Difference between revisions of "4th Annual Digital Data Conference, Indiana University"

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Revision as of 15:12, 7 May 2020

Social Media

Twitter: #digidata, @idigbio

Conference Resources

Conference Registration

For those who would like to support the sustainability of in-person Digital Data Conferences, registration fees are $100.00 for professionals, $50.00 for students. Those who wish not to make a financial contribution to the conference may select the free option.

Registration is open - Click here to register through Eventbrite.

Final registration deadline: May 22.

Abstract Submissions

Options for submission include: discussion, oral, or poster presentations.

You must register to submit an abstract. The abstract submission link will be sent to you in your registration confirmation email.

Abstract submission deadlines: 24 April 2020

The conference will be structured to allow live presentations among different time zones. Recording of presentations are additionally being requested to be posted on the wiki to ensure their availability to any timezone.

Posters

All posters will be electronic and linked to this wiki page. There will not be a live session for posters. We are requesting that poster presenters provide a recorded description with their poster presentation.

Oral Presentations

Oral presentations should be 10 minutes long. Each oral presentation will be presented live and pre-recorded presentations will be posted on the wiki page. In the live sessions an additional 5 minutes will be given for questions.
Click here to view an example

Discussion sessions

Discussion sessions may be up to one hour long. These may begin with a presentation or introduction followed by discussion or may be completely devoted to open discussion.

Conference Abstracts

Submitted abstracts can be found by clicking the following links:

Draft Agenda - Schedule Subject to Change

Monday, 1 June 2020

Day One - Block One
9:00AM - 12:00PM EDT / 1:00PM - 4:00PM UTC

Keynote Session 9:00 - 9:30 a.m.
Time Room 1 Room 2 Room 3
9:00 Welcome - Michael McRobbie, President of Indiana University
Logistics - Gary Motz, Indiana University, Indiana Geological and Water Survey

Conference Framing - Jill Goodwin, iDigBio, University of Florida

9:30 How Large Fossil Databases Are Rewriting the Early Evolution of Vertebrates
Lauren Sallan, Martin Meyerson Assistant Professor in Interdisciplinary Studies, University of Pennsylvania, 2019 TED Senior Fellow
10:00

Digital Data 2020: The critical role of specimens in emerging zoonotic pathogen discovery and mitigation
Joseph A. Cook, Regents Professor and Curator of Mammals, Museum of Southwestern Biology and Biology Department, University of New Mexico

10:30-11:00 Break - Rooms open for discussion
Concurrent Sessions 1-3 11:00 a.m. - 12:00 p.m.
11:00 Concurrent Session 1A

Developing Data infrastructures for environmental archaeology, palaeoecology and conservation palaeobiology
Philip Buckland, Umea University; Francesca Pilotto
Concurrent Session 2A

A joint effort for the quality control of herbarium specimen data
Ashton Welcome, South African National Biodiversity Institute (SANBI);
Concurrent Session 3A

The step beyond: from scientific work environment to reliable and effective conservation genomic tools
Jutta Buschbom, Statistical Genetics
11:20 Concurrent Session 1B

Reliable data use in R
Jorrit Poelen, Ronin Institute; Carl Boettiger, UC Berkeley
Concurrent Session 2B

Rodents from Eastern Amazon, Brazil: specimens and digital data
Alexandra M. R. Bezerra, Museu Paraense Emílio Goeldi
Concurrent Session 3B

Developing the digitization practices of parasitic arthropod specimens from a university collection
Jenna O'del, University of New Hampshire; Isaac A. Bergfalk, UNH; Holly A. Hoag, UNH; István Mikó, UNH
11:40 Concurrent Session 1C

Increasing the usefulness of crowd-sourced citizen science data to monitor and understand biodiversity
Giovanni Rapacciuolo, California Academy of Sciences; Alison Young, California Academy of Sciences; Michael Esgro, California, Ocean Protection Council; Sara Worden, California Department of Fish and Wildlife; Rebecca Johnson, California Academy of Sciences
Concurrent Session 2C

Florida plants and climate change: Scripts and pitfalls for utilizing digitized data in course-based undergraduate research
Michelle Gaynor, University of Florida; Douglas E. Soltis, Department of Biology and Florida Museum of Natural History, University of Florida; Pamela S. Soltis, Florida Museum of Natural History, University of Florida
Day One - Block Two
1:00PM - 4:00PM EDT / 5:00PM – 9:00PM UTC
Discussion Sessions 1&2
Time Room 1
1:00 - 2:15 Discussion Session 1

