Lawrence F. Gall - US grants

Understanding future environmental change requires researchers to access and integrate data from the geological and biological sciences, in order to answer questions about how environmental change will affect life on Earth. In many cases the data needed to answer these questions already exists but, unfortunately, technology has not kept pace with research needs. This places increasing demands on researchers, who have to search for and download data from multiple separate online databases; compile published information from many different literature sources; and track down specimens housed in museum and other collections scattered around the world. The time needed to search and retrieve this information is enormous and, once found, the data often have to be standardized before they can be used. This project will tackle this problem by developing software tools to connect three established, well-supported, and critically important data sources: the Paleobiology Database (PBDB, paleontological, literature based), iDigPaleo (paleontological, specimen based) and iDigBio (neontological, specimen based). This project will allow users of any one of these databases to access and query the others at the same time, returning a much richer, combined set of data to the user. Connecting these resources will open up a whole host of research questions that are currently difficult to answer, even by multiple researchers working as a team. The development of this system will allow scientists to ask and answer new research questions affecting fields as diverse as biogeographic/niche modeling, systematics, functional morphology, evolutionary biology, ecology, climatology, conservation biology, oceanography, and petroleum geology. This project will fundamentally change the nature of the research questions that can be addressed by the scientific community.

The connectivity between modern and fossil, and specimen and literature-based resources does not currently exist. The digital infrastructure provided by the composite ePANDDA application programming interfaces (APIs) will streamline and normalize data acquisition, including retrieval from disparate data sources, and will facilitate coordination with future data initiatives. Rather than creating another portal for the aggregation of data, ePANDDA will unify results that normally would have required multiple searches on numerous platforms. For the researcher, this eliminates a significant barrier to data collection and processing. Researchers will now have the ability to collaborate across disciplinary boundaries to study earth system processes and the nature of biotic response to environmental change across both space and time. Linking publications to specimens will enrich the potential of museum collections and augment their value for both research and education. The ePANDDA project also provides an opportunity to build collaborative programs that leverage existing education and outreach activities in addition to the primary research goals.

Lepidoptera (butterflies and moths) are one of the most diverse groups of organisms on the planet: worldwide there are approximately 160,000 species, including around 14,300 species in North America. Moths and butterflies are a conspicuous component of terrestrial habitats and one of the most diverse groups of plant-feeding animals worldwide. This group insect includes species of great economic importance. Their juveniles feed on plants useful to humans, including grains, cotton, tobacco, and timber and shade trees. However, many of the adults are beneficial as pollinators and are icons of conservation as evidenced by Monarch butterflies. Given their economic importance and sheer beauty, butterflies and moths are one of the most abundant insect group in museum collections, but only a fraction of the approximately 15 million specimens in non-federal collections have had their specimen label information digitally recorded and accessible to researchers and educators. Of those specimens that have been digitized, fewer than 10% of the North American Lepidoptera species have sufficient, accessible occurrence data to make reliable predictions about habitat use, susceptibility to global change impacts, or other ecologically important interactions. This project will digitize and integrate existing, unconnected collections of lepidopterans to leverage the outstanding potential of this group of organisms for transformative research, training and outreach.

The Lepidoptera of North America Network (LepNet) comprises 26 research collections that will digitize approximately 2 million specimen records and integrate these with over 1 million existing records. LepNet will digitize 43,280 larval vial records with host plant data, making this the first significant digitization of larvae in North American collections. LepNet will produce ca. 82,000 high-quality images of exemplar species covering 60% of North American lepidopteran species. These images will enhance remote identifications and facilitate systematic, ecological, and global change research. In collaboration with Visipedia, LepNet will create LepSnap, a computer vision tool that can provide automated identifications to the species level. Museum volunteers and student researchers equipped with smartphones will image >132,000 additional research-quality images through LepSnap. Up to 5,000 lepidopteran species will be elevated to a "research ready" status suitable for complex, data-driven analyses. LepNet will build on the existing data portal (SCAN) in consolidating data on Lepidoptera to the evolution of lepidopteran herbivores in North America. Access to these data will be increased through integration with iDigBio. Data for a broad range of research, including the evolutionary ecology of Lepidoptera and their host plants in the context of global change processes affecting biogeographic distributions will be generated. The LepXPLOR! program will spearhead education and outreach efforts for 67 existing programs, engaging a diverse, nationwide workforce of 400+ students and 3,500+ volunteers. Overall, LepNet will generate a sustainable social-research network dedicated to the creation and maintenance of a digital collection of North American Lepidoptera specimens (http://www.lep-net.org/).

