7th Annual Digital Data Conference, Arizona State University

From iDigBio
Jump to navigation Jump to search

Digital Data in Biodiversity Research Conference


Social Media

Twitter: #digidata, @idigbio
Shortened URL for sharing on social media, https://bit.ly/3GGj6Xw

Conference Resources

Advertising Materials

Traveling to Tempe, AZ: Lodging, Logistics, and area information

Information about getting around Tempe, where to stay, and things to do in Phoenix can all be found on the Conference Logistics Page.

Conference Registration

Registration is open.
Visit Eventbrite to register.

Registration fees
Registration fees include the conference, workshops, and refreshments and hors d'oeuvres at poster session and reception:
In-person, Non-student Registration (including virtual participation): $100 In-person, Student Registration (including virtual participation): $50 Virtual Participation Only: *Optional

  • Optional virtual registration fees will support the digital format technology, the editing and publication of abstracts, and keeping the conference sustainable. Registration fees are optional for virtual participants but encouraged. When registering, those who wish not to make a financial contribution to the conference will have that option. Although registration is optional, your registration information, even if you opt out of the fee, will allow us to keep you updated about conference activities.

Conference Abstracts

The conference will be structured to allow live presentations among different time zones. Live presentations will be organized by theme and format. Concurrent session blocks will include virtual and in-person presentations. All presenters will additionally be asked to submit a recording of their presentations to be posted on this wiki to ensure their availability to any time zone.

Poster Specifications

Poster Specifications: Posters should not exceed 3’ tall and 4’ feet wide and should be displayed in landscape orientation. Virtual viewing options will additionally be provided.


Monday, 5 June 2023

Day One - Block One
9:00AM - 12:00PM PDT
Plenary Session
Time Room 1: Auditorium
Click here to join Zoom
9:00 - 9:30 Welcome -
Conference framing - Gil Nelson, Director, iDigBio
Conference logistics - Jill Goodwin, Conference Manager, iDigBio
9:30 - 10:00 A computer vision for organismal biology
Arthur Porto, Assistant Professor at the Department of Biological Sciences and the Center for Computation and Technology at Louisiana State University, Baton Rouge, LA.
Click for Bio
10:00 - 10:30 Before the Pharaohs: Breaking New Ground in the Study of Egypt's Ancient Prehistory
Sanaa El-Sayed, Co-founder of the Mansoura University Vertebrate Paleontology center (MUVP), Mansoura University, Egypt & Department of Earth and Environmental Sciences, University of Michigan, USA
Click for Bio
10:30 - 11:00 Break
Concurrent Sessions
Time Room 1: Auditorium (In-person)
Concurrent 1:Implementing the use of digital data in basic biodiversity research
Click Here to Join Zoom for Day 1 , Room 1
Room 2 (In-person)
Concurrent 2: Digital extended specimens as paradigms for data integration
Click Here to Join Zoom for Day 1, Room 2
Room 3 (Virtual)
Concurrent 3:Innovative imaging techniques for enhancing specimen-based discoveries
[Click Here to Join Zoom for Day 1, Room 3]
11:00 - 11:15 Merging digitized collections information with open-access spatial data to identify priorities for future collection efforts (Lombardi) What’s our DEStination? Collaborating to develop a globally network of people and data - the “Digital Extended Specimen” (Buschbom) Standardizing and Adding Micrographs into Herbarium Workflow to Extend the Digital Specimen (Harmon)
11:15 - 11:30 The Pilosity Problem: Using Computer Vision Methods to Define a Complex Phenotype in Bees (Seltmann) Expanding biodiversity occurrence data for ecological collections (Yule) Standardizing Stacked Focus Imaging of Herbarium Specimens (Czako)
11:30 - 11:45 Signed Biodiversity Data Packages: A Method to Cite, Verify, Mobilize, and Future Proof, Large Image Corpora. (Poelen) Mobilizing Imagery of Fossil and Extant Specimens from the Treatise on Invertebrate Paleontology on the Digital Media Repository MorphoSource (López Carranza) USCH Bryophyte Digitization and Revitalization Project (Harmon)
11:45 - 12:00 Taxonomic translation of bat-virus interaction data via automated alignment tools (Upham) Data cleaning process in historical collections - Georeference combines old labels and artificial intelligence (Chang) A Course and Tutorial on Creating 3D Models Using methods in Focus-Stacking and Photogrammetry for Extending Research through Image and Trait Digitization (Big-Bee) (Smith)
Day One - Lunch Break
12:00 - 1:00 PM PDT
SEINet Networking Lunch
The Symbiota Support Hub invites all personnel involved with the SEINet Network to a community-building lunch. Get to know your fellow local curators, collections managers, regional botanists, and other plant folks. Lunch will be provided for attendees who pre-register here by Thursday, June 1st.
Day One - Block Two
1:00PM - 4:00PM PDT
Discussion Sessions
Time Room 1
1:00 - 2:15 Discussion Session 1