Taxonomically intelligent biodiversity data: Taking stock of our progress and next steps to scale up implementation
Beckett Sterner, Arizona State University; Nate Upham, Arizona State University; Steffi Ickert-Bond, University of Alaska Fairbanks; Jeff Gerbracht, eBird; Atriya Sen, Arizona State University; Nico Franz, Arizona State University
2:15 – 2:45 Break - Rooms open for discussion
2:45 – 3:30 Discussion Session 2

Reliable dataset identifiers are essential building blocks for reproducible research

Jorrit Poelen, Ronin Institute; Michael Elliott, Advanced Computing and Information Systems Laboratory (ACIS) Department of Electrical and Computer Engineering, University of Florida; Jose Fortes, Advanced Computing and Information Systems Laboratory (ACIS) Department of Electrical and Computer Engineering, University of Florida, Gainesville, FL

Day One - Block Three
6:00PM - 9:00PM EDT / 10:00 PM - 1:00 AM

Evening Reception
Time Room 1 Room 2 Room 3
6:00 - 6:20 Welcome
Description of Evening
6:20 - 6:50 Scientifically Speaking with Irene Moon presents, You the Charmer
Since 1997, Scientifically Speaking with Irene Moon has been presenting The Lectography: musical lectures about insects and other arthropods in an attempt to elevate Entomology as a rock genre. Performing at basement house shows and famous music venues like the Knitting Factory, Cafe Otto and the San Francisco Electronic Music Festival, Irene Moon has toured the US, Europe and Australia. She created over 30 musical volumes (including pressed vinyl records) during her career and performed live radio broadcasts dealing with entomological topics on WFMU in New York and other radio stations.

Irene Moon (a.k.a Katja C. Seltmann, PhD) is the Director of the Cheadle Center for Biodiversity and Ecological Restoration at the University of California Santa Barbara. She brings the aesthetics from the entomology laboratory in front of alternative audiences in the form of an absurd, factual presentations about insects. Performance and lecture are a means of connecting the public to entomology and increasing awareness of the art and creativity intrinsic to the scientific process. The power point presentation for the Digital Data in Biodiversity Research Conference is a New Wave lecture on cockroaches titled “You, the Charmer” that incorporates psychedelic imagery, pop styled torch songs, and comedy. Find out more at: begoniasociety.org

6:50 -7:30 IU Virtual Collection Tour
7:30 - 8:30 Natural History Show and Tell and Happy Hour
Theme #1
Natural History Show and Tell and Happy Hour
Theme #2
Natural History Show and Tell and Happy Hour
Theme #3

Tuesday, 2 June 2020

Day Two - Block One
9:00AM - 12:00PM EDT / 1:00PM - 4:00PM UTC
Discussion Session 3&4
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Time Room 1
9:00 - 10:00 Discussion Session 3
Research Data Support for Small Projects
Ali Krzton, Auburn University
10:00 - 10:30 Break
10:30 – 11:45 Discussion Session 4
Zooming in on COVID-19 In Our Lives
Deborah Paul, Florida State University; Pamela Soltis, University of Florida
Day Two - Block Two
1:00PM - 4:00PM EDT / 5:00PM – 8:00PM UTC

Plenary Session 1:00 - 2:00 p.m.
Time Room 1 Room 2 Room 3
1:00 - 1:30 Revealing Morphological Diversity with 3D Digitization
Katie Stanchak, Graduate Student/Postdoctoral Scholar, Department of Biology, University of Washington
1:30 - 2:00 Michelle LeFebvre, Assistant Curator of Archaeology, Florida Museum of Natural History, University of Florida
2:00 – 2:30 Break
Concurrent Sessions 4-7 2:30 – 4:00 p.m.
2:30 Concurrent Session 4A

Context R-CNN: Long Term Temporal Context for Object Detection in Camera Traps
Sara Beery, Caltech; Guanhang Wu, Google; Vivek Rathod, Google; Ronny Votel, Google; Jonathan Huang, Google
Concurrent Session 5A

Creating New Data, Questions, and Scientists: A New Phenology-focused CURE using Herbarium Specimen Data
Katie Pearson, Cal Poly State University; Jenn Yost, Cal Poly State University; Natalie Love; Tadeo Ramirez Parada
Concurrent Session 6A

