Digital Data in Biodiversity Research Conference: Full Schedule

Please join us for the 8th Annual Digital Data in Biodiversity Research Conference: Synthesizing & Harmonizing Data for Integrated Biodiversity Research.

9:00am CDT

Welcome

Speakers

Jillian Goodwin

Wednesday May 29, 2024 9:00am - 9:15am CDT
Burge Union

9:15am CDT

Managing Biodiversity Data in the Blockchain: Full Tracking of All Data Transactions Through Time in Managing Systematic Collections

Biodiversity data management is achieved via a single, correct, authoritative version. Other than inclusion of a few fields to preserve “verbatim” versions of key information, in largest part, current protocols in managing biodiversity data do not preserve the “lineage” of previous versions of information, much less the attribution of who did what and when. A collaborative effort between the Institute for Information Sciences and the Biodiversity Institute at the University of Kansas has been exploring blockchain-based technology solutions as a means of preserving a much-richer suite of information in the process of creating and managing biodiversity information records, and specifically data records associated with natural history museum specimens. We have developed a working prototype that allows large specimen datasets to be imported, edited, and batch-updated; the system logs all values and changes made to the data, along with information about the specific user who made the changes. User accounts can be created with different levels of permission and supervision. As a consequence, one can now create reports of what has been done by whom over the entire history of a data record. The result is a far-richer suite of information associated with data records in biodiversity informatics.
Co-authors:
Fernando Machado-Stredel, Department of Biology, University of New Mexico;
Ali Khalighifar, Center for Bioimage Informatics, Department of Developmental Neurobiology, St. Jude Children’s Research Hospital;
Drew Davidson, Institute for Information Sciences, University of Kansas

Speakers

Andrew Townsend Peterson

University Distinguished Professor, University of Kansas

Wednesday May 29, 2024 9:15am - 9:45am CDT
Burge Union

Plenary Speaker

9:45am CDT

Hosts, parasites, and microbiomes: A system for studying natural complexity in a changing world.

Natural history collections offer necessary, but underutilized, infrastructure for monitoring and addressing emerging disease threats. For example, the extended specimen captures not only host responses to pathogen infection, but also the potential role of ectoparasites in transmitting a pathogen, and the impact of beneficial microorganisms on infection success in both host and ectoparasite vector. Through associated sample metadata, we can examine how these nested communities of interacting hosts, ectoparasites, and microorganisms respond to habitat loss or geographic distance. We can additionally apply advanced sequencing technologies and protocols developed for ancient samples to the historical holdings of museums to understand how host-pathogen dynamics have changed through time. While these collections offer obvious value toward building resiliency to zoonoses, we can also improve the ways natural history museums sample, document, and share components of the extended specimen. By enhancing collections that specialize on parasites, pathogens, or microorganisms, we also build the power of natural history collections to address pressing zoonotic threats. This type of holistic, relationship-based approach will allow biodiversity and public health researchers to better leverage natural history collections toward the goals of interdisciplinary collaboration, open science, pathogen surveillance, and zoonotic resilience.

Speakers

Kelly Speer

Director, Michigan Pathogen Biorepository & Assistant Professor, Department of Ecology & Evolutionary Biology, University of Michigan

Dr. Kelly Speer (she/her) is an Assistant Professor in the Department of Ecology and Evolutionary Biology at the University of Michigan and the Director of the Michigan Pathogen Biorepository. Speer’s research leverages the extended specimen to examine the impact of environmental... Read More →

Wednesday May 29, 2024 9:45am - 10:15am CDT
Burge Union

Plenary Speaker

10:30am CDT

Exploring Harmful Algal Blooms in the Caloosahatchee River

The Calooshatchee River Estuary is a unique ecosystem with watershed that contributes to the Everglades. The river, along with other waterways in southwest Florida, has seen a rise in Harmful Algal Blooms (HAB), a common explanation for this trend is large agricultural practices and water run off from Lake Okeechobee. Through the use of time series analysis of Landsat satellite imagery, this project aims to be an exploratory study to identify other potentially contributing factors that are correlated, directly or inversely, with the presence of HABs by focusing on a few Regions of Interest (ROIs) in the Caloosahatchee River and Lee County Florida. Methods and tools being used include but are not limited to NDVI, reflectance metrics, emissivity metrics, and floating algal index.

The presentation will also include future applications that could contribute to better understanding this area's biodiversity such as sample collection, drone imagery, and structural imaging.

Speakers

Kit Lewers

Conference Coordinator, iDigBio

Wednesday May 29, 2024 10:30am - 10:45am CDT
Burge Union

Concurrent 1: Using digital data for conservation stewardship and management

10:30am CDT

Overcoming large scale challenges in tomography: introducing resources from the Non-Clinical Tomography Users Research Network (NoCTURN)

Our ability to visualize and quantify the internal structures of objects via Computed Tomography (CT) has fundamentally transformed science. Communities utilizing CT are numerous and diverse, with thousands of researchers producing thousands of tomographic datasets annually. The varied objectives of research groups and differing laboratory and data sharing protocols have resulted in a fragmented CT imaging environment across the world. The Non-Clinical Tomography Users Research Network (NoCTURN) is where the science of collecting and interpreting CT data meets the ‘nuts and bolts’ of good policies and best practices that ensure those data remain available and understandable by a broad community. NoCTURN has been working to address barriers to FAIR (Findability, Accessibility, Interoperability, Reuse) and open science principles for tomographic data, by leveraging input from a coordination network of more than 100 tomography educators, researchers and industry stakeholders, all gathering regularly to exchange experiences and ideas. Here, we demonstrate how NoCTURN is working to agree upon and aggregate community standards for tomographic data. We develop resources to help our community achieve their tomographic goals and facilitate the broader use of CT data among non-scientists. We share some of those resources, and highlight the benefits of working in a far-reaching coordination network.

Speakers

Jaimi Gray

Post-doc, Florida Museum of Natural History

Wednesday May 29, 2024 10:30am - 10:45am CDT
Burge Union

Concurrent 2: Innovative imaging techniques for enhancing specimen-based discoveries

10:30am CDT

Innovations in Collections-Focused Education and Outreach

The iDigBio Education and Outreach team has recently resumed open online meetings where invited members of the natural history education community highlight their innovative approaches to STEM programs. Some of the presenters have included members of the Yale Peabody Museum’s EVOLUTIONS (Evoking Learning and Understanding through Investigations of the Natural Sciences, or EVO for short) program and Bishop Museum’s PILSBry (Pacific Island Land Snail Biodiversity Repository) Thematic Collections Network (TCN). The iDigBio Education and Outreach team has also been focusing on incorporating social media platforms as a vital tool for science communication to broad audiences. This presentation will explore the varied new and exciting ways that iDigBio and TCN communities are advancing STEM education and outreach, how science communication can be effectively used in museum settings, the importance of mobilizing and making use of collections data in education, and ways to implement this work at other institutions and programs.

Co-authors: Norine Yeung, Bishop Museum; Elizabeth Ellwood, iDigBio

Speakers

Shyla Davidson

Wednesday May 29, 2024 10:30am - 10:45am CDT
Burge Union

Concurrent 3

10:45am CDT

Combining Museum Collections and Predictive Modeling to Survey a Cryptic Taxon

Surrogate species can be used to predict distributions where data on target species are limited or difficult-to-obtain. We examined if historical museum records of three crayfish species which exhibit the same burrowing behavior, similar habitat associations, and sympatric ranges could be used as surrogate species in ecological niche models (ENMs) to predict habitat suitability for each other. Further, we examined if a supraspecific ENM trained on the historical presences of all three species could successfully predict habitat suitability for burrowing crayfish in Missouri, USA. Taxonomic revisions, subterranean lifestyles, and a paucity of distributional data on burrowing crayfish currently limit biologists from confidently determining the ranges of species and geographic areas of conservation importance. We discuss how digital data, museum specimens, and current statistical methods can assist with the conservation of cryptic and undersampled species.

Speakers

Caitlin Bloomer

Wednesday May 29, 2024 10:45am - 11:00am CDT
Burge Union

Concurrent 1: Using digital data for conservation stewardship and management

10:45am CDT

Sphaeroptica: A tool for 3D taxonomy and geometric morphometrics on arthropods

Digitizing collections is a major challenge for natural science institutions. Thanks to various techniques developed over the years, most collection specimens can now be efficiently digitized. However, arthropods present a unique challenge due to their complex textures and structures, which can be tiny, transparent, hairy, shiny or dark. Consequently, existing workflows are limited to the scientific study of specimens requiring measurements, such as morphometric geometry. In response to this challenge, Sphaeroptica was developed with the aim of returning to the fundamental principles of photogrammetry. Sphaeroptica serves as a 3D viewer of a sphere of oriented 2D images, enabling users to visualize specimens and perform geometric measurements. It effectively displays complex structures such as chaetae and setae, using high-resolution stacked images instead of an approximate, simplified 3D model. Metric comparison of measurements obtained with Sphaeroptica on several case studies shows that differences with those measured on high-resolution 3D models derived from microcomputed tomography images are less than 1%, making Sphaeroptica's workflow suitable for accurate measurements of small and complex specimens such as arthropods.

