scholarly journals The history and impact of digitization and digital data mobilization on biodiversity research

2018 ◽  
Vol 374 (1763) ◽  
pp. 20170391 ◽  
Author(s):  
Gil Nelson ◽  
Shari Ellis
Keyword(s):  
Natural History ◽  
The United States ◽  
Digital Data ◽  
National Commission ◽  
Rapid Rise ◽  
Biodiversity Data ◽  
Scientific Enterprise ◽  
Global Biodiversity Information Facility ◽  
Scientific Publications ◽  
Biodiversity Research

The first two decades of the twenty-first century have seen a rapid rise in the mobilization of digital biodiversity data. This has thrust natural history museums into the forefront of biodiversity research, underscoring their central role in the modern scientific enterprise. The advent of mobilization initiatives such as the United States National Science Foundation's Advancing Digitization of Biodiversity Collections (ADBC), Australia's Atlas of Living Australia (ALA), Mexico's National Commission for the Knowledge and Use of Biodiversity (CONABIO), Brazil's Centro de Referência em Informação (CRIA) and China's National Specimen Information Infrastructure (NSII) has led to a rapid rise in data aggregators and an exponential increase in digital data for scientific research and arguably provide the best evidence of where species live. The international Global Biodiversity Information Facility (GBIF) now serves about 131 million museum specimen records, and Integrated Digitized Biocollections (iDigBio) in the USA has amassed more than 115 million. These resources expose collections to a wider audience of researchers, provide the best biodiversity data in the modern era outside of nature itself and ensure the primacy of specimen-based research. Here, we provide a brief history of worldwide data mobilization, their impact on biodiversity research, challenges for ensuring data quality, their contribution to scientific publications and evidence of the rising profiles of natural history collections. This article is part of the theme issue ‘Biological collections for understanding biodiversity in the Anthropocene’.

scholarly journals The Impact of Digitization and Digital Data Mobilization on Biodiversity Research and Outreach

2018 ◽  
Vol 2 ◽  
pp. e28470
Author(s):  
Gil Nelson ◽  
Shari Ellis
Keyword(s):  
Natural History ◽  
The United States ◽  
Digital Data ◽  
National Commission ◽  
Data Generation ◽  
Rapid Rise ◽  
Scientific Enterprise ◽  
Scientific Publications ◽  
Biodiversity Research ◽  
The Impact

The first two decades of the 21st Century have seen a rapid rise in the creation, mobilization, research, and educational use of digital museum data, especially in the natural and biodiversity sciences. This has thrust natural history museums and especially the biodiversity specimen collections they hold into the forefront of biodiversity research in systematics, ecology, and conservation, underscoring their central role in the modern scientific enterprise. The advent of such digitization and data mobilization initiatives as the United States National Science Foundation’s Advancing the Digitization of Biodiversity Collections program (ADBC), Australia’s Atlas of Living Australia (ALA), Mexico’s National Commission for the Knowledge and Use of Biodiversity (CONABIO), Brazil’s Centro de Referência em Informação (CRIA), Europe’s SYNTHESYS, and China’s National Specimen Information Infrastructure (NSII) has led to a rapid rise in regional, national, and international digital data aggregators and has precipitated an exponential increase in the availability of digital data for scientific research. The international Global Biodiversity Information Facility (GBIF) now serves about 130 million museum specimen records, and Integrated Digitized Biocollections (iDigBio), the U.S. national biodiversity portal, has amassed over 109 million records representing over 300 million specimens that are international in scope. These digital resources raise the profiles of museums, expose collections to a wider audience of systematic and conservation researchers, provide the best biodiversity data in the modern era outside of nature itself, and ensure that specimen-based research remains at the forefront of the biodiversity sciences. Here we provide a brief overview of worldwide digital data generation and mobilization, the impact of these data on biodiversity research, new data underscoring the impact of worldwide digitization initiatives on citation in scientific publications, and evidence of the roles these activities play in raising the public and scientific profiles of natural history collections.