Extracting phenology and life history data from digitized specimens
Alexis Garretson, George Mason University
2:50 Concurrent Session 4B

Computer vision for biodiversity database image processing
Katherine Wolcott, Encyclopedia of Life, Smithsonian Institution; Jennifer Hammock, Encyclopedia of Life; Katja Schulz, Encyclopedia of Life; Thomas Orrell, Encyclopedia of Life
Discussion Session 5 (2:30 -3:30)

Developing a Course-based Undergraduate Research Experience (CURE) using digitized natural history collections data in response to the transition to online teaching
Carly Jordan, The George Washington University; Janice L. Krumm, Widener University; Elizabeth Shea, Delaware Museum of Natural History; Jean Woods, Delaware Museum of Natural History
Concurrent Session 6B

Attribute facets for specimen data search
Jen Hammock, National Museum of Natural History; Katja Schulz, National Museum of Natural History
3:10 Concurrent Session 4C

Object Detection for Moth Sheet Identification
Chandra Earl, University of Florida
Discussion Session 5
Continued
Concurrent Session 6C

Establishing a pipeline for the application of machine learning to biodiversity specimen records for anomaly detection
Mikayla Buckley, Florida State University; Dr. Zhe He, Florida State University; Dr. Allen Romano, Florida State University; Dr. Austin Mast, Florida State University;
3:30 Discussion Session 5
Continued
Concurrent Session 6D

iDigBio’s Directory of Genetic Resources Enhances Discoverability of Materials for COVID-19 and Beyond
Maria Cortez, University of Florida; Pam Soltis, University of Florida
Day Two - Block Three
6:00PM – 8:30PM EDT / 10:00pm – 12:30AM UTC
R and the iDigBio API Workshop

Facilitators:Erica Krimmel, iDigBio, Florida State University and Ronald Canepa, ACIS Lab, University of Florida
This workshop will focus on using the iDigBio API (Application Programming Interface) to work with biodiversity occurrence data in R. Topics will be determined unconference-style by workshop attendees, but could include those related to collections management, e.g. reviewing specimen data quality issues, and to downstream research, e.g. facilitating reproducible and reusable methods. Community members of all backgrounds (collections staff, researchers, IT, etc.) and levels of programming experience (including R novice!) are encouraged to attend this workshop as a way to discover and discuss API data access, issues, and solutions. This workshop is a product of the iDigBio API User Group (R-based).

Time Room 1
6:00 - 7:00 R and the iDigBio API Workshop
7:00 - 7:30 Break
7:30 – 8:30 R and the iDigBio API Workshop Continued

Wednesday, 3 June 2020

Day Three - Block One
9:00AM - 12:00PM EDT / 1:00PM – 4:00PM UTC
Unconference: Biodiversity Science from Perspectives in Other Disciplines

Facilitators:Deb Paul, iDigBio, Florida State University; Kimberly Cook and Gary Motz, Indiana University
Biodiversity Information Science (BIS) is an inherently multidisciplinary science that is supported by a wealth of perspectives and expertise in diverse fields such as data science, information and library science, computer science, and many others. This unconference session is intended to explore mechanisms by which we can increase and enhance the diversity of people working to advance biodiversity information science in ways that were NOT addressed in the formal program of the Digital Data conference. Unconferences are intentionally unstructured meetings where YOU, the participants (including and especially students), tell the organizers what is important to you and should be better represented in future programming and opportunities for practitioners in our field.

Time Room 1
9:00 - 10:00 Unconference: Biodiversity Science from Perspectives in Other Disciplines
10:00 - 10:30 Break
10:30 - 11:30

Unconference: Biodiversity Science from Perspectives in Other Disciplines Continued

Day Three – Block Two
1:00PM – 4:00PM EDT / 5:00PM - 9:00PM UTC
Discussion Sessions 6&7
Theme: Gaps and deficiencies in currently available digital data that hinder effective use
Time Room 1
1:00 – 2:15 Discussion Session 6

Sharing fossil locality data for paleontological research
Erica Krimmel, iDigBio / Florida State University; Talia Karim, University of Colorado Boulder; Holly Little, National Museum of Natural History; Carrie Levitt-Bussian, Natural History Museum of Utah; Deb Paul, iDigBio / Florida State University