Speakers

Yann Pollet

Wednesday May 29, 2024 10:45am - 11:00am CDT
Burge Union

Concurrent 2: Innovative imaging techniques for enhancing specimen-based discoveries

10:45am CDT

New Professional Development Offerings from the iDigBio Digitization Academy

iDigBio (the US National Science Foundation’s National Resource for Advancing Digitization of Biodiversity Collections) is working towards a sustainable Digitization Academy that offers a set of complementary professional development courses on topics relevant to the digitization of biodiversity observations and specimens. The offerings began in 2021 with two 4-day courses: (i) Introduction to Biodiversity Specimen Digitization and (ii) Public Participation in Digitization of Biodiversity Collections. In 2022 and 2023, three additional courses were developed: (i) Digital Imaging for Biodiversity Collections, (ii) Introduction to Photogrammetry for Biodiversity Specimen Collectors, and (iii) Introduction to Immersive Media for Biodiversity Collections. With this poster, we will introduce the 2024 course offerings and other Digitization Academy resources for the community. Stop by to meet iDigBio’s new Workforce Development Manager, Kalina Jakymec.

Co-authors: Austin Mast, Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, FL 32306

Speakers

Kalina Jacymec

Wednesday May 29, 2024 10:45am - 11:00am CDT
Burge Union

Concurrent 3

11:00am CDT

Further Development of SC Herbarium Data Entry Standards to Streamline Data Entry & Species Tracking

The South Carolina Department of Natural Resources Natural Heritage Trust (SCDNR NHT) Botany and Plant Conservation Program partnered with the University of South Carolina A.C. Moore Herbarium to supplement data standards for the SERNEC (Symbiota based SEINET portal) database, specifically for South Carolina (SC) herbarium specimen data. Herbarium data managers frequently receive questions about how to enter data from herbarium specimens that do not match any of the provided fields. This may occur because fields were written broadly to accommodate many different types of specimens. SCDNR NHT strives to come up with unambiguous data standards for SC herbarium specimens to facilitate concise data entry and provide a usable resource for all SC and interested herbaria . These data standards will be integrated into R scripts used to process data downloaded from SERNEC to assist with ‘rare’ and ‘species of conservation concern’ tracking. All SC herbaria and a few of our neighboring states’ herbaria were contacted to set up a virtual meeting to discuss data standards and provide feedback. After hearing from herbaria representatives, we compiled data standards into an indexed PDF with examples and made it available to all herbaria. Data processors will be following these data standards going forward.

Speakers

Csilla Czako

Botany Data Specialist, SCDNR NHT Botany and Plant Conservation Program

Wednesday May 29, 2024 11:00am - 11:15am CDT
Burge Union

Concurrent 1: Using digital data for conservation stewardship and management

11:00am CDT

A Novel Cryptogam Herbarium Specimen Imaging Procedure Prioritizing Both Specimen and Label

The South Carolina Department of Natural Resources Natural Heritage Trust (SCDNR NHT) Botany and Plant Conservation Program tracks vascular and non-vascular imperiled species and species of conservation interest in SC. Data on species occurrences comes from various sources; however, herbarium specimens are of special interest because they are physical records of occurrences that can be re-examined to confirm identifications. SCDNR conservation partner, University of South Carolina Herbarium (USCH), is currently repackaging and imaging cryptogam specimens. To preserve the integrity of this collection, specimen packets are being created and the specimens will be rehoused in the new filing system. While identifying specimens from these images is not favorable, there are benefits to imaging, like identifying reproductive structures and quantifying available material for future testing. SCDNR has developed a procedure to image the specimen label material, as well as the creation of image tags in collaboration with ASU, UTENN, and DUKE for Bryophyte Portal. Tags can be applied in batch and through individual examination to help researchers identify images with label data, an organism, sporophyte present and more. Tags related to image workflows, like microscope and stacked focus photography, can be utilized to highlight diagnostic characteristics to confirm species identification.

Speakers

Hannah Berberich

Wednesday May 29, 2024 11:00am - 11:15am CDT
Burge Union

Concurrent 2: Innovative imaging techniques for enhancing specimen-based discoveries

11:15am CDT

Entomology meets engineering: Deciphering the workings of the bee stinger and beyond

Many of us will have had the unpleasant experience of being stung by a bee. What we may not realise in that instant is the remarkable feat of evolution that the bee stinger constitutes. When a bee stings the stinger comes away from the bee body and continues to sting autonomously. Its piercing parts move in a reciprocating motion, propagating the stinger deeper into tissue while simultaneously pumping venom by moving a set of two collapsible pistons. We set out to understand the kinematics and fluid flow patterns of this unusual micropump. We started by studying the 3D morphology of the stinger using microCT. This allowed us to create upscaled 3D printed models to replicate stinger pumping behaviours using measurements obtained from high-speed videography analysis. The stinger is challenging to observe and difficult to manipulate. The combination of microCT and 3D printing brings this system into the realm of tractable study. Using the same research framework we are starting to examine other stingers/ovipositors within the Hymenoptera. We are working in collaboration with ANIC and the Australian Synchrotron to image a large range of specimens specialised in piercing/sawing into different kinds of substrates.

Speakers

Fiorella Esquivel

UNSW

Wednesday May 29, 2024 11:15am - 11:30am CDT
Burge Union

Concurrent 2: Innovative imaging techniques for enhancing specimen-based discoveries

11:30am CDT

Using TaxonWorks Visualization Tools to Improve Data Quality at the INHS Insect Collection

The INHS Insect Collection currently exports data from about 1.2 million collection objects representing over 2.7 million specimens to various data aggregators. However, the data has been created piecemeal over the last 30 years from various grant-funded projects, and has numerous quality issues resulting from uneven effort and funding, differences in digitization specialist training effort, and legacy migration issues.

Recently, we have been attempting to solve a number of data quality issues using tools in TaxonWorks, GBIF, and iDigBio. In this talk, we demonstrate improvements in quality using a some of these tools.

Speakers

Thomas "Tommy" McElrath

Wednesday May 29, 2024 11:30am - 11:45am CDT
Burge Union

Concurrent 1: Using digital data for conservation stewardship and management

11:30am CDT

MorphoSource 3D Data Repository: New Features and Capabilities Empowering Media Contributors and Consumers

MorphoSource is a publicly accessible 3D data repository where subject experts, educators, and the public can find, view, interact with, and download 3D/2D media representing physical objects important to the world’s natural history, cultural heritage, and scientific collections. Over 193,000 media datasets have been contributed by ~2,150 contributors and have been downloaded over 595,500 times by a community of ~21,000 registered users. MorphoSource is under active development, with a team of developers continually improving the platform. We will discuss new and upcoming MorphoSource features. Features that have already been added include anonymous reviewer access links, improved media download review, 3D viewing and measurement improvements, a new collection type called a “media list” akin to a “playlist”, standardized data vocabularies, API metadata query and file downloading, and remote records hosted by external (e.g., institutional) file servers. A major feature to be released in Q2 2024 is an overhaul to how museum teams manage their media in MorphoSource, simplifying workflows and expanding team capabilities, and empowering imaging facilities. Other features that will be released in the future include automated tiering of data between hot and cold storage, decreasing storage costs significantly, and substantial site speed increases.

Speakers

Julie Winchester

Wednesday May 29, 2024 11:30am - 11:45am CDT
Burge Union

Concurrent 2: Innovative imaging techniques for enhancing specimen-based discoveries

11:30am CDT

On the problems of databasing indigenous knowledge

The Biodiversity Institute (BI) has a project to add a non-European perspective to the Panorama Exhibit. This contains 213 species, all accessioned and databased by the BI. It has been proposed to add Native American names and knowledge of uses to the labels of the species. This begs a number of questions: (1) in what languages. (2) With what alphabet (3) Who should be the partners. (3) What parts of the knowledge are "proprietary" of a nation or tribe. And last but not least, (4) knowledge is only a part of a world view. How one represents a world view in a database? These problems are discussed and exemplified in the context of the Panorama

Speakers

Jorge Soberon

Wednesday May 29, 2024 11:30am - 11:45am CDT
Burge Union

Concurrent 3

11:45am CDT

The impact of digital data on systematic, phylogenetic, and genomic research Quantifying the impact of MorphoBank on systematic and phylogenetic research

MorphoBank is a digital database and workspace for evolutionary research with content generated by scientists and published in peer-reviewed research articles. MorphoBank has aided taxonomic experts studying biodiversity by providing access to 1,019 morphological character matrices and 170,026 2D and 3D images for systematic and phylogenetic research through 1,586 public projects that meet the Findable, Accessible, Interoperable, and Reusable (FAIR) data principles. These open-access MorphoBank projects are associated with data from 236 different sources, including papers from subscription journals such as the Journal of Vertebrate Paleontology, Cladistics, Zoological Journal of the Linnean Society, and Journal of Systematic Palaeontology. Since 2020, MorphoBank has been cited at least 566 times, and within the last year has been cited 160 times. Here, we examined the use and impact of MorphoBank data on systematic and phylogenetic research and found that most data are used in phylogenetic analyses, describing new species, and examining diversification of taxonomic groups which spans a wide-range organisms from vertebrates such as dinosaurs, reptiles, and mammals (including studies of human evolution) to plants, invertebrates, and micro-organisms.

