Biodiversidata: an open-access biodiversity database for Uruguay – IRep – Nottingham Trent University

Abstract

Background

The continental and marine territories of Uruguay are characterised by a rich convergence of multiple biogeographic ecoregions of the Neotropics, making this country a peculiar biodiversity spot. However, despite the biological significance of Uruguay for the South American subcontinent, the distribution of biodiversity patterns in this country remain poorly understood, given the severe gaps in available records of geographic species distributions. Currently, national biodiversity datasets are not openly available and, thus, a dominant proportion of the primary biodiversity data produced by researchers and institutions across Uruguay remains highly dispersed and difficult to access for the wider scientific and environmental community. In this paper, we aim to fill this gap by developing the first comprehensive, open-access database of biodiversity records for Uruguay (Biodiversidata), which is the result of a large-scale collaboration involving experts working across the entire range of taxonomic diversity found in the country. 

New information

As part of the first phase of Biodiversidata, we here present a comprehensive database of tetrapod occurrence records native from Uruguay, with the latest taxonomic updates. The database provides primary biodiversity data on extant Amphibia, Reptilia, Aves and Mammalia species recorded within the country. The total number of records collated is 69,380, spanning 673 species and it is available at the Zenodo repository: https:// doi.org/10.5281/zenodo.2650169. This is the largest and most geographically and taxonomically comprehensive database of Uruguayan tetrapod species available to date and it represents the first open repository for the country.

ZooArchNet: Connecting zooarchaeological specimens to the biodiversity and archaeology data networks

Abstract:  Interdisciplinary collaborations and data sharing are essential to addressing the long history of human-environmental interactions underlying the modern biodiversity crisis. Such collaborations are increasingly facilitated by, and dependent upon, sharing open access data from a variety of disciplinary communities and data sources, including those within biology, paleontology, and archaeology. Significant advances in biodiversity open data sharing have focused on neontological and paleontological specimen records, making available over a billion records through the Global Biodiversity Information Facility. But to date, less effort has been placed on the integration of important archaeological sources of biodiversity, such as zooarchaeological specimens. Zooarchaeological specimens are rich with both biological and cultural heritage data documenting nearly all phases of human interaction with animals and the surrounding environment through time, filling a critical gap between paleontological and neontological sources of data within biodiversity networks. Here we describe technical advances for mobilizing zooarchaeological specimen-specific biological and cultural data. In particular, we demonstrate adaptations in the workflow used by biodiversity publisher VertNet to mobilize Darwin Core formatted zooarchaeological data to the GBIF network. We also show how a linked open data approach can be used to connect existing biodiversity publishing mechanisms with archaeoinformatics publishing mechanisms through collaboration with the Open Context platform. Examples of ZooArchNet published datasets are used to show the efficacy of creating this critically needed bridge between biological and archaeological sources of open access data. These technical advances and efforts to support data publication are placed in the larger context of ZooarchNet, a new project meant to build community around new approaches to interconnect zoorchaeological data and knowledge across disciplines.

Extending U.S. Biodiversity Collections to Promote Research and Education

“Our national heritage of approximately one billion biodiversity specimens, once digitized, can be linked to emerging digital data sources to form an information-rich network for exploring earth’s biota across taxonomic, temporal and spatial scales. A workshop held 30 October – 1 November 2018 at Oak Spring Garden in Upperville, VA under the leadership of the Biodiversity Collections Network (BCoN) developed a strategy for the next decade to maximize the value of our collections resource for research and education. In their deliberations, participants drew heavily on recent literature as well as surveys, and meetings and workshops held over the past year with the primary stakeholder community of collections professionals, researchers, and educators.

Arising from these deliberations is a vision to focus future biodiversity infrastructure and digital resources on building a network of extended specimen data that encompasses the depth and breadth of biodiversity specimens and data held in U.S. collections institutions. The extended specimen network (ESN) includes the physical voucher specimen curated and housed in a collection and its associated genetic, phenotypic and environmental data (both physical and digital). These core data types, selected because they are key to answering driving research questions, include physical preparations such as tissue samples and their derivative products such as gene sequences or metagenomes, digitized media and annotations, and taxon- or locality-specific data such as occurrence observations, phylogenies and species distributions. Existing voucher specimens will be extended both manually and through new automated methods, and data will be linked through unique identifiers, taxon name and location across collections, across disciplines and to outside sources of data. As we continue our documentation of earth’s biota, new collections will be enhanced from the outset, i.e., accessioned with a full suite of data. We envision the ESN proposed here will be the gold standard for the structured cloud of integrated data associated with all vouchered specimens. These permanent specimen vouchers, in which genotypes and phenotypes link to a particular environment in time and space, comprise an irreplaceable resource for the millennia….”