2:15 – 2:45 Break
2:15 - 3:30 Discussion Session 7
Digital Data: integration of infrastructure for representational data
Doug Boyer, Duke University; Julie Winchester, Duke University; David Blackburn, Florida Museum of Natural History
Day Three - Block Three
6:00PM - 9:00PM EDT / 10:00PM - 1:00 AM UTC

Plenary Session 6:00 - 6:45 p.m.
Time Room 1 Room 2 Room 3
6:00 - 6:15 Gil Nelson, Director, iDigBio
6:15 – 6:45 Open Science in Biodiversity: the Challenge and the Promise
Beth Plale, Science Advisor for Public Access, National Science Foundation; Michael A. and Laurie Burns McRobbie Bicentennial Professor of Computer Engineering at Indiana University Bloomington, Bloomington Indiana; Co-founder of the Research Data Alliance (RDA) and past inaugural chair
6:45 – 7:15 Break - Rooms open for discussion
Concurrent Sessions 8-10 7:15 – 8:30 p.m.
Session 7 - Use of digitized biodiversity specimen data within ecological research and practice Session 8 - Part I- Gaps and deficiencies in currently available digital data that hinder effective use
7:15 Concurrent Session 7A

Leveraging Digitized Trait Data for New Insight into Small Mammal Phenology across North America
Bryan McLean, University of North Carolina; Robert Guralnick, Florida Museum of Natural History

Concurrent Session 8A

Building a Global Index of Arthropod Collections
Neil Cobb, Northern Arizona University; Nicole Fisher, CSIRO; Neal Evenhuis, Bishop Museum; Jesús Napoles, UNAM; Petra Sierwald, FMNH; Evin Dunn, Biodiversity Outreach Network; Lindsie McCabe, USDA-ARS; Paige Chesshire, NAU

Discussion Session Follow - Up Panel with Plenary Speakers
7:35 Concurrent Session 7B

Paleobiology in Novel Ecosystems: lessons for conservation from beneath the pavement and diverse digital data sources
Alexis Mychajliw, University of Oklahoma; Libby Ellwood, La Brea Tar Pits & Museum, Emily Lindsey, La Brea Tar Pits & Museum; PiNE Working Group

Concurrent Session 8B

Open Access and Digital Availability of Biodiversity Data Literature: Case of New Discovery of Indonesian Fauna in 2015-2019
Raden Pramesa Narakusumo, Museum Zoologicum Bogoriense, Indonesia Institute of Sciences; Encilia, Museum Zoologicum Bogoriense; Agmal Qodri, Museum Zoologicum Bogoriense; Cahyo Rahmadi, Museum Zoologicum Bogoriense

Discussion Session Follow - Up Panel with Plenary Speakers
Continued
7:55 Concurrent Session 7C

Using Botanical Collections and Digital Herbaria Interfaces to Inform Restoration Efforts for Mining Sites
Larry Schmidt, University of Wyoming; Kristina M. Hufford, University of Wyoming

Session 8 - Part II - Standards and practices for depositing and documenting open access digital datasets

Concurrent Session 8C
Scalable, extensible, and light-weight data sharing with schema.org
Dave Vieglais, University of Kansas