Speakers

Brooke Long-Fox

MorphoBank Data Curation Scientist, Phoenix Bioinformatics

Wednesday May 29, 2024 11:45am - 12:00pm CDT
Burge Union

Concurrent 1: Using digital data for conservation stewardship and management

12:00pm CDT

M-PABI: A Database Model for the Extended Specimens of a Pathogen Biorepository

Natural history collections serve as vital infrastructure for monitoring and combating emerging zoonotic diseases by documenting wildlife-pathogen interactions through time and space. Flexible and searchable databases are essential for storing and facilitating access to the object data, preparation types, and collection occurrences that document the full story of the extended specimens within these collections. This poster presents the development of a Specify database and Darwin Core metadata schema for the Michigan Pathogen Biorepository (M-PABI), addressing this need for accommodating various specimen data types and complex host-pathogen relationships. The challenges and solutions discussed provide insights into creating flexible data architectures applicable to interconnected organismal collections. Holistic databases such as the one detailed here can enable interdisciplinary collaboration, open science, and enhanced pathogen surveillance, ultimately contributing to zoonotic resilience and biodiversity research.

Speakers

Summer Mengarelli

Wednesday May 29, 2024 12:00pm - 12:15pm CDT
Burge Union

Concurrent 1: Using digital data for conservation stewardship and management

12:30pm CDT

Lunch

Wednesday May 29, 2024 12:30pm - 2:00pm CDT
Burge Union

Lunch

2:00pm CDT

Neural Radiance Field and Gaussian Splatting techniques for 3D modeling of biodiversity

This presentation will cover emergent AI-assisted, 3D visualization and surface reconstruction pipelines and contextualize these tools alongside the older methods of structure-from-motion (sometimes called photogrammetry). A brief overview of this field and an example pipeline for implementation will be demonstrated. Initial results from Neural Radiance Field and Gaussian Splatting algorithms with surface reconstruction capabilities will be compared, and these algorithms will be assessed for their fitness for morphometric analyses and other uses. Some of the key differences between these methods and "work-horse" structure-from-motion methods will be highlighted, with recognition of cases where these cutting-edge methods succeed where structure-from-motion previously failed.

Speakers

Alex Adkinson

Wednesday May 29, 2024 2:00pm - 2:15pm CDT
Burge Union

Discussion Session: Utilizing Innovative Media Technologies for Research

2:00pm CDT

Discussion Session: Trait data from herbarium specimens: What is needed?

Herbarium specimens have long been at the heart of plant taxonomy and systematics but are increasingly appreciated as immense sources of trait data across space, time, and phylogeny. This discussion session will open with a summary on the past and current state of herbarium-based functional trait research, outlining past successes, potential limitations, and future promise. The discussion will focus on guiding question such as: What is needed to advance herbaria as centers for plant functional trait research? How should extracted trait data be archived to allow effective re-use? What new approaches might enable new trait-based discoveries in the many millions of existing specimens? How can we anticipate future needs by re-thinking our methods during new field collecting? Though focused on plant collections, the discussion extends well beyond herbaria to other biological collections, and a wide diversity of perspectives are encouraged.

Speakers

Rob Guralnick

Vertnet | University of Florida | University of Colorado Museum of Natural History

Mason Heberling

Associate Curator of Botany, Carnegie Museum of Natural History

Will Weaver

Wednesday May 29, 2024 2:00pm - 3:30pm CDT
Burge Union

Discussion Session: Trait data from herbarium specimens: What is needed?

2:15pm CDT

The diffusion diaries: using diffusible iodine-based contrast-enhanced Computed Tomography for high-throughput imaging of the anatomy of natural history specimens in 3D

Each specimen housed within natural history collections represents a treasure trove of anatomical knowledge waiting to be uncovered. To reveal soft tissues inside fluid-preserved specimens, diffusible iodine-based contrast-enhanced CT (diceCT) is a commonly used method that involves staining specimens with an iodine solution, increasing the radiopacity of soft tissues so they can be imaged using X-ray CT. The recent diceCT effort at the Florida Museum of Natural history is one of the largest and most taxonomically broad soft tissue imaging efforts in the world, with over 200 datasets produced covering fishes, amphibians, reptiles, and mammals. As part of the openVertebrate (oVert) Thematic Collections Network, these datasets are freely available via MorphoSource for research, education, art, and other purposes. We have refined methods for the application of diceCT for natural history collections, and we explore best practices informed by recent work in the field. We present recommendations including predictions for staining duration, suggestions for optimal staining techniques, and recommendations for scanning and post-processing. As diceCT continues to be a widely employed method for non-destructively documenting the soft anatomy of alcohol-preserved museum specimens, we hope that these datasets and methods will contribute towards the growing stock of digital anatomy in online repositories.

Speakers

Jaimi Gray

Post-doc, Florida Museum of Natural History

Wednesday May 29, 2024 2:15pm - 2:30pm CDT
Burge Union

Discussion Session: Utilizing Innovative Media Technologies for Research

2:30pm CDT

NASA BioSCape: Modeling Biodiversity and Invasion in the Greater Cape Floristic Region Using Advanced Remote Sensing and MultiScale Imagery Techniques

In the face of increasing ecological threats posed by invasive species, accurate detection and modeling are essential for effective management and mitigation. This presentation details a groundbreaking study focused on the invasion of non-native tree species in the Greater Cape Floristic Region(GCFR) of South Africa, a biodiversity hotspot, where these species threaten the native fynbos vegetation. Traditionally, hyperspectral techniques have been used in local spatial settings (Durán et al., 2019; Schneider et al., 2017) so this is not only exploring the questions of how we can model invasion using hyperspectral data and multiscale imagery at a large scale, but also how effective it is at predicting low density invasion when using validated, ground truth data? Utilizing an integrated remote sensing approach, this research leverages data from the Sentinel Satellite, alongside advanced airborne imaging sensors mounted on NASA’S G3 and G5 research aircraft. Notably, this project marks NASA's inaugural Biodiversity field campaign that integrates airborne imaging spectroscopy, lidar, and field observations, setting a new standard for ecological monitoring and biodiversity conservation using remote sensing technologies.

The study employs innovative analytical techniques, including band dimensionality reduction and principal component analysis to enhance the understanding of spectral signatures that differentiate invasive from native plant species. The spectral data is used to calculate three diversity metrics: alpha, beta, and gamma diversity to understand diversity in and between communities. By analyzing these diversity metrics, the research identifies specific areas most at risk and provides crucial data to inform conservation strategies.

Co-authors: Peter Adler, Alanna Rebello, Elisa Van Cleemput, Katie Suding, Ben Poulter, Ayia Lindquist, Meghan Hayden, Cibele Hummel do Amaral, Laura Dee

Speakers

Kit Lewers

Conference Coordinator, iDigBio

Wednesday May 29, 2024 2:30pm - 2:45pm CDT
Burge Union

Discussion Session: Utilizing Innovative Media Technologies for Research

2:45pm CDT

Bridging historical museum collections with evolutionary and medical applications

Our knowledge of developmental biology and its implications to medical and evolutionary realms is limited to a handful of organisms, commonly known as "model organisms". Because of their evolutionary history and the limited range of morphologies represented by these organisms, our current understanding of how development shapes evolution and the mechanisms shaping morphological variation is limited. However, a different source of data can fill this gap: museum collections. Indeed, hundreds of years of sampling allowed us to accumulate largely unexplored collections that contain both genomic and morphological information. I predict that museum collections will be increasingly important for not only resolving long standing questions related to the history of life, but also the mechanisms and rules dictating underpinning its function.

Speakers

Matteo Fabbri

Wednesday May 29, 2024 2:45pm - 3:00pm CDT
Burge Union

Discussion Session: Utilizing Innovative Media Technologies for Research

3:00pm CDT

Documenting Biodiversity with 360-degree Photography and Videography

Capturing omnidirectional digital media potentially documents individuals, populations, and habitats in far richer ways than text descriptions, traditional digital images/video, and other strategies. Here, we present protocols that we are developing that apply the latest consumer- and professional-grade technologies and best-practice recommendations to biodiversity research and conservation needs. Our protocols have the additional benefit of producing media that can be used for immersive media delivery (e.g., using a VR headset), as well as 3D modeling of a site using structure-from-motion photogrammetry. The benefits of 360 cameras might reasonably make it an essential tool for biodiversity collecting expeditions and similar in the future.

