scholarly journals Workforce Capacity Development and the Digital Extended Specimen

2021 ◽  
Vol 5 ◽  
Author(s):  
Anna Monfils ◽  
Elizabeth R. Ellwood
Keyword(s):  
Natural History ◽  
Best Practices ◽  
Capacity Development ◽  
Workforce Training ◽  
Educational Materials ◽  
Biodiversity Data ◽  
Natural History Collections ◽  
Workforce Capacity ◽  
Future Work ◽  
And Training

As we look to the future of natural history collections and a global integration of biodiversity data, we are reliant on a diverse workforce with the skills necessary to build, grow, and support the data, tools, and resources of the Digital Extended Specimen (DES; Webster 2019, Lendemer et al. 2020, Hardisty 2020). Future “DES Data Curators” – those who will be charged with maintaining resources created through the DES – will require skills and resources beyond what is currently available to most natural history collections staff. In training the workforce to support the DES we have an opportunity to broaden our community and ensure that, through the expansion of biodiversity data, the workforce landscape itself is diverse, equitable, inclusive, and accessible. A fully-implemented DES will provide training that encapsulates capacity building, skills development, unifying protocols and best practices guidance, and cutting-edge technology that also creates inclusive, equitable, and accessible systems, workflows, and communities. As members of the biodiversity community and the current workforce, we can leverage our knowledge and skills to develop innovative training models that: include a range of educational settings and modalities; address the needs of new communities not currently engaged with digital data; from their onset, provide attribution for past and future work and do not perpetuate the legacy of colonial practices and historic inequalities found in many physical natural history collections. Recent reports from the Biodiversity Collections Network (BCoN 2019) and the National Academies of Science, Engineering and Medicine (National Academies of Sciences, Engineering, and Medicine 2020) specifically address workforce needs in support of the DES. To address workforce training and inclusivity within the context of global data integration, the Alliance for Biodiversity Knowledge included a topic on Workforce capacity development and inclusivity in Phase 2 of the consultation on Converging Digital Specimens and Extended Specimens - Towards a global specification for data integration. Across these efforts, several common themes have emerged relative to workforce training and the DES. A call for a community needs assessment: As a community, we have several unknowns related to the current collections workforce and training needs. We would benefit from a baseline assessment of collections professionals to define current job responsibilities, demographics, education and training, incentives, compensation, and benefits. This includes an evaluation of current employment prospects and opportunities. Defined skills and training for the 21st century collections professional: We need to be proactive and define the 21st century workforce skills necessary to support the development and implementation of the DES. When we define the skills and content needs we can create appropriate training opportunities that include scalable materials for capacity building, educational materials that develop relevant skills, unifying protocols across the DES network, and best practices guidance for professionals. Training for data end-users: We need to train data end-users in biodiversity and data science at all levels of formal and informal education from primary and secondary education through the existing workforce. This includes developing training and educational materials, creating data portals, and building analyses that are inclusive, accessible, and engage the appropriate community of science educators, data scientists, and biodiversity researchers. Foster a diverse, equitable, inclusive, and accessible and professional workforce: As the DES develops and new tools and resources emerge, we need to be intentional in our commitment to building tools that are accessible and in assuring that access is equitable. This includes establishing best practices to ensure the community providing and accessing data is inclusive and representative of the diverse global community of potential data providers and users. Upfront, we must acknowledge and address issues of historic inequalities and colonial practices and provide appropriate attribution for past and future work while ensuring legal and regulatory compliance. Efforts must include creating transparent linkages among data and the humans that create the data that drives the DES. In this presentation, we will highlight recommendations for building workforce capacity within the DES that are diverse, inclusive, equitable and accessible, take into account the requirements of the biodiversity science community, and that are flexible to meet the needs of an evolving field.

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 Natural history collections-based research: progress, promise, and best practices

2015 ◽  
Vol 97 (1) ◽  
pp. 287-297 ◽  
Author(s):  
Bryan S. McLean ◽  
Kayce C. Bell ◽  
Jonathan L. Dunnum ◽  
Bethany Abrahamson ◽  
Jocelyn P. Colella ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Natural History ◽  
Best Practices ◽  
Scientific Community ◽  
Scientific Progress ◽  
Research Progress ◽  
Weak Links ◽  
Natural History Collections ◽  
Stable Isotope Ecology ◽  
Associated Data

Abstract Specimens and associated data in natural history collections (NHCs) foster substantial scientific progress. In this paper, we explore recent contributions of NHCs to the study of systematics and biogeography, genomics, morphology, stable isotope ecology, and parasites and pathogens of mammals. To begin to assess the magnitude and scope of these contributions, we analyzed publications in the Journal of Mammalogy over the last decade, as well as recent research supported by a single university mammal collection (Museum of Southwestern Biology, Division of Mammals). Using these datasets, we also identify weak links that may be hindering the development of crucial NHC infrastructure. Maintaining the vitality and growth of this foundation of mammalogy depends on broader engagement and support from across the scientific community and is both an ethical and scientific imperative given the rapidly changing environmental conditions on our planet.