BCoN Report: Extending U.S. Biodiversity Collections to Promote Research and Education

The Biodiversity Collections Network has released its new report, Extending U.S. Biodiversity Collections to Promote Research and Education.  You are invited to download and share the summary brochure and to review the longer report that provides additional detail about this vision for the future. …”

Report urges massive digitization of museum collections | Science | AAAS

“The United States should launch an effort to create an all-encompassing database of the millions of stuffed, dried, and otherwise preserved plants, animals, and fossils in museums and other collections, a U.S. National Science Foundation (NSF)–sponsored white paper released today urges. The report, titled Extending U.S. Biodiversity Collections to Promote Research and Education, also calls for new approaches to cataloging digitized specimens and linking them to a range of other data about each organism and where it was collected. If the plan is carried out, “There will be [a] huge potential impact for the research community to do new types of research,” says NSF biology Program Director Reed Beaman in Alexandria, Virginia.

The effort could take decades and cost as much as half a billion dollars, however, and some researchers are worried the white paper will not win over policymakers. “I just wish that the report focused more on the potential benefits for noncollections communities,” says James Hanken, director of the Harvard Museum of Comparative Zoology in Cambridge, Massachusetts.

For the past 8 years, NSF has sponsored the $100 million, 10-year Advancing Digitization of Biodiversity Collections program, which has paid for nearly 62 million plant and animal specimens to be digitally photographed from multiple angles for specific research studies. New technology has greatly sped up the process. Already, researchers studying natural history and how species are related are reaping the benefits of easy access to a wealth of information previous locked in museums….”

Expanded access to images in the Biodiversity Literature Repository

“The Biodiversity Literature Repository at Zenodo is holding now over 160,000 figures originally included in scientific publications and is daily updated. Each image is open access. It has a link to the original source – also included in the image metadata – and to related items, such as the taxonomic treatment that cites the image. Originally, Zenodo has been created as a repository for the deposition of single documents, research data, files, but with an option to automate the upload (and download) automatically using its API….”

Do not publish | Science

“Biologists have long valued publishing detailed information on rare and endangered species. Until relatively recently, much of this information was accessible only through accessing specialized scientific journals in university libraries. However, much of these data have been transferred online with the advent of digital platforms and a rapid push to open-access publication. Information is increasingly also available online in public reports and wildlife atlases, and research published behind paywalls can often be found in the public domain. Increased data and information accessibility has many benefits, such as helping to improve repeatability in scientific studies and enhancing collaboration (1, 2). However, such readily accessible information also creates major problems in the context of conserving endangered species….”

Scientists Keep Accidentally Doxxing Endangered Species – Vocativ

“Publishing information about the specific locations of endangered species helps scientists, but it’s also putting those same animals at risk. A team of researchers, writing in the journal Science, is sounding the alarm bell.

In the past, it was really only scientists who read scientific journals. They were physical copies, sent to a researcher’s mailbox or the library of an academic institution. So there wasn’t much risk to publishing the exact places where rare species lived — it helped others in the field learn more about these ephemeral creatures.

Today, the stakes are different. Journal articles new and old are published online, and the rise in open access journals make more information available to the public. In some fields of science, sharing data is considered a good thing. But in the study of endangered species, it sometimes does more harm than good….”

Biodiversity Heritage Library – Expanding Access to Biodiversity Literature

“Expanding Access to Biodiversity Literature, which is funded generously by the Institute of Museum and Library Services (IMLS), will significantly increase online access to biodiversity material by positioning BHL as an on-ramp for biodiversity content providers that would like to contribute to the national digital library infrastructure through the Digital Public Library of America (DPLA). The grant proposes to address challenges facing content providers—including insufficient amounts of content, indexing of scientific names, and metadata creation—and make necessary digital infrastructure enhancements by creating an innovative model for open access to data and to support collaboration among these institutions. The project would meet the goals of the IMLS National Leadership Grants for Libraries Program by increasing access to digital services, expanding the range and types of digital content available, improving discoverability, and supporting open access….The project runs from October 1, 2015 to September 30, 2017 and will be conducted by the New York Botanical Garden in partnership with Harvard University, the Missouri Botanical Garden, and the Smithsonian Institution Libraries….”

Opening up the Natural History Heritage for Europeana

“Countless natural history treasures are deposited in museums across the world, many hidden away beyond easy access. The OpenUp! project creates a free access to these resources, offering over one million items belonging to the world’s biodiversity heritage. The objects made available through OpenUp! consist of high quality images, videos and sounds, as well as natural history artworks and specimens, and also include many items previously inaccessible to visitors. Information provided through OpenUp! is checked by scientists and made available through the Europeana portal at www.europeana.eu….”