Co-authors: Nicole James, Florida State University

Speakers

Austin Mast

Wednesday May 29, 2024 3:00pm - 3:15pm CDT
Burge Union

Discussion Session: Utilizing Innovative Media Technologies for Research

3:15pm CDT

Advances in Digital Media Discussion

Discussion session to engage with all presenters

Wednesday May 29, 2024 3:15pm - 3:30pm CDT
Burge Union

Discussion Session: Utilizing Innovative Media Technologies for Research

6:00pm CDT

Reception: Collection Tours and Networking Event

Join us for an evening reception at the KU Biodiversity Institute and Natural History Museum. Drinks and hors d'oeuvres will be provided. Collection tours and visiting opportunities will be available for the following collections:
Ichthyology
Herpetology
Ornithology
Mammalogy
Vertebrate Paleontology
Informatics/Specify

Wednesday May 29, 2024 6:00pm - 9:00pm CDT

Evening Reception

9:00am CDT

Outer membrane protein identification and AI generation.

Speakers

Joanna Slusky

Associate Professor, Molecular Biosciences, University of Kansas

Joanna graduated magna cum laude in chemistry from Princeton University. While there she synthesized superconductors and geometrically frustrated magnets that resulted in her co-authoring 5 papers in Nature. She then focused on membrane protein design and completed her PhD in Bill... Read More →

Thursday May 30, 2024 9:00am - 9:30am CDT
Burge Union

Plenary Speaker

10:00am CDT

Bridging the gap: connecting biodiversity data to other disciplines

Speakers

Jocelyn Colella

Robert W. and Geraldine Wilson Assistant Professor of Ecology & Evolutionary Biology and Curator of Mammals, KU Biodiversity Institute and Natural History Museum

Jocelyn Colella, PhD, is an Assistant Professor of Ecology & Evolutionary Biology and Curator of Mammals at the University of Kansas Biodiversity Institute & Natural History Museum. Colella is an evolutionary biologist who uses mammals as models to understand how organisms and communities... Read More →

Thursday May 30, 2024 10:00am - 10:30am CDT
Burge Union

Plenary Speaker

10:29am CDT

Discussion Session: Sustaining Access to Biodiversity Data

Sustaining the good work and outcomes the collections community has achieved in creating, disseminating, and using digital biodiversity data has become an increasing challenge for collections professionals. This session will address numerous issues associated with sustainability through a series of talks followed by a moderated panel discussion of those who have found or are seeking effective sustainability strategies.
10:30 - 10:40 Planning for Sustainability - David Jennings, iDigBio Project Manager, Florida Museum of Natural History, University of Florida
10:40 - 10:55 MorphoSource: Sustaining 3D Data Access - Doug M. Boyer, Assistant Professor, Duke University, Department of Evolutionary Anthropology
10:55 - 11:05 Sustaining Access to Biodiversity Occurrence Data – Jose Fortes, AT&T Eminent Scholar and Professor of Electrical and Computer Engineering, University of Florida
11:05 - 11:15 Open Source Software, Stakeholders and $ustainability – Jim Beach, Executive Director, Specify Collections Consortium, University of Kansas
11:15 - 11:25 Accelerating biotechnology development and translation: NSF and NobleReach EmergePilot
– Charlene Marini, Senior Commercialization Advisor, NobleReach Foundation
11:25 - 11:35 EDI
11:35 - 11:45 Adventures in sustaining the USA National Phenology Network, Theresa Crimmins, Director, USA National Phenology Network, University of Arizona
11:45 - 11:55 iDigBio: Sustaining the digitization, mobilization, accessibility, and use of biodiversity specimen data in U.S. museum and academic collections – Dunrie Greiling, Principal,Scientific Ink & Consulting. Embedded Entrepreneur, iDigBio
11:55 - 12:30 Sustainability Discussion

Thursday May 30, 2024 10:29am - 12:30pm CDT
Burge Union

Sustainability Discussion: Cultural, Discussion Session: Sustaining Access to Biodiversity Data | Ethical, Discussion Session: Sustaining Access to Biodiversity Data | Legal and Social Issues for biodiversity data, Discussion Session: Sustaining Access to Biodiversity Data

10:30am CDT

Planning for Sustainability

This introductory talk by the session moderator will provide an overview of the sustainability concept and its multiple facets as they relate to our community. The talk will also discuss the important roles of strategic and implementation planning along the path towards sustainability.

Moderators

David Jennings

Project Manager, UF / Florida Museum / iDigBio

David is the iDigBio Project Manager based at the Florida Museum of Natural History at the University of Florida. iDigBio is an NSF-funded effort to enable digitization and online access to U.S. natural history collections. David is responsible for oversight of iDigBio operations... Read More →

Thursday May 30, 2024 10:30am - 10:40am CDT
Burge Union

10:30am CDT

Curation, Digitization, and Digital Extended Specimen: Sustaining a template for basic biodiversity research in the Caraga Region, Philippines Sanguila

The island of Mindanao in the southern Philippines is home to rich biodiversity that nourishes the country’s culture, heritage, economy, and national development. Sustained biotic inventories in Mindanao are a challenge because of security, logistics, and a lack of guiding themes, especially in regions plagued by poverty and severe habitat destruction. In northeastern Mindanao, the Caraga Region, biotic inventories provide fundamental biodiversity data needed for effective biodiversity information products. Nevertheless, the curation, and integration of such data types into the public domain, remain deficient. Here, we illustrate our ongoing efforts for the curation, digitization, and maintenance of Digital Extended Specimen, with an example from herpetological inventories in three watersheds and one wetland ecosystem. Vouchers are curated in a Reference Natural History Collection and their individual specimen-associated information and metadata are managed by a locally accessible Collections Management System via a Specify database and are published in GBIF. Together with long-term international collaborators, our current efforts are geared towards building a community of Filipino students, teachers, and other local stakeholders informed by open-access, locally available infrastructure for sustained biodiversity research programs in the Caraga Region and beyond.

Speakers

Marites Sanguila

Thursday May 30, 2024 10:30am - 10:45am CDT
Burge Union

Concurrent 1: Implementing the use of digital data in basic biodiversity research

10:40am CDT

MorphoSource: Sustaining 3D Data Access

MorphoSource is the only online repository that allows stakeholders from research, education, publishing, collections, and imaging communities to interactively contribute, manage, and access 3D data representing natural history and cultural heritage objects. In the 11 years since MorphoSource launched, it has had a transformative impact on research, education and data management. MorphoSource has been cited for data access or archiving in >2,000 academic articles. Datasets represent specimens from ~1,000 museum organizations, scanned at ~500 different global facilities. Almost 200 of these organizations (representing about 60 institutions) have active management teams. These teams manage more than half of all data existing in MorphoSource, imbuing a unique potential for verifying data quality. In addition, MorphoSource has a sophisticated API that is increasingly relied upon by third party initiatives to query and access data for specific communities and uses. Finally, MorphoSource is leading by example in pushing data standards with a fully published data model and up-to-date, RDF data vocabulary.

Despite its integral role, MorphoSource faces a major challenge of switching from a grant and university-funded operating model to a model that increasingly incorporates community funding in the next 3-5 years. We discuss this model and how it will be implemented.

Co-authors: Julie Winchester

Speakers

Doug Boyer

Thursday May 30, 2024 10:40am - 10:55am CDT
Burge Union

10:45am CDT

Consolidating diatom ecology and trait data to decipher their hieroglyphic forms and enigmatic functions

A great deal of progress has made to document the biodiversity of diatoms via diatoms.org. The diatoms.org project is a collaborative effort to provide accurate in diatom identification that supports researchers, federal, state, tribal, and local agencies to assess their waters and keep taxonomic keys relevant by continuous updates. To date there are 1099 species within 192 genera described on the diatoms.org website. It has become the largest single resource for species identification of diatoms and continues to grow. However, the ecological information within the website remains sparse, highly selective, and unconsolidated. Integrating ecological information and primary data with taxonomic and phenotypic data is critically important to understand the distribution of biodiversity across biological and spatio-temporal scales. Herein I present the results of a preliminary study linking diatoms.org data with a trait and environmental database revealing links of trait-form to ecosystem function. My goals are to provide a platform for open access to trait and consolidated environmental data to enhance testing capacity of realized and theoretical niche that will fully realize the potential of diatoms as model organisms for understanding how form follows function in ecology and evolution. Herein, I present a study from a preliminary diatom environmental data portal.