Arthropod parasites (specifically, insects and their relatives) are responsible for economically critical issues in human health, wildlife conservation, and livestock productivity. Because natural history collections are permanent repositories for past and present parasite specimens, these collections and their data can help address these significant societal challenges in human and animal health and safety. Natural history collections often contain specimens and ancillary materials that are completely unknown to the broader community, yet represent irreplaceable knowledge about organismal habitats, distributions, and parasite-host associations. Further, these collections yield information that can be used to model ecological processes and changes in species distributions, predict the future spread of human and animal disease, update taxonomy, and help identify under-represented parasite groups in urgent need of sampling and threatened parasite diversity in need of conservation. This project will provide digital records (i.e., specimen label data and images) of invaluable arthropod parasite collections to make research-ready baseline data accessible online, catalyzing new research and education initiatives. These newly digitized data will have immediate and long-lasting benefits for our understanding of organismal associations, biodiversity, and beyond.

The Terrestrial Parasite Tracker Thematic Collection Network (TPT-TCN) will digitize over one million arthropod specimens representing species that are significant parasites and disease vectors of vertebrates in the United States. The TPT-TCN is a collaboration among 26 research collections, and includes vertebrate and invertebrate taxonomists and curators, epidemiologists, ecologists, data-scientists, and biodiversity informatics specialists. This Partners to Existing Networks (PEN) grant allows the Yale Peabody Museum to join the collaboration, and digitize specimens that fill critical gaps in geographic and taxonomic coverage in the existing TPT-TCN. This project will integrate arthropod data with millions of vertebrate host records with vector and disease monitoring data shared by state and federal agency collaborators, creating a novel foundation for integrative, long-term research. It will also empower ongoing citizen science and public awareness campaigns with tools for understanding distribution changes of arthropod vectors and associated diseases due to environmental change and global movement. Educational initiatives include partnering with natural history museums to educate the public about parasites via science-focused lectures, exhibits, summer youth programs, informal presentations, and developing new online educational resources for teachers in underserved communities. All specimen images generated by this project will be shared with iDigBio.org and used in developing a rapid parasite identification tool, which will be accessible over the internet and smartphone apps. The TPT-TCN will also develop and implement undergraduate teaching modules focused on data held in natural history collections. These modules will be disseminated to academic institutions across the United States and made available online.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

Insects are the largest and most diverse class of animals on our planet where they play essential roles in ecosystems and the services those provide to society. Entomologists have long been engaged in collecting, preserving and depositing nearly one billion insect specimens at natural history museums around the globe. These collections form the basis for much of our knowledge about insects and provide critical information about the past from which scientists can assess current and future global change impacts. To fully realize the value of these collections, data from insect specimens must first be digitized. However, their small size, delicate structures, and traditional storage and labeling methods creates enormous challenges for large-scale digitization. Consequently, at present, only 5% of specimens have transcribed labels and less than 1% of specimens are imaged. The LightningBug project will break through this digitization bottleneck by establishing a semi-automated workflow involving advancements in robotic multi-view imaging, information extraction and 3D reconstruction. Results from this work will provide researchers with the unprecedented capability to capture specimen metadata representing time, place and taxonomic identity along with accurate three-dimensional surface morphology representing color and shape. These investigators expect LightningBug and related technologies will promote ecomorphological studies at a scale that has not been possible to date.

The LightningBug project seeks to create an end-to-end pipeline for high-throughput data acquisition from pinned insects in entomological collections. To accomplish this goal, it will: (1) further develop an existing hardware and software platform to capture multi-view imagery of both labels and specimens; (2) build robust algorithms to automatically process fragmentary views of multiple labels into separate integrated “virtual labels;" (3) connect virtual labels to structured text extraction services; and (4) apply photogrammetric analysis to assemble the 3D shape and structure of specimens. Guided by real-world science use cases that highlight the use of specimen-based multi-view imaging in studies of global change and functional morphology, the entomological collections of the Yale Peabody Museum and the Harvard Museum of Comparative Zoology will be used in rigorous test-case implementations. Results will include robust sets of annotated multi-view images, 3D models of specimens (point clouds, textured meshes), 2D reconstructed “virtual labels” and digitized specimen metadata generated from those labels. These digital specimens will present new challenges for data preservation and access, but they will also catalyze new solutions for large-scale storage and delivery of research imagery. This challenge will be addressed via a partnership with MorphoSource to develop a linked institutional repository model for data access to large digital assets such as those produced by multi-view imaging. Ultimately, the ability to capture multi-view image suites and generate virtual specimens at scale will permit new avenues for remote access to research resources, and enable the application of computer vision and machine learning to trait identification and evolution, species recognition and new species discovery. Label data from pinned insects will give researchers access to critical temporal and geospatial information necessary for relating changes in biodiversity to other biotic and environmental variables. It will also provide collections staff with a complete digital portrait of their holdings, which can enable historical research, streamline collections use and tracking, and improve data quality control. Results from this project will also have applications beyond the natural history collections and research communities, such as computer graphics, product imaging, motion pictures, 3D animation, virtual and augmented realities, and education. More information and results from this project can be found at http://lightningbug.tech

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.