Discussion Session Follow - Up Panel with Plenary Speakers
Continued

Remote Poster Session

Title Authors
Expanding Tools for Ecological and Trait-based Discovery Within Eukaryotic High-Throughput Sequence Datasets Scott T. Bates, Purdue University Northwest; Phil Anders, University of Illinois, Illinois Natural History Survey; Andrew N. Miller, University of Illinois, Illinois Natural History Survey
Digitization of plant structures used in Geometric Morphometry to differentiate native and introduced reforested species of the Polylepis genus in the Illinizas Ecological Reserve-Ecuador. Joselin Caiza Guamba, University of Fuerzas Armas-ESPE; Jean Herdoiza, University of Fuerzas Armadas-ESPE; Michelle Santillán, University of Fuerzas Armadas-ESPE; Cristina Galárraga, University of Fuerzas Armadas-ESPE; Daniel Corredor, University of Fuerzas Armadas-ESPE; Cristian Armas, University of Fuerzas Armadas-ESPE; Belén Alulema, University of Fuerzas Armadas-ESPE; Marco Córdova, University of Fuerzas Armadas-ESPE; Cinthya Jiménez, University of Fuerzas Armadas-ESPE; Mónica Jadán, University of Fuerzas Armadas-ESPE; María Claudia Segovia Salcedo, University of Fuerzas Armadas-ESPE
Transcribed Ornithological Field Notes in the Biodiversity Heritage Library Joseph DeVeer, Harvard University, Museum of Comparative Zoology, Ernst Mayr Library; Constance Rinaldo, Harvard University, Museum of Comparative Zoology, Ernst Mayr Library
Using the ANIC digitisation pipeline to assemble research datasets: analysis of Australian Mutillidae mimicry from museum specimens Nicole Fisher, CSIRO; Claudia Schipp; Thekla Pleines; Juanita Rodriguez
Augmenting the Research Areas Stimulated by Specimen Digitization Maura Flannery, St. John's University NY;
Towards an open data paradigm to address the pollination crisis in Chile Francisco Fonturbel, Pontificia Universidad Catolica de Valparaiso; Manuel Lopez-Aliste, Pontificia Universidad Catolica de Valparaiso; Giselle Muschett, Pontificia Universidad Catolica de Valparaiso
Extracting life stage and behavioral data from digital biodiversity data reveals spatiotemporal trends in milkweed bug ecology Alexis Garretson, George Mason University; Tedra Cuddy, George Mason University; Rebecca Forkner, George Mason University
Digitized herbarium specimen document changes in the timing and duration of phenophases and pathogen damage in Eastern United States maples Alexis Garretson, George Mason University; Rebecca Forkner, George Mason University
Beyond the Building : Inside out (A physic Garden for the 21st Century) Irene Hallyburton, University of Dundee; Ali Floyd, University of Dundee, Wellcome Centre for Anti-Infectives research; Kevin Frediani, University of Dundee, Botanic Gardens
Bats in a Box: Bringing Museums to the Classroom Aditi Jayarajan, Florida Museum of Natural History, University of Florida; David Reed, University of Florida, Florida Museum of Natural History
The beginner’s guide to 3D data processing: A pipeline for computed tomography (CT) data Anne Kort, Indiana University; Elizabeth Hicks, Indiana University; Tara Smiley, Indiana University
Phylogenetic Tree Analysis of Bucephalandra in aquatic biota market using CP-DNA RBCL Marker Media Fitri Isma Nugraha, Indonesian Research Centre for Ornamental Fish Culture - Ministry Marine and fisheries; Ina Erlinawati, Indonesian Institute of Science (LIPI); Deni Sahroni, Indonesian Institute of Science (LIPI); Wening Enggarini, Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD); Rossa Yunita, ICABIOGRAD; Reflinur, ICABIOGRAD; Muhammad Yamin, Indonesian Research Centre for Ornamental Fish Culture - Ministry Marine and fisheries
New life for old data: compiling global diet data of freshwater fishes Jacob Ridgway, University of South Dakota; Jeff Wesner, University of South Dakota; Justin Pomeranz, Colorado Mesa University
Management of biotic interaction data in the Encyclopedia of Life Katja Schulz, Smithsonian National Museum of Natural History; Jennifer Hammock, Smithsonian National Museum of Natural History; Jorrit Poelen, Global Biotic Interactions; Eli Agbayani, Encyclopedia of Life
BCEENET: a network to support the development and implementation of Course-based Undergraduate Research Experiences (CUREs) using digitized natural history collections. Elizabeth Shea, Delaware Museum of Natural History; Janice Krumm, Widener Univeristy; Carly Jordan, The George Washington University; Jean Woods, Delaware Museum of Natural History
Enhanced Species Distribution Models with Digital Extant and Extinct Biodiversity Data Reveal the Shifted Baselines of Avifauna under Climate Change Ashwin Sivakumar, Flintridge Preparatory School; Alexis Mychajliw, La Brea Tar Pits and Museum
Safeguarding Our Specimens (SOS): Improving Research Collections Stewardship of the Jurica-Suchy Nature Museum Karly Tumminello, Jurica-Suchy Nature Museum at Benedictine University; Colleen Filipek, Jurica-Suchy Nature Museum at Benedictine University; Jack Purcell, Benedictine University; Tanya Rasha, Benedictine University; Stephanie Slagle, Benedictine University; Sarah Jablonski, Benedictine University
Addressing Challenges in Seadragon Conservation with Artificial Intelligence Chrissy Tustison, Scripps Institution of Oceanography, UC San Diego;
Cyborg matching of taxonomic names Campbell Webb, University of Alaska Museum of the North; Stefanie Ickert-Bond, University of Alaska Museum of the North