Speakers

Joseph Mohan

Thursday May 30, 2024 10:45am - 11:00am CDT
Burge Union

Concurrent 1: Implementing the use of digital data in basic biodiversity research

10:55am CDT

Sustaining Access to Biodiversity Occurrence Data

Speakers

Jose Fortes

Professor, University of Florida

I am on the faculty of the ECE Department of the U. of Florida. I work on distributed computing, cyberinfrastructure and biodiversity informatics. I am the Founding Chair of the CENTRA Steering Committee.

Thursday May 30, 2024 10:55am - 11:05am CDT
Burge Union

Sustainability Discussion: Cultural Ethical Legal and Social Issues for biodiversity data

11:00am CDT

Enabling biodiversity research in Guatemala with a customized Symbiota portal

Since its development in 2020, the Guatemala Biodiversity Symbiota portal (biodiversidad.gt) has turned into an outstanding resource to facilitate the digitization, mobilization and use of specimen records from local natural history collections. Close to 50,000 records and several thousands of images from Guatemalan collections have been shared online for the first time in this portal. The bilingual interface Spanish-English, and the increased accessibility to biodiversity data and specialized tools like checklists and datasets generators, interactive search in collections and maps, among other resources, has also encouraged users from undergraduate students to professional researchers to develop their own studies on Guatemalan natural diversity. An integrated installation allows further data mobilization to GBIF, amplifying its impact on biodiversity research at international level and, at the same time, promoting visibility and recognition for Guatemalan collections and researchers.

Speakers

Samanta Orellana

PhD Candidate, Symbiota Support Hub, Arizona State University

Fungus weevils, entomology, collections, biodiversity data, Symbiota, Guatemala :)

Thursday May 30, 2024 11:00am - 11:15am CDT
Burge Union

Concurrent 1: Implementing the use of digital data in basic biodiversity research

11:05am CDT

Open Source Software, Stakeholders and $ustainability

For 30 years, the Specify Project and its predecessor the MUSE Project operated on grant funding from the U.S. National Science Foundation. In retrospect, the NSF and its reviewers deserve rich acknowledgement for their decades-long commitment to the extended incubation of these collection informatics initiatives. At the time though, managing and sustaining a collections cyberinfrastructure on 3-year competitive grants was challenging, and too probabilistic for comfort or complacency.

While being supported by NSF, software development and helpdesk support were our highest daily priorities. Community or open-source organization building was of relatively low importance as the only actual stakeholder in a financial sense was the NSF. Proposal reviewers could be considered indirect stakeholders but with no financial skin in the game.

Over the years and through the grant cycles, motivation to reduce our dependency on NSF ebbed and flowed. In 2017, we were again encouraged by NSF to look for additional revenue sources and a business model based on a demonstration of our value to collections institutions. Then, in a serendipitous discovery process we explored alternate organizational and economic models. That exploration culminated with the establishment of the Specify Collections Consortium (SCC) in 2018. Now in its sixth year, the SCC has flourished into an international community of over 105 institutional stakeholder museums.

The transformation to a self-sustaining, research community organization has made Specify more responsive to its stakeholders. It has caused us to focus on collaborative governance structure and to improve the quality of our technical methods, software products, community engagement, and support services.

Speakers

Jim Beach

Executive Director, Specify Collections Consortium, University of Kansas

OK, if Sched insists, people should talk to me about: Serious issues. How humans and Earth will survive global warming. Where to store biodiversity collections forever when universities decide they are not vital intellectual resources worth maintaining in perpetuity. Duke. And life... Read More →

Thursday May 30, 2024 11:05am - 11:15am CDT
Burge Union

Sustainability Discussion: Cultural Ethical Legal and Social Issues for biodiversity data

11:15am CDT

Accelerating biotechnology development and translation: NSF and NobleReach EmergePilot

As part of the collaboration between NobleReach and NSF, 11 projects have been selected to accelerate bringing innovative research to the market and society. NobleReach Emerge helps government research organizations transform mission-critical research and innovations into market-ready organizations and products. A unique feature of the Emerge program, is that it matches each Principal Investigator and their team with an Embedded Entrepreneur to help them assess market need, opportunities, and approaches to translating research into the market with a sustainable model. This talk will provide an overview of the NobleReach Emerge model, the journey our biodiversity data focused participants are undertaking and a set of common considerations for biodiversity data platforms based on the program progress to date.

Speakers

Charlene Marini

Senior Commercialization Advisor, NobleReach Foundation

Thursday May 30, 2024 11:15am - 11:25am CDT
Burge Union

Sustainability Discussion: Cultural

11:15am CDT

Georeferenced herbarium specimen data improve NatureServe global conservation assessments

NatureServe is a US nonprofit organization dedicated to unlocking the power of science to guide biodiversity conservation. NatureServe and its public-private network gather and maintain a unique body of detailed scientific information on the location, condition, and status of the at-risk (G1-G3) plants, animals, and ecosystems of the United States and Canada. NatureServe Conservation Status Ranks indicate relative extinction risk from “Critically Imperiled, globally” (G1) to “Secure, globally” (G5) using occurrence data from the network, natural history collections, and iNaturalist. For newly described, resurrected, or cryptic taxa, NatureServe relies heavily on natural history collections to calculate conservation status ranks. A summary of georefencing work for at least 25 taxa and over 1,600 herbarium specimens will be provided, and conservation stories and impacts resulting from recently assessed taxa will be shared.

Speakers

Diana Soteropoulos

Thursday May 30, 2024 11:15am - 11:30am CDT
Burge Union

Concurrent 1: Implementing the use of digital data in basic biodiversity research

11:25am CDT

Sustaining the future of science with open data at EDI

The future of science requires expanded access to a rapidly growing corpus of data by a more diverse community of users. Access and use of these data depend on a suite of repository services that enable the data lifecycle to work more seamlessly with the research lifecycle. These services include curation, publication, search and discovery, harmonization, and analytics, as well as expertise and training that grows the capacity of the science community to participate in new science. Each of these data repository services is costly. The current model for funding repositories, including both operations and the future costs of maintaining a long-term archive, does not match repository needs or the needs of the scientific community. Here we discuss how EDI intends to approach sustainable funding issues. A portfolio of funding sources will be required to develop and deliver services to the scientific community at the size and breadth required by federal FAIR mandates. For research communities funded by federal agencies, both the scientists and the agencies need to recognize, account for, and build in a range of data services, including those provided by repositories, as part of the business model.

Speakers

Gregory Maurer

Data Scientist/Data Manager, New Mexico State University

An ecologist and the information manager for the Jornada Basin LTER, with research interests in global change, drylands, and data science.

Thursday May 30, 2024 11:25am - 11:35am CDT
Burge Union

Sustainability Discussion: Cultural

11:30am CDT

Niche Overlap in American Asclepias: The use of herbarium data in broad-scale ecological niche modeling

Niche divergence is considered an important driver of speciation and diversification that has consequences for species coexistence. By characterizing niches of species across a whole group it becomes possible to assess niche differences among closely related species and gain insight into the role niches play in lineage diversification. To evaluate the role of niche differentiation in lineage diversification, I studied the American Clade of Asclepias (milkweeds), which contains approximately ~130 species. These species exhibit a broad range of ecological variation and can be found across much of North, Central, and South America. I hypothesized that 1) species diverged mainly along niches axes associated with climate (temperature and precipitation) with a small contribution from soil characteristics, and 2) niche overlap among American Asclepias are not indicative of niche conservatism. Here, I characterized niches by utilizing 19 bioclimatic variables, elevation, % clay content, % silt content, % sand content, coarse fragment content, nitrogen content, pH, and electrical conductivity. I used multivariate analyses, including principal component analysis (PCA), and ecological niche modeling, to characterize niches and evaluate species differences. The degree of niche overlap between species was measured using Warren’s I and to determine signal for niche conservatism a Mantel test was used.

Speakers

David Kunkel

Thursday May 30, 2024 11:30am - 11:45am CDT
Burge Union

Concurrent 1: Implementing the use of digital data in basic biodiversity research

11:35am CDT

Adventures in sustaining the USA National Phenology Network

The USA National Phenology Network (USA-NPN) is a national-scale monitoring and research initiative focused on collecting, organizing, and delivering phenological data, information, and forecasts to support decision-making, to advance science, and to promote understanding by a wide range of audiences. From when the Network was established in 2007 until the end of 2019, was primarily supported by the US Geological Survey. In 2020, the USGS dramatically reduced support for the Network because of internal budget reductions. At that time, USA-NPN leadership chose to seek alternative forms of support rather than shut the program down. The program has since sustained operations with a reduced staff thanks to short-term funding provided by the NSF Sustaining Biological Infrastructure program, multiple federal appropriations, and project grants from several federal agencies and competitive programs. However, the effort and uncertainty associated with grant funding make supporting the USA-NPN primarily using this mode over the long term unsustainable.
The USA-NPN is fortunate to have been selected for a pilot effort, funded by NSF and the NobleReach Foundation, to help projects to establish financial footing and stand on their own. The USA-NPN team is currently working with an embedded entrepreneur and experts in the field of philanthropy to identify opportunities for more sustainable support for the enterprise. In this presentation, I will share updates on the USA-NPN’s journey to diversifying funding models. The experience, outcomes, and findings from this intense effort will have applicability to other programs struggling with program sustainability.