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 Engaging K-12 Audiences with Biodiversity Data through Advancing Digitization for Biodiversity Collections

2018 ◽  
Vol 2 ◽  
pp. e26473
Author(s):  
Molly Phillips ◽  
Anne Basham ◽  
Marc Cubeta ◽  
Kari Harris ◽  
Jonathan Hendricks ◽  
...  
Keyword(s):  
Natural History ◽  
The United States ◽  
Lessons Learned ◽  
Educational Resources ◽  
Digital Data ◽  
Science Standards ◽  
Global Biodiversity Information Facility ◽  
Digital Collections ◽  
Natural History Collections ◽  
K 12

Natural history collections around the world are currently being digitized with the resulting data and associated media now shared online in aggregators such as the Global Biodiversity Information Facility and Integrated Digitized Biocollections (iDigBio). These collections and their resources are accessible and discoverable through online portals to not only researchers and collections professionals, but to educators, students, and other potential downstream users. Primary and secondary education (K-12) in the United States is going through its own revolution with many states adopting Next Generation Science Standards (NGSS https://www.nextgenscience.org/). The new standards emphasize science practices for analyzing and interpreting data and connect to cross-cutting concepts such as cause and effect and patterns. NGSS and natural history collections data portals seem to complement each other. Nevertheless, many educators and students are unaware of the digital resources available or are overwhelmed with working in aggregated databases created by scientists. To better address this challenge, participants within the National Science Foundation Advancing Digitization for Biodiversity Collections program (ADBC) have been working to increase awareness of, and scaffold learning for, digitized collections with K-12 educators and learners. They are accomplishing this through individual programs at institutions across the country as part of the Thematic Collections Networks and collaboratively through the iDigBio Education and Outreach Working Group. ADBC partners have focused on incorporating digital data and resources into K-12 classrooms through training workshops and webinars for both educators and collections professionals, as well as through creating educational resources, websites, and applications that use digital collections data. This presentation includes lessons learned from engaging K-12 audiences with digital data, summarizes available resources for both educators and collections professionals, shares how to become involved, and provides ways to facilitate transfer of educational resources to the K-12 community.

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 DiSSCo, iDigBio and the Future of Global Collaboration

2019 ◽  
Vol 3 ◽  
Author(s):  
Gil Nelson ◽  
Deborah L Paul
Keyword(s):  
Working Group ◽  
Application Programming Interface ◽  
The United States ◽  
Common Source ◽  
Data Generation ◽  
Biodiversity Data ◽  
Global Biodiversity Information Facility ◽  
Data Accessibility ◽  
The Us ◽  
Biodiversity Information

Integrated Digitized Biocollections (iDigBio) is the United States’ (US) national resource and coordinating center for biodiversity specimen digitization and mobilization. It was established in 2011 through the US National Science Foundation’s (NSF) Advancing Digitization of Biodiversity Collections (ADBC) program, an initiative that grew from a working group of museum-based and other biocollections professionals working in concert with NSF to make collections' specimen data accessible for science, education, and public consumption. The working group, Network Integrated Biocollections Alliance (NIBA), released two reports (Beach et al. 2010, American Institute of Biological Sciences 2013) that provided the foundation for iDigBio and ADBC. iDigBio is restricted in focus to the ingestion of data generated by public, non-federal museum and academic collections. Its focus is on specimen-based (as opposed to observational) occurrence records. iDigBio currently serves about 118 million transcribed specimen-based records and 29 million specimen-based media records from approximately 1600 datasets. These digital objects have been contributed by about 700 collections representing nearly 400 institutions and is the most comprehensive biodiversity data aggregator in the US. Currently, iDigBio, DiSSCo (Distributed System of Scientific Collections), GBIF (Global Biodiversity Information Facility), and the Atlas of Living Australia (ALA) are collaborating on a global framework to harmonize technologies towards standardizing and synchronizing ingestion strategies, data models and standards, cyberinfrastructure, APIs (application programming interface), specimen record identifiers, etc. in service to a developing consolidated global data product that can provide a common source for the world’s digital biodiversity data. The collaboration strives to harness and combine the unique strengths of its partners in ways that ensure the individual needs of each partner’s constituencies are met, design pathways for accommodating existing and emerging aggregators, simultaneously strengthen and enhance access to the world’s biodiversity data, and underscore the scope and importance of worldwide biodiversity informatics activities. Collaborators will share technology strategies and outputs, align conceptual understandings, and establish and draw from an international knowledge base. These collaborators, along with Biodiversity Information Standards (TDWG), will join iDigBio and the Smithsonian National Museum of Natural History as they host Biodiversity 2020 in Washington, DC. Biodiversity 2020 will combine an international celebration of the worldwide progress made in biodiversity data accessibility in the 21st century with a biodiversity data conference that extends the life of Biodiversity Next. It will provide a venue for the GBIF governing board meeting, TDWG annual meeting, and the annual iDigBio Summit as well as three days of plenary and concurrent sessions focused on the present and future of biodiversity data generation, mobilization, and use.