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.

scholarly journals Uncertain Geo-Uncertainty: Ecological research and public biodiversity data repositories

2019 ◽  
Vol 3 ◽  
Author(s):  
Arnald Marcer ◽  
Elspeth Haston ◽  
Quentin Groom ◽  
F. Xavier Picó ◽  
Agustí Escobar ◽  
...  
Keyword(s):  
Natural History ◽  
Spatial Information ◽  
Species Distribution Modelling ◽  
Location Information ◽  
Ecological Research ◽  
Biodiversity Data ◽  
Data Repositories ◽  
Ecological Requirements ◽  
Natural History Collections ◽  
Wide Range

Natural history collections represent a vast and superb wealth of information gathered and curated across centuries by institutions such as natural history museums and botanical gardens around the world. The relatively recent advent and maturation of accessible computer technology has allowed the initiation of major digitization projects aimed at making the contents of these collections publicly available for education and research purposes. The final destinations of these newly digitized data are public biodiversity data repositories, of which, GBIF is the main one. These respositories are gateways where researchers can access and retrieve the data for use in a wide range of analyses. This unprecedented volume of information on biodiversity represents an extraordinary asset for research in ecology and evolution. A particularly important part of the digitized data for any given specimen is its collection location, as it indirectly gives information on the species’ habitat and thus, its ecological requirements. Many specimens in natural history collections come from a time where the collecting event, which includes the location information, was hand-written on physical tags attached to the specimen. This location information was given as a description of a place, e.g. a site name, and could be a rather precise or vague description. In order to convert this description of locality into a digitized research-grade georeferenced record, the research community has come up with a set of guidelines and recommendations; the most prominent one the point-radius method devised by Wieczorek et al. in 2004. However, and despite the public availability of this know-how, the end result is that the data available at the end of the pipeline, e.g. GBIF, often lacks georeferencing information with enough quality to be used for research purposes. Occurrence records from natural history collection datasets held at GBIF, often lack spatial coordinates and, if present, in most cases their precision and uncertainty fields are blank. The final consequence of this lack of complete georeferencing information is that the affected records are rendered useless for many kinds of research. For example, the flourishing field of species distribution modelling absolutely depends on accurate spatial information in order to be able to retrieve information on the environmental conditions in which the species live. The availability of global environmental and remote sensing datasets together with the sophisticated geospatial tools at the disposal of the researcher become powerless if no quality geoinformation is available. In this study, we perform a preliminary analysis on the status and availability of geoferencing information in datasets originated from specimens in natural history collections held at GBIF, discuss how the quality of this spatial info may affect ecological research, and conclude with some recommendations on how to better describe the georeferencing process within public digital biodiversity repositories.

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.

LepNet: The Lepidoptera of North America Network

Zootaxa ◽  
2017 ◽  
Vol 4247 (1) ◽  
pp. 73 ◽  
Author(s):  
KATJA C. SELTMANN ◽  
NEIL S. COBB ◽  
LAWRENCE F. GALL ◽  
CHARLES R. BARTLETT ◽  
M. ANNE BASHAM ◽  
...  
Keyword(s):  
United States ◽  
North America ◽  
Natural History ◽  
North American ◽  
Evolutionary Biology ◽  
Biodiversity Data ◽  
Natural History Collections ◽  
Digital Formats ◽  
Global Research

The Lepidoptera of North America Network, or LepNet, is a digitization effort recently launched to mobilize biodiversity data from 3 million specimens of butterflies and moths in United States natural history collections (http://www.lep-net.org/). LepNet was initially conceived as a North American effort but the project seeks collaborations with museums and other organizations worldwide. The overall goal is to transform Lepidoptera specimen data into readily available digital formats to foster global research in taxonomy, ecology and evolutionary biology. 

scholarly journals Describing Living Collections and Specimens 

2021 ◽  
Vol 5 ◽  
Author(s):  
Patricia Mergen ◽  
Maarten Trekels ◽  
Frederik Leliaert ◽  
Matt Woodburn ◽  
Gabriele Droege ◽  
...  
Keyword(s):  
Natural History ◽  
Best Practices ◽  
Group Living ◽  
World Federation ◽  
Culture Collections ◽  
Controlled Vocabularies ◽  
Cost Action ◽  
Botanical Gardens ◽  
Natural History Collections ◽  
Voucher Specimens

Many institutions harbor living collections in the form of living plants, animals, microrganisms or seeds. In the framework of the TDWG collections and specimen descriptions standards, it has become important to align exisiting standards for living collections and specimens or to identify where concepts or controlled vocabularies would be needed in the current TDWG standards. In September 2021 a workshop was organized in the framework of the COST Action Mobilise (https://www.mobilise-action.eu/) to get a better common understanding of the different types of living collections to consider and set the scene for further work on standards alignments. The EU COST Action CA17106 on “Mobilising Data, Experts and Policies in Scientific Collections”. Invited experts to these workshop were representatives of the TDWG Collection Description Group, the GGBN and TDWG molecular collections group, living plants collections and seed banks (Botanic Gardens Conservation International: BGCI, https://www.bgci.org/), living animal and biobanks (European Association of Zoos and Aquaria: EAZA, https://www.eaza.net/) and the culture collections (World Federation for Culture Collections: WFCC, http://www.wfcc.info/), who gave presentations on their currently used standards and challenges. The second day was devoted to break out sessions to brainstorm the specific needs for the different living collections with the aim to check and update the controlled vocabularies and concepts as needed. Identified topics were : Session 1: Voucher specimens of living accessions. Session 2: Living collections and GBIF. Session 3: How do we compare botanical gardens with herbaria? Session 4: How do we compare zoos and aquaria with natural history collections? Session 5: Culture collections: best practices and guidelines. Session 1: Voucher specimens of living accessions. Session 2: Living collections and GBIF. Session 3: How do we compare botanical gardens with herbaria? Session 4: How do we compare zoos and aquaria with natural history collections? Session 5: Culture collections: best practices and guidelines. The goal of this presentation is to address the outcome of these sessions and recommend future steps in collaboration with TDWG and the different identified stakeholders.

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