Speakers

Theresa Crimmins

Director, USA National Phenology Network

Rob Guralnick

Thursday May 30, 2024 11:35am - 11:45am CDT
Burge Union

Sustainability Discussion: Cultural Ethical Legal and Social Issues for biodiversity data

11:45am CDT

Balancing Mission, Opportunity, and Sustainability for iDigBio

Human societies and ecological communities are facing wicked problems at local, state, national, and global scales. The United Nations recognizes a “triple planetary crisis” in the intertwined challenges of “climate change, pollution, and biodiversity loss.” These challenges cause and extend into others including pandemics and threats to food security. Species occurrence and trait data from digitized biological collections have the potential to provide a critical baseline for better decisions. As part of its sustainability planning, iDigBio has been interviewing researchers and environmental decision makers to assess demand for data products, services, and platforms. These interviews have pointed to several opportunities and directions which now must be prioritized against the mission and capabilities of the team and community. Future project phases will include acquiring pilot customers.

Speakers

Dunrie Greiling

Consultant, Scientific Ink

Sustainability of biological collections.

Thursday May 30, 2024 11:45am - 11:55am CDT
Burge Union

Sustainability Discussion: Cultural Ethical Legal and Social Issues for biodiversity data

11:45am CDT

Making RBG Kew Collection Data Globally Accessible

RBG Kew Digitisation Programme is ensuring digital access to 8.25M plant and fungi specimens, from over 250 years of collection and curation into a digitised database with free access to all by 2026. Since 2019 RBG Kew has undertaken a programme of work to- 1. Digitise and transcribe Kew’s specimens. 2. Build and implement a new Integrated Collection Management System (ICMS) 3. Develop a new online Data Portal to provide global access to all of Kew’s unrestricted collection data. Why Now? - Over 6.75M (6M Herbarium and 725k Fungarium specimens) of the 8.25M did not have a digital representation of the specimen or associated metadata. - RBG Kew were managing and supporting outdated and uncompliant databases, carrying the risk of data loss and limited accessible data for science and research. - Online access was restricted due to out-of-date data portals which provided less than 20% of Kew’s collection data Sharing our Challenges - Mobilisation, building the Teams and procuring effective Suppliers. - How to capture and adapt to the multiple business requirements to support collections and ongoing transactions records. - How to establish and manage QA standards - Setting sustainable Key Performance Indicators

Speakers

John Adcock

Thursday May 30, 2024 11:45am - 12:00pm CDT
Burge Union

Concurrent 1: Implementing the use of digital data in basic biodiversity research

12:00pm CDT

The impact of digital data on systematic, phylogenetic, and genomic research Why designing UCEs probes is necessary for weevil museomics?

Insects are becoming more challenging to collect or may never be collected again due to extinction, habitat loss and fragmentation, climate change, politics, funding, security, among other reasons. If many species are not to be collected again, the use of historical samples will be the only way to study them. This is particularly critical for hyperdiverse groups such as weevils. Despite the various weevil phylogenies available, most of the mid-level weevil lineages (i.e., recognized tribes and genera) remain tentative due to incomplete taxon sampling; thus leading to shifting, non-consensus classification schemes. Nevertheless, target enrichment of Ultraconserved Elements (UCEs) allows us to improve taxon sampling through inclusion of museum specimens in phylogenomic analyses. Because UCEs probe set utility decreases with increasing phylogenetic distance from target taxa, novel probe design that leverages museum specimens is needed to effectively represent weevil genomic diversity. Here we document the design of UCEs probes for 23 weevil genomes available to date, including five newly sequenced and assembled genomes of specimens accessed through the Arizona State University Charles W. O’Brien Collection (ASUCOB; https://doi.org/10.15468/eeqtx0) available at https://ecdysis.org/. We discuss the prospect of our work for further leveraging natural history museum specimens through digital platforms and genomic data.

Speakers

Kevin Cortes Hernandez

Thursday May 30, 2024 12:00pm - 12:15pm CDT
Burge Union

Concurrent 1: Implementing the use of digital data in basic biodiversity research

12:15pm CDT

eDNA Explorer: Designing a digital tool for unlocking biodiversity secrets

Environmental DNA (eDNA) is recognized as a valuable tool for understanding biodiversity but has not seen broad acceptance. Sliced Bread Design, a user experience agency, CALeDNA at UCSC, and Oceankind conducted a user research study with sixteen scientists and researchers to understand opportunities for breaking down barriers to eDNA use.

The research revealed a gap between land managers' need for trustworthy data, the uncertainties associated with eDNA, and the lack of access to geneticists to help with data interpretation. There were many unknowns about how to set up an effective study and analyze unexpected results. Furthermore, while interviewees collaborated extensively as a normal course of work, many did not yet have that network built up for eDNA .

Based on these insights, we designed eDNA Explorer, an easy to use digital platform to help people plan eDNA projects, understand the results visually without the help of a geneticist, and collaborate with others. The platform also integrates complementary geospatial data and facilitates comparisons with other biomonitoring methods.

The platform has seen high engagement and early success. As a next step, the team is applying ML across eDNA and geospatial data on the platform to inform biodiversity health assessments and predictions.

Co-authors: Julie Stanford, Principal, Sliced Bread Design, CEO, eDNA Explorer; Rachel Meyer, Assistant Professor, UC Santa Cruz. Director of CALeDNA, CSO, eDNA Explorer; Jennifer Kim, UX Designer and Researcher, Sliced Bread Design; Jenny Mailhot, Director of Design, Sliced Bread Design; Audrey Yang, UX Designer and Researcher, Sliced Bread Design

Speakers

Jennifer Kim

Thursday May 30, 2024 12:15pm - 12:30pm CDT
Burge Union

Concurrent 1: Implementing the use of digital data in basic biodiversity research

12:30pm CDT

Lunch

Thursday May 30, 2024 12:30pm - 2:00pm CDT
Burge Union

Lunch

2:00pm CDT

The ecocomDP R package: Tools to facilitate biodiversity data FAIRness in ecological synthesis

The Environmental Data Initiative (EDI) and the National Ecological Observatory Network (NEON) have developed a flexible intermediate data design pattern for ecological community data called “ecocomDP”. Implementation of this data model is intended to enhance the discoverability of and access to biodiversity data from NEON and EDI data holdings, including data from the Long Term Ecological Research (LTER) program. The data model is applied in the ecocomDP R package, which provides tools for independent researchers to format their data following the ecocomDP standard, as well as tools to search and visualize data from NEON and EDI data holdings. The flexibility of the ecocomDP data model allows for ancillary data associated with observations to be preserved. Here we provide an overview of the tools available to data users. We also describe a modular workflow that is under development to map ecocomDP to the Darwin Core Archive (DwC-A) format and expose ecocomDP data packages in the Global Biodiversity Information Facility (GBIF) data portal, and how this workflow can facilitate the discovery of NEON biodiversity data through GBIF. These tools are intended to lower the barriers for researchers in ecology and the environmental sciences to access and work with long-term biodiversity data.

Speakers

Eric Sokol

Ecologist, NEON, Battelle

Thursday May 30, 2024 2:00pm - 2:15pm CDT
Burge Union

Concurrent 2: Facilitating ecological discovery and understanding

2:00pm CDT

Digital Collections Data and Tracking Disease Workshop

The COVID-19 pandemic impacted our entire way of life, including how we do science and our understanding of what we need in such situations. The potential role of natural history specimens in pathogen discovery and mitigation is recognized in the museum world (DiEuliis et al. 2016, Dunnum et al., 2017) and by at least some disease ecologists (e.g. Mills and Childs 1998). Renewed efforts to align pathobiology with biodiversity discovery initiatives are critical (Kading and Kingston 2020). Moreover, linking both biodiversity infrastructure and capacity-building more closely to zoonotic (and other) pathogen surveys in biodiverse countries would substantially improve proactive responses to pathogen-related events before they once again wreak havoc across the globe. From a collections and observations point-of-view, what have we learned about our own administrative and scientific processes for gathering and integrating the data and expertise needed, across borders and departments? What problems do our researchers and decision-makers continue to face in addressing the need for access to data, specimens, and expertise for answering key research questions for these events? What new policies and procedures have groups put into place for “next time” or to prevent “next time”? We need to share otherwise tacit or localized experiences so that we can work on how to foster adoption and implementation of practices that change how a local-to-global community ecosystem conducts its science. Please join our session to listen and to add your experiences to inform key elements for moving forward.

