Life on earth—its biodiversity—has been documented for hundreds of years with specimens in natural history collections, photographs, sound recordings, textual accounts, and a wide variety of other media. These physical objects provide information about thousands of species from all around the world. Records of biodiversity have been used in scientific publication and analyses, genetic sampling, and even artwork and literature. In recent decades, digital data has been added to physical biodiversity information–allowing researchers, educators, and policy makers to access these data without needing to visit or borrow from the collection.
Importantly, digital records also provide the opportunity to link information about biodiversity across databases, such that analysis beginning with a 200-year-old bird specimen, for example, can lead researchers to studies that have used that specimen, environmental data from the location where the specimen was collected, genetic sequences from the specimen, parasites of the bird species, and other data. In an article published in BioScience, a team of collaborators including Deborah Paul, biodiversity informatics community liaison with the Species File Group at the Illinois Natural History Survey (INHS), describes this network of information with biodiversity data at its core as the Digital Extended Specimen (DES).
Linking biodiversity data, and even linking biodiversity data with other types of information, is not new. Researchers have a long history of manually doing this to get a better picture of an organism, its environment, and connections within complex ecosystems. However, making these linkages manually is time-consuming, error-prone, and generally difficult to accomplish at scale or reproduce. The DES brings automation and harmonization to this, presenting a structure for a global network that spans data types, follows community FAIR guidelines (that is, ensuring data are findable, accessible, interoperable, and reusable), and engages diverse communities.
“Added features and updates to our local and international databases and data-sharing infrastructures offer researchers and collections worldwide new possibilities and potentially novel discoveries,” said Paul. “Making the Digital Extended Specimen a reality means local to global improvements for people and specimens. For specimens and their data, Digital Extended Specimens provide a richer out-of-the cabinet existence, and they also provide more sophisticated ways to foster expertise-sharing and credit humans and organizations for their work.”
The DES will transform the way science is done and will greatly advance work that addresses global change, biodiversity loss, zoonotic diseases, food and water security, and the sustainable management of natural resources. Each of these fields, and a host of others, benefit from the inclusion of biodiversity data, though all are currently limited by the degree to which these data can be accessed and incorporated into cross-disciplinary analyses.
“The DES can have its own kind of existence on the Internet as a processable entity, and is therefore not limited by the bounds of a particular data source, research initiative, or data management system,” said lead author Alex Hardisty of Cardiff University.
Implementing Digital Extended Specimens requires both social and technical steps. The social side requires collaboration and buy-in from individuals and institutions in biological and environmental data-oriented fields. While the DES will not require a change in workflow from practitioners, it will involve community-wide input, acceptance, use, and feedback along with continued data contribution.
Technically, the DES requires a standardized framework that is robust to handling legacy data, growth via new data sources, linkages that are maintained over time, and accessibility that is open yet follows legal and ethical regulations. Experimental pilots are testing these features.
Linking biodiversity data with associated information through the DES and making it a processable entity on the Internet adds incredible value to natural history collections and to the connected data, thereby supporting the cross-disciplinary research necessary for tackling today’s wicked problems. This is an active area of research, and the authors encourage broad discussion and involvement in DES development and activities.
"Here at the University of Illinois Urbana-Champaign a unique blend of world-class physical collections housed at INHS and the Prairie Research Institute intersect with biodiversity informatics expertise in the Species File Group. This synergy positions our stakeholders, our specimens, and biodiversity data firmly within this evolving network," Paul said.
The paper “Digital Extended Specimens: Enabling an extensible network of biodiversity data records as integrated digital objects on the Internet” is available online. https://doi.org/10.1093/biosci/biac060
This work has been supported by the National Science Foundation (DBI 2027654) and the European Union’s Horizon 2020 research and innovation programme (grant agreement number 871043-DiSSCo Prepare).
For more information, contact Deborah Paul at dlpaul@illinois.edu or 217-265-0419.