Symbiota Skillshare and Capacity Building Workshop
Symbiota portals–including the SEINet Network, the Consortium of Lichen Herbaria, the Consortium of Bryophyte Herbaria, and many more–include a variety of features that enable efficient data management, access, and curation. In this workshop, we will provide hands-on training in using Symbiota tools that allow users to, for example, upload data, manage annotations, manage loans, print label data, crowdsource data transcription, and create checklists. Desired topics and questions will be solicited before the workshop for focus during the session. We will invite all current or potential users of Symbiota portals to participate in the workshop, especially local (SW US) data managers from the SEINet Network, so they can build data management skills. Kaitlin Pearson, Arizona State University; Lindsay Walker, Arizona State University; Ed Gilbert, Arizona State University; Greg Post, Arizona State University; Samanta Orellana, Arizona State University

2:15 - 2:45 Break
2:45 - 3:45 Discussion Session 2

Focus group: How a Biological Collections Action Center can Engage Researchers
Moderators: Libby Ellwood, Gil Nelson, John Bates
The collections community is in the midst of a series of webinars, workshops, and focus groups focusing on Envisioning a Biological Collections Action Center as proposed in the recent NASEM report and authorized by the U.S. Congress in summer 2022 as part of the CHIPs and Science Act. We have conducted three webinars and one workshop to date and are very interested in including a range of voices from the biodiversity sciences community, including researchers and other users of digital biodiversity data. We aim to bring together U.S. collections and research professionals to consider how such a center could engage with and provide services to researchers to enhance the quality of collections-based researcher and to sustain U.S. biodiversity collections. We are scheduling this in-person focus/discussion group during this year's Digital Data Conference to broaden the input into the Action Center concept. We hope you can attend.

Day One - Block Three
6:00 pm PDT
Reception & Tours of ASU Collections

The ASU Natural History Collections consist of nine different collections that support the university's teaching, research and public outreach functions. Our collections emphasize flora and fauna from the arid southwest of North America. Since 2018, we operate the National Ecological Observatory Network (NEON) Biorepository, which contains a diversity of nearly 70 collections with close to 400,000 organismal and environmental samples. Since 2021, we manage the iDigBio Symbiota Support Hub, which supports more than 1,000 live-managed collections.

Join us on Monday evening for a private tour of the different collections; including the mammalian, insect, mollusk, herbarium, fossil plants, symbiota, beetles, wet collection, as well as the state of the art NEON Biorepository cryo collections. A reception with light appetizers will take place on the patio after the tours. Complimentary buses will be provided to and from the collections site.

The ASU Natural History Collections house preserved and dried biospecimens including plants, mollusks (shells), insects, fishes, amphibians, reptiles, birds, and mammals. Sensitivities and allergies may occur in certain individuals. Please consult with a healthcare provider to discuss any concerns before attending tours.

Tuesday, 6 June 2023

Day Two - Block One
9:00AM - 12:00PM PDT
Discussion Sessions
Time Room 1
Room 2
Room 3
9:00 - 10:00 (Hybrid) Symposium:
Addressing Roadblocks and Envisioning Solutions of the Digital Extended Specimen Concept

This two-hour session will bring together biodiversity informatics and data experts from throughout our community to address some of the possibilities and challenges implementing the Digital Extended Specimen concept. This session will address solutions to date and additionally look to the community for input and discussion.

10:00 – 10:15 (Virtual) Oral Presentation:
Engaging the community in FAIR taxonomic data liberation: an overview of training resources at Plazi (Giora)
(In-person only) Discussion:
Addressing Roadblocks and Envisioning Solutions of the Digital Extended Specimen Concept
10:15 – 11:00 (Virtual) Discussion Session:
Reimagining the future of natural history museums with compassionate collection (Byrne)
(In-person only) Discussion:
Addressing Roadblocks and Envisioning Solutions of the Digital Extended Specimen Concept
Day Two - Block Two
1:00PM - 4:00PM PDT
Plenary Session
Time Room 1
1:00 - 1:30 Crop Wild Relatives and the Role of Herbaria in Future Food Crop Security
Makenzie Mabry, iDigBio, Florida Museum of Natural History, University of Florida
Click for Bio & Abstract
1:30 - 2:00 Data for Whom? Intellectual Property, Biodiversity, and Indigenous Genomic Data Sovereignty
Krystal Tsosie, Assistant Professor, School of Life Sciences, Arizona State University
Beckett Sterner, Assistant Professor, School of Life Sciences, Arizona State University
Click for Bios
2:00 - 2:15 Break
Concurrent Sessions
Time Room 1 (Virtual)
Concurrent 1 cont.
Implementing the use of digital data in basic biodiversity research
Room 2 (In-person?)
Concurrent 4:
Facilitating ecological discovery and understanding
Room 3 (In-person)
Concurrent 3 cont:
Innovative imaging techniques for enhancing specimen-based discoveries
2:15 - 2:30 Using collection data to determine harvesting hotspots for the most traded and threatened medicinal plants of the Eastern Cape province in South Africa (Welcome) A workflow for capturing ichthyology collections’ information (Cruz) Automated Multi-View Imaging of Pinned Insects (Tran)
2:30 - 2:45 Monarch Migration Models: Visualizing Global and Local Priorities for Western Land Managers (Young) Fish-AIR - A FISH IMAGE DATASET WITH BUILT-IN IMAGE QUALITY MANAGEMENT SYSTEM (Wang) Building a Pipeline for Label Reconstruction on the Pin (Hereld)
2:45 - 3:00 Comparing perspectives of academics and government professionals on their use of online information systems and their reuse of species occurrence data (Martin) Leveraging deep computer vision to inform conservation assessments and the response of North American butterfly communities to global change (Shirey) Using robotics to 3D-scan pinned insects and storing models in PlutoF platform: A six-axis tool to acquire focus-stacked macroscopical images for photogrammetrical digitization (Ylinampa)
3:00 - 3:15 Break
3:15 - 3:30 Completeness analysis for over 3000 United States bee species identifies persistent data gaps (Chesshire) A New, Global Estimate for Biocrust Carbon and Nitrogen Flux from Terrestrial Ecosystems (Janapaty) Availability of image preprocessing metadata terms and their effects on calculation of suitability of datasets for machine learning pipelines (Altintas)
3:30 - 3:45 R Program to Remap & Clean Downloaded SERNEC Data (Czasko) The California Biodiversity Sentinel Site Network (Bucciarelli) Digitization efforts at a small Ecuadorian herbarium focused on Applied Botany (Freire-Fierro)
3:45 – 4:15 Describing the bee biodiversity in Baja California: An analysis of current and historical data (de Pedro) echinopscis: an extensible notebook for open science on specimens (Nicolson)
Day Two - Block Three
Dinner on your own