Speakers

Pam Soltis

University of Florida at Gainsville

Deb Paul

Informatics Liaison / Past TDWG Chair, University of Illinois Urbana Champaign / Prairie Research Institute / Illinois Natural History Survey

In my current position, I serve as the Biodiversity Informatics Community Liaison for the Species File Group. Prior to this, I was at iDigBio as Digitization and Workforce Development Manager. It's exciting to be working to connect INHS and PRI collections and taxonomic projects... Read More →

Cody Thompson

Mammal Collection Manager & Associate Research Scientist, University of Michigan Museum of Zoology

My research centers on the patterns and processes of mammalian diversity, focusing primarily on the effects of hybridization on the species boundary. In doing such, I incorporate fieldwork and a strong laboratory component (i.e., karyotyping, Sanger sequencing, fragment analysis... Read More →

Thursday May 30, 2024 2:00pm - 5:00pm CDT
Burge Union

2:15pm CDT

Visualizing Mongolian Mammal Specimens and their Parasites Through Time

Interactive online visualization tools increase accessibility of mammalian natural history databases for users of all backgrounds, aiding education, research, and policy assessment. Intuitive mapping algorithms can streamline access to and visualization of species distributions or species interactions. I built interactive maps for the Steppe Parasite Networks (STEPP-Net) project, a National Science Foundation funded grant that is focused on developing a better understanding of mammals and their associated parasites in Mongolia and other areas in Central Asia. My thesis applies interactive mapping techniques to the growing Mongolian mammal and parasite datasets held at the Museum of Southwestern Biology by using georeferenced mammal and parasite specimens to map 1) host distributions and 2) parasite distributions and associations. This interactive platform, available in both English and Mongolian, supports future research, within the STEPP-Net consortium and more broadly, by enabling visualization of host-parasite interactions across spatiotemporal scales. The maps also serve to enrich educational activities for students and community scientists, by providing opportunities to explore biodiversity interactions across Central Asia. The platform is accompanied by a module intended for classroom use that guides educators and students through the process of using the map, Global Biotic Interactions website, and Arctos database. By translating the platform into Mongolian, it enhances place-based classroom usability and facilitates education, research, and management efforts for Mongolian and Central Asian biodiversity on regional and international scales.

Speakers

Litsa Wooten

Thursday May 30, 2024 2:15pm - 2:30pm CDT
Burge Union

Concurrent 2: Facilitating ecological discovery and understanding

2:30pm CDT

Data-centric species distribution modeling of invasive European frog-bit (Hydrocharis morsus-ranae L.)

Twenty-first century ecologists have an extensive suite of analyses and data types available to answer complex questions about endangered species decline, potential consequences of climate change across ecosystems, and the progression of biological invasions. Decisions in data selection and processing could create significant downstream consequences; however, many of these decisions are hidden in modeling algorithms or not reported in literature, potentially hindering reproducibility and biological interpretations. Species distribution models (SDMs), which bridge multiple data types to model relationships between species and their environments, provide an interesting example of the interaction of data complexity with model results. We selected several points throughout the SDM process to investigate their influence on model performance, outcomes, and interpretation using invasive European frog-bit (Hydrocharis morsus-ranae L.) in North America as a case study. Concerns about the impacts of European frog-bit on native ecosystems catalyzed targeted monitoring efforts across the invasive range, which have produced heterogenous occurrence data that are well-suited to the questions addressed. Our data-centric analysis pipeline integrated data discovery throughout the modeling process to identify and account for the effects of input data features on model outcomes, which ultimately impacted our interpretations relative to European frog-bit biology and ecology.

Speakers

Sara Hansen

Thursday May 30, 2024 2:30pm - 2:45pm CDT
Burge Union

Concurrent 2: Facilitating ecological discovery and understanding

2:45pm CDT

Deep Data Analysis for Exploring the Deep Ocean: Using Aggregated Specimen Records to Explore Deep-Sea Ecology

Sampling the deep ocean is analogous to trying to catch cockroaches in the streets of New York, from a helicopter, with a bucket. The inaccessibility these ecosystems along with the low frequency with which target species are collected, coupled with the low volume of specimens able to be captured leaves many gaps in our knowledge. This is where biodiversity data aggregators come in. Using the data we have amassed over hundreds of years across thousands of collecting events we can get a much clearer picture of the ecology in the deep sea, specifically with regards to depth. Join us as we explore and share these data and insights with you - no need for a boat or submarine!

Speakers

Randal Singer

Thursday May 30, 2024 2:45pm - 3:00pm CDT
Burge Union

Concurrent 2: Facilitating ecological discovery and understanding

3:00pm CDT

Dynamics of Carabid Beetle Communities: Initial Insights from NEON Data Products

As important bioindicators, ground beetles (Carabidae) remain one of the most widely studied families of insects. However, aside from their general morphology, little else is known about a significant portion of less studied species. Their inclusion as one of two targeted insect groups collected by the National Ecological Observatory Network (NEON) has the potential to greatly expand our collective understanding of their community composition, diversity, and species abundance.

In this presentation, we will explore ground beetle population and community dynamics in relation to environmental variables including precipitation, temperature, and humidity. We will focus on emergence patterns observed at the Santa Rita Experimental Range (SRER). Finally, issues and solutions concerning the quality and overall ease of use of specific data products will be examined.

Speakers

Brennan Hays

Thursday May 30, 2024 3:00pm - 3:15pm CDT
Burge Union

Concurrent 2: Facilitating ecological discovery and understanding

3:15pm CDT

AnnotateVid.Io: A platform for crowd-annotation of behavioral videos

AnnotateVid.Io is a web application where users create public or private video collections that can be annotated by invited users. Any user who has access to the collection can add annotations (a.k.a., events) to any video in the collection. The annotations can then be analyzed in order to discover novel insights about behaviors in the collection.

Each video is associated with a collection. In turn, individuals and events are associated with each video. Individuals are also associated with events, such that in any event, there is at least one actor with an optional one or several recipients/subjects.

Collection owners can customize the kinds of intake questions they ask of users for all three core objects: individuals, videos, and events, thereby allowing for great flexibility in the types of videos and behaviors that can be annotated.

During annotation, a user indicates when a behavior is begun, and then marks when that behavior is ended in the video. Data for the behaviors recorded per video and per collection as a whole are filterable and sortable by each custom attribute in the video. These filtered data could facilitate analyses of frequency, duration, success rates, or even association of various behaviors across time.

Speakers

Mark Fisher

Thursday May 30, 2024 3:15pm - 3:30pm CDT
Burge Union

Concurrent 2: Facilitating ecological discovery and understanding

4:00pm CDT

Exploring the AI kaleidoscope with VoucherVision: a spectrum of techniques for specimen label transcription

Facing considerable digitization backlogs and limited resources, natural history collections stand to benefit from recent advancements in computer vision and natural language processing. Our project investigates the application of Large Language Models (LLMs) to facilitate the transcription of specimen labels into digitally searchable formats, utilizing the VoucherVision platform. First, we evaluate four distinct optical character recognition (OCR) techniques for extracting text from specimen images. Then, we leverage the adaptability and capabilities of LLMs to transform the extracted unstructured text into structured JSON dictionaries, which can then be ingested into existing collections software like Symbiota, Specify, and BRAHMS. To do this, we test the capabilities of three separate AI-powered workflows to determine the most effective transcription methodologies: (1) the utilization of prompt engineering coupled with API calls to more than 15 different well-known foundational LLMs (such as ChatGPT, Mistral, Gemini, etc.), (2) an agent-based strategy employing multiple LLM bots for the transcription and subsequent recursive validation of each LLM-generated output, (3) the application of LLMs that are fine-tuned with natural history transcription datasets. We demonstrate that each of the three AI methods can produce a properly formatted JSON dictionary, but that content accuracy varies with the LLM version, hyperparameter settings, and prompting style. To complement VoucherVision, we also worked with 15 partner institutions to develop an easy-to-use editing tool for correcting transcription errors. This collaborative effort highlights the potential of integrating AI to streamline the digitization of natural history collections but also underscores the importance of iterative testing and customization in achieving high transcription accuracy and efficiency.