scholarly journals Unlocking the Entomological Collection of the Natural History Museum of Maputo, Mozambique

2021 ◽  
Vol 9 ◽  
Author(s):  
Domingos Sandramo ◽  
Enrico Nicosia ◽  
Silvio Cianciullo ◽  
Bernardo Muatinte ◽  
Almeida Guissamulo
Keyword(s):  
Natural History ◽  
Crucial Role ◽  
Development Programme ◽  
Natural History Museum ◽  
Biodiversity Data ◽  
Global Biodiversity Information Facility ◽  
History Museum ◽  
Data Portal ◽  
Global Biodiversity ◽  
Biodiversity Information

The collections of the Natural History Museum of Maputo have a crucial role in the safeguarding of Mozambique's biodiversity, representing an important repository of data and materials regarding the natural heritage of the country. In this paper, a dataset is described, based on the Museum’s Entomological Collection recording 409 species belonging to seven orders and 48 families. Each specimen’s available data, such as geographical coordinates and taxonomic information, have been digitised to build the dataset. The specimens included in the dataset were obtained between 1914–2018 by collectors and researchers from the Natural History Museum of Maputo (once known as “Museu Alváro de Castro”) in all the country’s provinces, with the exception of Cabo Delgado Province. This paper adds data to the Biodiversity Network of Mozambique and the Global Biodiversity Information Facility, within the objectives of the SECOSUD II Project and the Biodiversity Information for Development Programme. The aforementioned insect dataset is available on the GBIF Engine data portal (https://doi.org/10.15468/j8ikhb). Data were also shared on the Mozambican national portal of biodiversity data BioNoMo (https://bionomo.openscidata.org), developed by SECOSUD II Project.

scholarly journals Unleash the Potential of your Website! 180,000 webpages from the French Natural History Museum marked up with Bioschemas/Schema.org biodiversity types

2020 ◽  
Vol 4 ◽  
Author(s):  
Franck Michel ◽  
Gargominy Olivier ◽  
Benjamin Ledentec ◽  
The Bioschemas Community
Keyword(s):  
Natural History ◽  
Search Engines ◽  
Critical Mass ◽  
Scientific Data ◽  
Third Party ◽  
Data Sources ◽  
Integrative Approach ◽  
Biodiversity Data ◽  
Major Step ◽  
Global Biodiversity Information Facility

