NSF News 12-082
NSF Awards Second Round of Grants to Advance Digitization of Biological Collections
Funding will shed light on current "dark data," and integrate genetic, organismal, ecological information--past and present
May 1, 2012
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Centuries of exploration and discovery have documented the diversity of life on Earth.
Records of that biodiversity are, for the most part, distributed widely across varied and distinct natural history collections. Until now, that has made assessing the information in these collections a difficult task.
Last year, the National Science Foundation (NSF), through its Advancing Digitization of Biological Collections (ADBC) program, responded to the need for greater accessibility of biological collections data by awarding four major grants.
The funding created a national resource of digital data documenting existing biological collections.
This year, NSF funded four, additional major grants, along with two smaller awards that link to and enhance one of last year's projects.
These awards increase the diversity of organisms to be digitized, the techniques that will be developed for processing specimens, and the scope of a paleontology project.
They also expand the research challenges that may be addressed by future scientists.
Biological diversity is important to the future of the planet. Incomplete information on species, their distributions and environmental and biological changes over time make it difficult, however, to assess the status of and changes in biodiversity.
Such information is critical in the face of changes in climate, invasive species and other threats.
Much of the relevant information exists in the nation's research collections. But because that information is not integrated as a searchable resource, it exists as "dark data"--not accessible online and therefore effectively hidden to most biologists, policymakers and the general public.
"The ADBC program continues to grow in the breadth of its collections, including fossils, and in the depth of additional information about each specimen," says John Wingfield, NSF assistant director for Biological Sciences.
"The collections being digitized are unprecedented in their worth to research and education, and hold huge potential for future development and integration with other biological data from genomes to phenomes," says Wingfield.
"With the diversity of information digitized, these projects are addressing issues of interoperability, access and analysis--'big data.' The benefits will be felt for many generations to come."
The ADBC program will result in more efficient and innovative ways to provide access to information in biodiversity research collections.
It will also speed up the process of integrating information on the paleontological, genetic, ecological, organismal and molecular biology of specimens in collections, and information on the ancient history of life on Earth.
A wealth of data is linked with these specimens. For example, standardized digital photos may be linked with DNA sequences, phenology information, host organisms, environmental variables at the collecting localities, and electron micrographs.
Training for future researchers on collections techniques, informatics technology and data integration is part of the efforts.
The awards provide graduate and undergraduate training opportunities, and outreach to K-12 educators, students, and non-scientists.
Each of four Thematic Collections Networks (TCNs) focuses on "grand challenge" (major scientific) questions in biodiversity and offers multiple research opportunities as data become widely available. The TCN awards include 64 institutions in 34 states.
New TCN awards this year are:
Mobilizing New England Vascular Plant Specimen Data to Track Environmental Changes
PI (Principal Investigator): Patrick Sweeney, Yale University
Collaborators: Christopher Neefus, University of New Hampshire; Charles Davis, Harvard University; Erika Edwards, Brown University; David Barrington, University of Vermont; Karen Searcy, University of Massachusetts Amherst; Richard Primack, Boston University; and scientists at eight other institutions
Summary: Natural history collections of pressed and dried plants assembled over the past three centuries contain a treasure trove of environmental information that will help understand global environmental change. The goal of this project is to digitally capture more than 1.3 million specimen images, and associated information about where and when these plants grew--and the timing of buds and flowers across New England.
The group will also develop novel high-throughput digitization technologies to increase efficiency and reduce the cost of harvesting pictures and data from specimens.
The data from this project will be of immediate use to scientists who study climate and land-use change, and will provide a better understanding of how global change will affect the distribution of native and introduced plant species.
The project will benefit research in taxonomy, ecology, morphology, biogeography and evolutionary history by making data available on an entire regional flora in an electronic format. The project will involve citizen scientists, school groups and students.
Digitizing Fossils to Enable New Syntheses in Biogeography - Creating a PALEONICHES-TCN
PI (Principal Investigator): Bruce Lieberman, University of Kansas
Collaborators: Alycia Stigall, Ohio University; Jonathan Hendricks, San Jose State University; and scientists at three other institutions
Summary: Museum collections of fossils hold millions of records, with data on the distribution of species over space and immense spans of time. They provide large amounts of data useful for studying what causes species to migrate, go extinct, or evolve.
These collections are of great relevance, scientists say, for considering how global change has and will continue to affect life on this planet.
However, to reach their scientific potential, the data need to be available online and in a format that facilitates quantitative biogeographic analyses.
This project will capture information in electronic form about the age and precise location of fossil specimens from several important paleontological collections; develop improved computer software to integrate paleontological specimens with modern specimen data; digitize nearly 450,000 specimens in 900 species from museums throughout the United States; and focus on three different time periods in the history of life over the past 500 million years.