Speakers

William Weaver

Thursday May 30, 2024 4:00pm - 4:15pm CDT
Burge Union

Concurrent 2: Facilitating ecological discovery and understanding

4:15pm CDT

Developing An Oriented Object Detection Model For Museum Image Datasets

Detecting and cataloging fish specimens in datasets of digitized museum specimens is essential for scientific research, biodiversity studies, and conservation efforts. In this study, we use a machine learning approach utilizing YOLOv8, a state of art object detection algorithm, for detection of fish specimens within the collection images. Our purpose is to solve problems in datasets where there are multiple specimens and/or specimens have different orientations.
Our method addresses the challenges posed by varying fish sizes, orientations, and positions within the dataset. Leveraging YOLOv8's capability to detect objects with different orientations, we annotated the museum images and trained a model showing diversity among the museums in Great Lakes Invasives Network (GLIN) dataset and compared the results with manually observed number of specimen values from FishAIR (http://www.fishair.org) database. We also developed a model for capturing non-specimen objects such as labels, scale bars, and color bars.
Our model resulted in 99.4% accuracy finding fish specimens with the parameters 75 epochs and 0.5 score threshold. This study presents a practical and efficient solution for automating the detection of multiple/oriented fish specimens as well as single specimens in museum image data, aiding researchers, curators, and conservationists in their endeavors to document and preserve biodiversity effectively.
This research is supported by: NSF-HDR #2118240 (Imageomics)

Co-author: Yasin Bakis ,Tulane University; Xiaojun Wang, Tulane University; Henry Bart , Tulane University

Speakers

Bahadir Altintas

Research software developer, Tulane University Biodiversity Research Institute

Thursday May 30, 2024 4:15pm - 4:30pm CDT
Burge Union

Concurrent 2: Facilitating ecological discovery and understanding

4:30pm CDT

Efficient Midline Detection for Enhanced Fish Species Profiling in AI Applications

In this study, we developed a novel method to detect the midline with high precision, focusing on the critical anatomical reference that bisects the fish longitudinally into dorsal and ventral halves. This enhanced midline detection is crucial for the morphological studies facilitated by the Fish-AIR dataset, a robust tool in biological research known for its comprehensive curation and detailed metadata. Employing the Archival Resource Key (ARK) system, Fish-AIR significantly boosts data provenance and affirms AI readiness, serving as a pivotal resource for advancing artificial intelligence applications in biology.

Our pipeline harnesses the power of a variational autoencoder to reconstruct images, with a specific focus on the fish's head and body, excluding fins and other non-essential elements. This strategic focus paves the way for the precise detection of the midline. In an experimental phase, convolutional Neural Networks (CNNs) were trained on a limited set of 100 images from the Fish-AIR dataset, yielding promising results that underscore the potential for scaling up to a more extensive training regimen. This initial training equips the CNNs to discern and isolate crucial anatomical features accurately, thereby elevating the precision of midline detection.

The improved process enhances the annotation of morphological landmarks—biologically significant points used for the morphometric analysis of shape, size, and structural differences—and supports the meticulous comparison of these landmarks across multiple specimens and species. Our findings, supported by the National Science Foundation's Harnessing the Data Revolution Institute Grant, demonstrate substantial improvements in automated fish profiling, enriching the Fish-AIR dataset's contributions to biological research and marking a pivotal advancement in the fusion of biology with artificial intelligence.

Speakers

Marcio Ferreira

Postdoc, Tulane University

Thursday May 30, 2024 4:30pm - 4:45pm CDT
Burge Union

Concurrent 2: Facilitating ecological discovery and understanding

9:00am CDT

From Digital Data to Causes of Extinction: Climate Change, Physiology, and the Survival of the Sluggish

Basal Metabolic Rate (BMR) is a key property of organisms known to influence their resource use and survival. Here we examine how BMR influences long term species survival by focusing on marine gastropods and bivalves from the fossil and extant biota of the West Atlantic (WA) region along the eastern coast of the United States. This region has a detailed and intensively sampled fossil record, and many species still alive today occur back to 3 million years ago, a time when ocean temperatures were relatively warm, approximating conditions expected to be reached within the next ~ century. Using information from paleoclimate and other variables, along with data from collection visits and digital museum records, BMR values were calculated and compared between those species that survived and those species that went extinct in the region. A highly statistically significant difference in BMR was found, with survivors having lower BMRs. This indicates that sometimes properties of organisms can be extrapolated upwards to explain species survival, and that in the face of climate change, species with organisms having lower activity levels and using fewer resources are more likely to survive. Using data from iDigBio we also examined BMR patterns at the assemblage level, and by contrast found that at this scale no significant changes in metabolic rate occurred through time. This suggests that even with substantial extinction, communities of Neogene mollusks were stable energetically, pointing out the disconnect that can exist between macroevolutionary and macroecological patterns.

Luke C. Strotz, Northwest University
Erin E. Saupe, Oxford University
Bruce S. Lieberman, University of Kansas

Speakers

Bruce Lieberman

Senior Curator, Invertebrate Paleontology; Professor, Ecology & Evolutionary Biology; Director, Paleontological Institute, KU Biodiversity Institute and Natural History Museum

Bruce S. Lieberman is an evolutionary biologist and invertebrate paleontologist who studies macroevolution, paleoecology, phylogenetics, biogeography, the Cambrian radiation, trilobites and other fossil arthropods. He has been extensively involved with the digitization of invertebrate... Read More →

Friday May 31, 2024 9:00am - 9:30am CDT
Burge Union

Plenary Speaker

9:30am CDT

Opportunities to Synthesize Data Provided by Long Term Research

Scale matters in biology. The National Science Foundation supports biological research at multiple scales, from molecules to ecosystems; from individual investigators to team science; from local studies to continental scale research; from short-term studies to decadal research. Two major areas of NSF investment covering different timescales and geographical scales are Long Term Ecological Research (LTER) sites and the National Ecological Observatory Network (NEON), both of which produce rich data that are open access. While LTER is site-based research that is often heterogenous, NEON is constructed to collect nearly identical data across all its sites. LTER has been in existence for over 40 years while NEON is relatively new but planned for a 30-year lifespan. ESIIL, the Environmental Data Science Innovation and Inclusion Lab, exists to facilitate the use of these data resources and to diversify environmental data science. I will discuss how NSF hopes these resources will be utilized.

There are many drivers for NSF investment in LTER, NEON, and ESIIL. First, ecological and biological processes often take longer than a typical 3 to 5-year grant. Thus, we make investments in long-term data. Second, surprises, by definition, can’t be predicted and usually can’t be defined except through a long-term lens. Third, LTER and NEON sites can provide context for understanding and interpreting disparate biological phenomena. Finally, as new technologies, opportunities, questions, and problems arise the existence of a stable dataset for new interrogation is invaluable.

Speakers

Allen Moore

Division Director in the Division of Environmental Biology, National Science Foundation

Allen Moore is a Distinguished Research Professor at the University of Georgia and currently serving as Director of the Division of Environmental Biology at NSF. He is an evolutionary geneticist, with a focus on the evolution of behavior. He has produced over 200 refereed journal... Read More →

Friday May 31, 2024 9:30am - 10:00am CDT
Burge Union

Plenary Speaker

10:00am CDT

Data Cleaning Break Out Room

Friday May 31, 2024 10:00am - 1:45pm CDT
Burge Union

10:30am CDT

Data cleaning for maximum impact: Tools and workflows for data providers to efficiently find and fix data quality issues.

In this workshop, data mobilization and data quality experts – including representatives of iDigBio, GBIF, Arctos, Specify, the Symbiota Support Hub, and TaxonWorks – will share training and resources to identify and fix common data quality issues using different tools (e.g., providers’ collection management system). Participants will gain experience with a toolbox of data quality flags and fixes that they will then be able to use or delegate to improve the quality of their biocollections datasets. Remote participation in this workshop will be allowed. Participants are encouraged to pre-register their interest (https://forms.gle/5W7PoWztpUYHMSfB7) and to bring a laptop for the hands-on portion.

Speakers

Katie Pearson

Project & Data Manager, Symbiota Support Hub

Friday May 31, 2024 10:30am - 2:30pm CDT
Burge Union

10:30am CDT

GBIF Workshop: eDNA Mobilization and Sharing to Global Biodiversity Data Portals

The collection of environmental DNA (eDNA) data is growing rapidly and the need to publish these data to biodiversity aggregators (e.g., GBIF, iDigBio, VertNet) is on the rise. In this workshop we will explore the relevance of eDNA data, the reasons why they should be published, and tools and processes needed to share these data publicly. The workshop agenda will include discussion about the source materials from which eDNA may be derived and how to maintain them, workflows recommended to organize, clean, and mobilize eDNA data, and an introduction to GBIF’s new tool, which allows users to reshape datasets in formats familiar to the DNA community into standardized datasets ready for publication to GBIF. Participants will be given time to work on their own datasets with the assistance of trainers. Participants should bring a laptop. A dataset will be provided to those who do not have data of their own.
Trainers/Mentors: David Bloom - GBIF NA Regional Representative, VertNet Node Manager; Laura Russell - GBIF Training Officer for Community and Capacity; Stephen Formel - US Node Manager, USGS; Sharon Grant - The Field Museum; Carole Sinou - Canadensys Node Manager; Teresa Mayfield - Arctos; David Jennings - iDigBio Node Manager
10:30am - 5:00pm (In-person only) Friday, May 31st, Digital Data Conference, Lawrence, KS
Workshop Size is Limited: Max 25 participants
CLICK HERE TO BE CONSIDERED

Friday May 31, 2024 10:30am - 5:00pm CDT
Burge Union