The challenge of finding, retrieving and making sense of biodiversity data is being tackled by many different approaches. Projects like the Global Biodiversity Information Facility (GBIF) or Encyclopedia of Life (EoL) adopt an integrative approach where they republish, in a uniform manner, records aggregated from multiple data sources. With this centralized, siloed approach, such projects stand as powerful one-stop shops, but tend to reduce the visibility of other data sources that are not (yet) aggregated. At the other end of the spectrum, the Web of Data promotes the building of a global, distributed knowledge graph consisting of datasets published by independent institutions according to the Linked Open Data principles (Heath and Bizer 2011), such as Wikidata or DBpedia. Beyond these "sophisticated" infrastructures, websites remain the most common way of publishing and sharing scientific data at low cost. Thanks to web search engines, everyone can discover webpages. Yet, the summaries provided in results lists are often insufficiently informative to decide whether a web page is relevant with respect to some research interests, such that integrating data published by a wealth of websites is hardly possible. A strategy around this issue lies in annotating websites with structured, semantic metadata such as the Schema.org vocabulary (Guha et al. 2015). Webpages typically embed Schema.org annotations in the form of markup data (written in the RDFa or JSON-LD formats), which search engines harvest and exploit to improve ranking and provide more informative summarization. Bioschemas is a community effort working to extend Schema.org to support markup for Life Sciences websites (Michel and The Bioschemas Community 2018, Garcia et al. 2017). Bioschemas primarily re-uses existing terms from Schema.org, occasionally re-uses terms from third-party vocabularies, and when necessary proposes new terms to be endorsed by Schema.org. As of today, Bioschemas's biodiversity group has proposed the Taxon type*1 to support the annotation of any webpage denoting taxa, TaxonName to support more specifically the annotation of taxonomic names registries, and guidelines describing how to leverage existing vocabularies such as Darwin Core terms. To proceed further, the biodiversity community must now demonstrate its interest in having these terms endorsed by Schema.org: (1) through a critical mass of live markup deployments, and (2) by the development of applications capable of exploiting this markup data. Therefore, as a first step, the French National Museum of Natural History has marked up its natural heritage inventory website: over 180,000 webpages describing the species inventoried in French territories have been annotated with the Taxon and TaxonName types in the form of JSON-LD scripts (see example scripts). As an example, one can check the source of the Delphinus delphis page. In this presentation, by demonstrating that marking up existing webpages can be very inexpensive, we wish to encourage the biodiversity community to adopt this practice, engage in the discussion about biodiversity-related markup, and possibly propose new terms related e.g. to traits or collections. We believe that generalizing the use of such markup by the many websites reporting checklists, museum collections, occurrences, life traits etc. shall be a major step towards the generalized adoption of FAIR*2 principles (Wilkinson 2016), shall dramatically improve information discovery using search engines, and shall be a key accelerator for the development of novel, web-scale, biodiversity data integration scenarios.

scholarly journals Improving Impact Metrics of Open and Free Biodiversity Data through Linked Metadata and Academic Outreach

2019 ◽  
Vol 3 ◽  
Author(s):  
Daniel Noesgaard
Keyword(s):  
Data Sharing ◽  
Citation Count ◽  
Open Data ◽  
Scientific Paper ◽  
Open Science ◽  
Digital Object Identifier ◽  
Biodiversity Data ◽  
Global Biodiversity Information Facility ◽  
Scientific Publications ◽  
Creative Commons

The work required to collect, clean and publish biodiversity datasets is significant, and those who do it deserve recognition for their efforts. Researchers publish studies using open biodiversity data available from GBIF—the Global Biodiversity Information Facility—at a rate of about two papers a day. These studies cover areas such as macroecology, evolution, climate change, and invasive alien species, relying on data sharing by hundreds of publishing institutions and the curatorial work of thousands of individual contributors. With more than 90 per cent of these datasets licensed under Creative Commons Attribution licenses (CC BY and CC BY-NC), data users are required to credit the dataset providers. For GBIF, it is crucial to link these scientific uses to the underlying data as one means of demonstrating the value and impact of open science, while seeking to ensure attribution of individual, organizational and national contributions to the global pool of open data about biodiversity. Every single authenticated download of occurrence records from GBIF.org is issued a unique Digital Object Identifier (DOI). These DOIs each resolve to a landing page that contains details of the search parameters used to generate the download a quantitative map of the underlying datasets that contributed to the download a simple citation to be included in works that rely on the data the search parameters used to generate the download a quantitative map of the underlying datasets that contributed to the download a simple citation to be included in works that rely on the data When used properly by authors and deposited correctly by journals in the article metadata, the DOI citation establishes a direct link between a scientific paper and the underlying data. Crossref—the main DOI Registration Agency for academic literature— exposes such links in Event Data, which can be consumed programmatically to report direct use of individual datasets. GBIF also records these links, permanently preserving the download archives while exposing a citation count on download landing pages that is also summarized on the landing pages of each contributing datasets and publishers. The citation counts can be expanded to produce lists of all papers unambiguously linked to use of specific datasets. In 2018, just 15 per cent of papers based on GBIF-mediated data used DOIs to cite or acknowledge the datasets used in the studies. To promote crediting of data publishers and digital recognition of data sharing, the GBIF Secretariat has been reaching out systematically to authors and publishers since April 2018 whenever a paper fails to include a proper data citation. While publishing lags may hinder immediate effects, preliminary findings suggest that uptake is improving—as the number of papers with DOI data citations during the first part of 2019 is up more than 60 per cent compared to 2018. Focusing on the value of linking scientific publications and data, this presentation will explore the potential for establishing automatic linkage through DOI metadata while demonstrating efforts to improve metrics of data use and attribution of data providers through outreach campaigns to authors and journal publishers.