Wednesday, 7 June 2023

Day Three - Block One
9:00AM - 12:00PM PDT
Discussion Sessions
Time Room 1
9:00 - 10:00 Open discussion: the NEON Biorepository infrastructure model

This discussion session is offered to complement the opportunity to visit the National Ecological Observatory Network, NEON Biorepository, in person during Digital Data 2023 at Arizona State University. Click here for a video introduction. The NEON project involves a structured, long-term plan to sample new, diverse, prioritized specimens across distributed sites of the North American subcontinent, process and store them a both intermediary peripheral facilities and a permanent centralized location, transform them into Darwin Core occurrences and published extended specimens, and actively make both samples and data available for loan to enable question-driven ecological and evolutionary research. To begin this session, we will offer an introductory presentation of the operational concept and implementation of the NEON Biorepository and of the associated data portal (https://biorepo.neonscience.org/portal/), which dynamically integrates standards from ecological and biodiversity data domains. We will then open the floor for discussion, based on an initial set of framing themes and questions, to jointly explore the prospects of this model in relation to current and future developments in the national and global biocollections infrastructure and data communities.
Kelsey Yule, Edward Gilbert, Azhar Husain, Andrew Johnston, Rosie Liao, Laura Rocha Prado, Laura Steger; all Arizona State University.

10:00 - 10:15 Break
10:15 - 11:15 Poster Session
Day Three - Block Two
1:00 PM – 2:00 PM PDT
Concurrent Sessions
Time Room 1 (In-person)
Concurrent 1 cont.
Implementing the use of digital data in basic biodiversity research
Room 2 (Virtual)
Concurrent 4 cont.
Facilitating ecological discovery and understanding
Room 3 (Virtual)
Concurrent 5:
The impact of digital data on systematic, phylogenetic, and genomic research
1:00 – 1:15 Harmonizing taxonomic resources is necessary for novel insights into bat roosting dataset (Sherman) Symbtk: A toolkit for Symbiota (Anders) MorphoBank: A digital repository of morphological data matrices with integrated phylogenetic analysis capabilities (Long-Fox)
1:15 – 1:30 Digital Herbarium for the Flora of United Arab Emirates: Novel database towards future plant conservation, biodiversity and sustainability (Mousa) Toward a global bee functional trait database (Ostwald) Matching material citations to occurrences: extending the biodiversity knowledge graph (Agosti)
1:30 – 1:45 Virtual presentation
Coordinating Digitization Efforts of Biological Collections in US & Beyond (Wilkins)
Digital Monographs as Products Exemplary of the Unification and Use of Digital Data (Yoder) DNA Barcoding of South Carolina Oaks (Czako)
Plenary Sessions
Time Room 1
2:00 – 2:30 Supporting Digitized Data through the National Science Foundation

Katharina Dittmar, National Science Foundation, Division of Environmental Biology

2:30 – 3:00 Communities of practice across the Americas

Samanta Orellana, International Community Coordinator, Symbiota Support Hub & Evolutionary Biology Ph.D. Student at Arizona State University
Jenn Yost, Community Lead, Symbiota Support Hub & Associate Professor, Cal Poly
Click for Bios

3:00 – 3:30 Penguin fieldwork and data collection in the age of extended specimens

Rachael Herman, NASA FINESST PhD student at Stony Brook University
John Bates, Curator of Birds at The Field Museum