are both much lower for arthropods when compared to chordates and plants. (2) The National Science Foundation’s decade-long ADBC program (Advancing Digitization of Biological Collections) has been transformational in promoting arthropod digitization. However, even if this program became permanent, at current rates, by the year 2050 only 38% of the existing arthropod specimens would be digitized, and less than 1% would have associated digital images. (3) The number of specimens in collections has increased by approximately 1% per year over the past 30 years. We propose that this rate of increase is insufficient to provide enough data to address biodiversity research needs, and that arthropod collections should aim to triple their rate of new specimen acquisition. (4) The collections we surveyed in the United States vary broadly in a number of indicators. Collectively, there is depth and breadth, with smaller collections providing regional depth and larger collections providing greater global coverage. (5) Increased coordination across museums is needed for digitization efforts to target taxa for research and conservation goals and address long-term data needs. Two key recommendations emerge: collections should significantly increase both their specimen holdings and their digitization efforts to empower continental and global biodiversity data pipelines, and stimulate downstream research.

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