scholarly journals Highlights and Outcomes of the 2021 Global Community Consultation

2021 ◽  
Vol 5 ◽  
Author(s):  
Elizabeth R. Ellwood ◽  
Andrew Bentley ◽  
Jutta Buschbom ◽  
Alex Hardisty ◽  
Austin Mast ◽  
...  
Keyword(s):  
Natural History ◽  
Data Integration ◽  
Phase 1 ◽  
The United States ◽  
Slight Variation ◽  
Phase 2 ◽  
Biodiversity Data ◽  
Data Infrastructure ◽  
Biodiversity Knowledge ◽  
Associated Data

International collaboration between collections, aggregators, and researchers within the biodiversity community and beyond is becoming increasingly important in our efforts to support biodiversity, conservation and the life of the planet. The social, technical, logistical and financial aspects of an equitable biodiversity data landscape – from workforce training and mobilization of linked specimen data, to data integration, use and publication – must be considered globally and within the context of a growing biodiversity crisis. In recent years, several initiatives have outlined paths forward that describe how digital versions of natural history specimens can be extended and linked with associated data. In the United States, Webster (2017) presented the “extended specimen”, which was expanded upon by Lendemer et al. (2019) through the work of the Biodiversity Collections Network (BCoN). At the same time, a “digital specimen” concept was developed by DiSSCo in Europe (Hardisty 2020). Both the extended and digital specimen concepts depict a digital proxy of an analog natural history specimen, whose digital nature provides greater capabilities such as being machine-processable, linkages with associated data, globally accessible information-rich biodiversity data, improved tracking, attribution and annotation, additional opportunities for data use and cross-disciplinary collaborations forming the basis for FAIR (Findable, Accessible, Interoperable, Reproducible) and equitable sharing of benefits worldwide, and innumerable other advantages, with slight variation in how an extended or digital specimen model would be executed. Recognizing the need to align the two closely-related concepts, and to provide a place for open discussion around various topics of the Digital Extended Specimen (DES; the current working name for the joined concepts), we initiated a virtual consultation on the discourse platform hosted by the Alliance for Biodiversity Knowledge through GBIF. This platform provided a forum for threaded discussions around topics related and relevant to the DES. The goals of the consultation align with the goals of the Alliance for Biodiversity Knowledge: expand participation in the process, build support for further collaboration, identify use cases, identify significant challenges and obstacles, and develop a comprehensive roadmap towards achieving the vision for a global specification for data integration. In early 2021, Phase 1 launched with five topics: Making FAIR data for specimens accessible; Extending, enriching and integrating data; Annotating specimens and other data; Data attribution; and Analyzing/mining specimen data for novel applications. This round of full discussion was productive and engaged dozens of contributors, with hundreds of posts and thousands of views. During Phase 1, several deeper, more technical, or additional topics of relevance were identified and formed the foundation for Phase 2 which began in May 2021 with the following topics: Robust access points and data infrastructure alignment; Persistent identifier (PID) scheme(s); Meeting legal/regulatory, ethical and sensitive data obligations; Workforce capacity development and inclusivity; Transactional mechanisms and provenance; and Partnerships to collaborate more effectively. In Phase 2 fruitful progress was made towards solutions to some of these complex functional and technical long-term goals. Simultaneously, our commitment to open participation was reinforced, through increased efforts to involve new voices from allied and complementary fields. Among a wealth of ideas expressed, the community highlighted the need for unambiguous persistent identifiers and a dedicated agent to assign them, support for a fully linked system that includes robust publishing mechanisms, strong support for social structures that build trustworthiness of the system, appropriate attribution of legacy and new work, a system that is inclusive, removed from colonial practices, and supportive of creative use of biodiversity data, building a truly global data infrastructure, balancing open access with legal obligations and ethical responsibilities, and the partnerships necessary for success. These two consultation periods, and the myriad activities surrounding the online discussion, produced a wide variety of perspectives, strategies, and approaches to converging the digital and extended specimen concepts, and progressing plans for the DES -- steps necessary to improve access to research-ready data to advance our understanding of the diversity and distribution of life. Discussions continue and we hope to include your contributions to the DES in future implementation plans.