Online digital atlases will be created, illustrating and describing these fossils and providing maps showing where they can be found.
A handheld device "app" will be developed to use these atlases in the field. The online and portable device digital atlases will educate amateur paleontologists and K-12 students about fossils.
The Macrofungi Collection Consortium: Unlocking a Biodiversity Resource for Understanding Biotic Interactions, Nutrient Cycling and Human Affairs
PI (Principal Investigator): Barbara Thiers, New York Botanical Garden
Collaborators: Joseph Ammirati, University of Washington; Donald Pfister, Harvard University; Andrew Miller, University of Illinois at Urbana-Champaign; Timothy James, University of Michigan; Thomas Bruns, University of California at Berkeley; Mark Cubeta, North Carolina State University; and scientists at 28 other institutions.
Summary: From wood-rotting fungi that clear the forest floor of dead wood to the chanterelles and truffles in our food, mushrooms and other large showy fungi (macrofungi) play a critical role in the lives of plants and animals, including the health and welfare of humans.
Yet the numbers of different species of these fungi are largely unknown.
Understanding the biodiversity of fungi will be critical in analyzing the effects of habitat change, nutrient cycling in ecosystems, and distributions and diversity of host organisms.
Scientists in the United States have been studying and collecting macrofungi for the past 150 years, which has produced a legacy of some 1.4 million dried scientific specimens, in 35 institutions in 24 states.
These institutions joined forces in an effort to digitize and share online data associated with these specimens.
The resulting resource will enable a national census of macrofungi, and will allow researchers to better understand the diversity of these organisms and the relationships between macrofungi and the other species, such as lichens, in which fungi and algae form a wide variety of biotic partnerships.
Citizen mycologists in clubs and nature societies across the country play an important role in documenting macrofungi diversity. They are a critical link between professional scientists and the general public.
In this project, a unique collaboration of citizen mycologists will combine forces with professional staff members at the scientific institutions housing collections of fungi to help to create online resources.
Southwest Collections of Arthropods Network (SCAN): A Model for Collections Digitization to Promote Taxonomic and Ecological Research
PI (Principal Investigator): Neil Cobb, Northern Arizona University
Collaborators: Wendy Moore Brusca, University of Arizona; M. Deane Bowers, University of Colorado at Boulder; Boris Kondratieff, Colorado State University; James Cokendolpher, Texas Tech University; John Oswald, Texas AgriLife Research; Nico Franz, Arizona State University; Frank Krell, Denver Museum of Nature and Science; Charles Bundy, New Mexico State University; Kelly Miller, University of New Mexico
Summary: From beetles to scorpions, spiders to ants, the ground-dwelling arthropods are a showcase of biodiversity. They're valuable players in the desert and mountain ecosystems of the Southwestern United States.
The Southwest Collections of Arthropods Network (SCAN) project brings together 10 arthropod collections at universities and museums throughout this region to create a virtual information network on ground-dwelling arthropods.
These 10 natural history collections document much of the Southwest's biodiversity, but currently the data associated with their millions of arthropod specimens are virtually inaccessible to researchers interested in this region.
SCAN will develop methods for integrating existing databases, catalogue-image specimens, new electronic identification techniques, and a virtual library of ground-dwelling arthropods (beetles, grasshoppers, spiders and ants).
The project members will work with an existing software project called Filtered Push that enhances the capacity of far-flung experts to contribute identifications and annotations of data that may be shared across the network.
The comprehensive SCAN online library and expert information will be available to the public as well as to professionals in taxonomy, ecology, and climate change science.
New Partners to Existing Networks (PENs)
This year, ADBC Partners to Existing Networks (PENs) were funded that will enhance projects begun with the initial round of funding last year. The new partners will add their collections to fill in gaps identified in the original network proposals.
The two PEN awards are:
Digitization of North American Bryophyte and Lichen Specimens from Florida Herbaria
PI: Norris William, University of Florida; and scientists at four other institutions in Florida
This PEN will add information on subtropical bryophytes (mosses and liverworts) and lichens to a broad-scale project on plant biodiversity.
Addressing Colorado Lichens and Bryophytes as Sensitive Indicators of Environmental Quality and Change
PI: Timothy Hogan, University of Colorado at Boulder
This PEN project focuses on high altitude collections of lichens, the group of fungi-algae biotic associations that are important environmental indicators of atmospheric pollution.
Marasmius, a fungus in the tropical rainforest of Belize, is important to its ecosystem.
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A researcher enters fossil locality data with georeferencing tools to reconstruct the past.
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Scientist Gertrude Burlingham wrote these field notes from a mid-20th century collecting trip.
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NSF is fostering development of a partially automated method for capturing specimen images.
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Careful positioning of specimens and labels is required for high-quality images.
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Cheryl Dybas, NSF, (703) 292-7734, email: email@example.com
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