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ASU Biocollections grant fuels digitization of millions of specimen records


ASU natural history collections director Nico Franz digitizing specimen info

BioKIC’s work with Symbiota represents a 10-year span of bringing individual bodies of data online, and the next phase will focus on interconnecting them.

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November 29, 2021

Arizona State University knows a thing or two about natural history. The ASU Natural History Collections are composed of nine different collections — ranking among the largest collections of Sonoran desert biota in the world. 

Thousands of specimens are tucked into trays, drawers and cupboards. And, while there will always be a need for accumulating and storing natural history specimens, digital access represents an increasingly urgent need in the world of research, education and innovation. 

Fortunately, ASU is ahead of the curve in that area as well. 

The Biodiversity Knowledge Integration Center at Arizona State University has joined Integrated Digitized Biocollections as a crucial partner supporting Phase 3 of its ongoing mission to digitize natural history collections throughout North America and beyond, making them available online to researchers, educators and community scientists around the world. 

Integrated Digitized Biocollections (iDigBio) is the national hub for digitizing and aggregating high-quality specimen data for the past 10 years — nearly 130 million individual records from close to 1,000 U.S. natural history collections. This massive undertaking has been the combined effort of dozens of separately funded thematic collections networks.

ASU’s Biodiversity Knowledge Integration Center (BioKIC) represents an expansive network of biodiversity data portals through its Symbiota software package, which accounts for about 20 million unique specimen records in iDigBio’s database. 

Symbiota is a collections management tool and currently provides the sole technical and social entry point for nearly 700 institutional research collections. It is also a data discovery engine, connecting over 1,400 natural history collections through the various portals.

The National Science Foundation recently awarded ASU BioKIC $2.5 million for Sustaining Infrastructure for Biological Research, part of a larger award to iDigBio’s partnered efforts to continue to bring natural history collections online through the 40 Symbiota portal installations currently hosted by the center.

“It’s a great validation of work that we’ve been doing here out of the collections group for more than 10 years,” said Nico Franz, biocollections director and Virginia M. Ullman Professor of Ecology in the School of Life Sciences.

“iDigBio is by design an aggregator,” he said. “But now we have been singled out as the engine to bring new collections into the fold.”

The Symbiota network

ASU was a leader in building the Symbiota network and has been developing the platform for over 20 years. Throughout this entire time, Edward Gilbert, biodiversity informatician and research associate in the School of Life Sciences, has led the development of software and data publishing services. 

“Twenty years ago, this began as a small ASU initiative with a focus on a few Arizona curated botanical collections,” Gilbert said. “The nationwide success we are seeing today is the result of committed interdisciplinary collaborations. After more than a decade of working alongside iDigBio, I am thrilled that we are able to continue this work in a more official and fully funded capacity.”

Gilbert and Franz combined forces in 2011 and are now also joined by Jenn Yost, associate professor and herbarium director at California Polytechnic State University.

“I am thrilled to be a part of the team that brings transformative solutions to new collections,” said Yost. “ASU has been vital in the success of bringing together the collections community." 

The software gives individual collections managers the tools to build their own portals for specimen and observation-based information, including maps of where specimens live, specimen images and interactive identification keys. Portals are often formed around a particular region like the Minnesota Biodiversity Atlas, or around types of organisms, like California plants, lichens of North America or Pacific islands invertebrates.

These data are publicly available and searchable, providing a valuable resource for research and education. 

Supported by NSF funding incentives, small networks of collections managers around the world mobilized to take their individual collections online and publish them to the iDigBio hub using Symbiota portals. 

"As a collections manager, getting my collection's data online in a Symbiota portal was a game-changer,” Yost said. “This was especially true during COVID when we couldn't access the physical collections. My team could continue digitizing them from our living rooms. We had over 200 volunteers helping transcribe our records during the pandemic.” 

New NSF funding will enable ASU to provide better infrastructure and support for the Symbiota portal communities moving forward, including establishing three new positions: a portal infrastructure manager, a portal data manager and a portal community manager. 

In addition to user support for all users of the Symbiota system, this team will also help lead a sustainable course forward as the project continues to expand.

Katelin Pearson, research analyst in the School of Life Sciences, has been brought on as data manager. She started her journey as a botanist, working in herbarium collections, where she gained a passion for data standards, curation and management. 

“I've been on the other side of the collections management pipeline, trying to manage data and digitize natural history collections, and I appreciate the opportunity to provide the technical and collaborative support that this community needs,” she said. “We have a stellar team at ASU and a fantastic broader community of natural history collections with which we will be working closely. I love the chance to help others succeed.”

The added support of the sub-award also positions ASU to remain at the forefront of developing new data products and services – such as linkages between specimens, trait data, DNA and ecological interactions (pollination, etc.).

Looking to the future

The sub-award sets up BioKIC to play an important role in the mission of the Julie Ann Wrigley Global Futures Laboratory, a transdisciplinary initiative at ASU that aims to generate new ideas and solutions in sustainability, use-inspired research and ensuring a habitable planet and future. 

“There was this idea that we are connecting information with decision-making at the societal level. We provide the biodiversity component to that,” said Franz.  

There is both an exploration component and a monitoring component to biodiversity. Exploring the diversity of species, what has lived where, and how they are distributed gives us the ability to then examine the data collected over time and ask questions about how environments and species interactions change, and what we can learn from those changes. 

“It’s a loop between knowledge about our environment, knowledge about trends in our environment — down to the species level, down to the specimen level — and then linked with decision-making on how to sustainably manage our future,” Franz said. 

For example, as plants start to flower earlier and earlier in certain regions, this will impact the pollinators who feed on those flowers, the other insects who control and feed on the pollinators, and on up the chain. 

BioKIC’s work with Symbiota represents a 10-year span of bringing individual bodies of data online, and the next phase will focus on interconnecting them. This will open up the ability to examine online data collections through their biological interactions, and eventually predict how environments and interactions are faring as documented through these collections. 

“This is our new frontier, building the Extended Specimen Network,” Franz said. “There’s a past, present and future to it.”

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