scholarly journals Towards a Global Collection Description Standard

2019 ◽  
Vol 3 ◽  
Author(s):  
Niels Raes ◽  
Emily van Egmond ◽  
Ana Casino ◽  
Matt Woodburn ◽  
Deborah L Paul
Keyword(s):  
Natural History ◽  
Large Scale ◽  
The United States ◽  
Fragmented Landscape ◽  
Global Biodiversity Information Facility ◽  
Classification Schemes ◽  
Natural History Collections ◽  
Natural History Collection ◽  
World Collection ◽  
Scientific Collections

With digitisation of natural history collections over the past decades, their traditional roles — for taxonomic studies and public education — have been greatly expanded into the fields of biodiversity assessments, climate change impact studies, trait analyses, sequencing, 3D object analyses etc. (Nelson and Ellis 2019; Watanabe 2019). Initial estimates of the global natural history collection range between 1.2 and 2.1 billion specimens (Ariño 2010), of which 169 million (8-14% - as of April 2019) are available at some level of digitisation through the Global Biodiversity Information Facility (GBIF). With iDigBio (Integrated Digitized Biocollections) established in the United States and with the European DiSSCo (Distributed Systems of Scientific Collections) accepted on the ESFRI roadmap, it has become a priority to digitize natural history collections at an industrialized scale. Both iDigBio and DiSSCo aim at mobilising, unifying and delivering bio- and geo-diversity information at the scale, form and precision required by scientific communities, and thereby transform a fragmented landscape into a coherent and responsive research infrastructure. In order to prioritise digitisation based on scientific demand, and efficiency using industrial digitisation pipelines, it is required to arrive at a uniform and unambiguously accepted collection description standard that would allow comparing, grouping and analysing natural history collections at diverse levels. Several initiatives attempt to unambiguously describe natural history collections using taxonomic and storage classification schemes. These initiatives include One World Collection, Global Registry of Scientific Collections (GRSciColl), TDWG (Taxonomic Databases Working Group) Natural Collection Descriptions (NCD) and CETAF (Consortium of European Taxonomy Facilities) passports, among others. In a collaborative effort of DiSSCo, ICEDIG (Innovation and consolidation for large scale digitisation of natural heritage), iDigBio, TDWG and the Task Group Collection Digitisation Dashboards, the various schemes were compared in a cross-walk analysis to propose a preliminary natural collection description standard that is supported by the wider community. In the process, two main user groups of collection descriptions standards were identified; scientists and collection managers. The classification produced intends to meet requirements from them both, resulting in three classification schemes that exist in parallel to each other (van Egmond et al. 2019). For scientific purposes a ‘Taxonomic’ and ‘Stratigraphic’ classification were defined, and for management purposes a ‘Storage’ classification. The latter is derived from specimen preservation types (e.g. dried, liquid preserved) defining storage requirements and the physical location of specimens in collection holding facilities. The three parallel collection classifications can be cross-sectioned with a ‘Geographic’ classification to assign sub-collections to major terrestrial and marine regions, which allow scientists to identify particular taxonomic or stratigraphic (sub-)collections from major geographical or marine regions of interest. Finally, to measure the level of digitisation of institutional collections and progress of digitisation through time, the number of digitised specimens for each geographically cross-sectioned (sub-)collection can be derived from institutional collection management systems (CMS). As digitisation has different levels of completeness a ‘Digitisation’ scheme has been adopted to quantify the level of digitisation of a collection from Saarenmaa et al. 2019, ranging from ‘not digitised’ to extensively digitised, recorded in a progressive scale of MIDS (Minimal Information for Digital Specimen). The applicability of this preliminary classification will be discussed and visualized in a Collection Digitisation Dashboards (CDD) to demonstrate how the implementation of a collection description standard allows the identification of existing gaps in taxonomic and geographic coverage and levels of digitisation of natural history collections. This set of common classification schemes and dashboard design (van Egmond et al. 2019) will be contributed to the TDWG Collection Description interest group to ultimately arrive at the common goal of a 'World Collection Catalogue'.

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