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In April and July 2024, interested members of the public were able to attend open tours at the University and Jepson Herbaria at the University of California, Berkeley, advertised to the public ahead of time. The tours of the herbarium including a demo of the digitizing lab, showing people the process of digitizing and using African specimens as an example. | In April and July 2024, interested members of the public were able to attend open tours at the University and Jepson Herbaria at the University of California, Berkeley, advertised to the public ahead of time. The tours of the herbarium including a demo of the digitizing lab, showing people the process of digitizing and using African specimens as an example. | ||
====[#AfricanPlants series]==== | ====[#AfricanPlants series]==== | ||
Revision as of 10:54, 21 August 2024
Collaborative Research: Digitization and Enrichment of U.S. Herbarium Data from Tropical Africa to Enable Urgent Quantitative Conservation Assessments
| Digitization and Enrichment of U.S. Herbarium Data from Tropical Africa to Enable Urgent Quantitative Conservation Assessments | |
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| Quick Links | |
| Project Summary | |
| Current Research | |
| Project Websites | |
| Publications | |
Project Summary
Biological diversity has been the subject of hundreds of years of work by botanists and zoologists, accumulating rich stores of specimens and associated data in museums and herbaria around the world. These rich information resources, however, too often remain in analog format only, and have not been digitized and “enabled” in the service of science. This project aims to digitize, enrich, and share openly the rich data resources held in United States herbaria that correspond to plants of tropical Africa. By the close of the project, it will have captured data from 1.1 million herbarium specimens, and will augment digital accessible data records for the African continent by more than 15-fold. It will also have created a broad, international, intercontinental network of scientists and students interested in and experienced with management and analysis of such data. This combination of information resources and human capacity will enrich and improve biodiversity conservation planning across Africa.
Herbarium specimens represent a rich source of data on plant diversity. This project will focus on the tropical African seed plant specimen holdings of 21 U.S. herbaria, which will be imaged, associated data captured, and data records georeferenced and quality-controlled. Imaging and data capture will be carried out at each of the herbaria, and data will be aggregated for efficient georeferencing. For most records, georeferencing will be performed automatically; however, a small portion will be georeferenced manually by plant scientists in Ghana, Rwanda, Malawi, and Gabon. Finally, project data will be subjected to detailed quality-control assessment, and served openly to the scientific community via a dedicated “African Plants” portal on Symbiota, as well as integration into iDigBio.org and the Global Biodiversity Information Facility (GBIF.org). These rich data resources will be used to understand the conservation status of African plant species in much greater detail than has been possible to date.
Current Research
Project Websites & Social Media
African Plants Collaborative Biodiversity Portal
The African Plants Portal provides a unique access point to millions of primary biodiversity records of plants from African countries.
https://african-plants.org/portal/index.php
Citizen Science & Outreach Projects
The Field Museum (FM) hosted community scientists to participate in digitization projects at the Field Museum Collections Club. Fourteen community scientists attended an event in December 2022, learned about this project and its main objectives, and barcoded ~1800 specimens of flowering plants from Africa; in January 2023, 32 community scientists barcoded a further 5271 specimens.
In April 2023, FM hosted a WeDigBio Event, wherein community scientists were invited to participate in digitization
projects at the Field Museum. FM also hosted a Bank of America Community Volunteering Program, where 18 people
attended and barcoded 2976 African plant specimens. Finally, FM Members' Night events provided FM members with the
opportunity to visit behind-the-scenes areas to meet scientists and learn about their research projects, including a display
about this project in the Imaging Lab.
In April and July 2024, interested members of the public were able to attend open tours at the University and Jepson Herbaria at the University of California, Berkeley, advertised to the public ahead of time. The tours of the herbarium including a demo of the digitizing lab, showing people the process of digitizing and using African specimens as an example.
[#AfricanPlants series]
https://twitter.com/WeDigBio/status/1619899508351201282 Tweet about outreach activities with volunteers who barcoded over 12,000 specimens as part of the African Plants Data Project.
Project Leadership
Project sponsor: National Science Foundation
Principal Investigators (PIs):[A. Townsend Peterson (PI/PD)] [Brent D. Mishler (PI)] [Mare Nazaire (PI)] [Nico M. Franz (PI)] [Alexander Linan (PI)] [Elena Kramer (PI)] [Nicole Tarnowsky (PI)]
Project Collaborators
University of Kansas
Principal Investigator (PI)/Project Director (PD): A. Townsend Peterson (NSF Award #2223875)
University of California, Berkeley, University Herbarium (UC) and Jepson Herbaria (JEPS)
Principal Investigator (PI): Brent D. Mishler (NSF Award #2223876)
California Botanic Garden, formerly Rancho Santa Ana (RSA) Botanic Garden
Principal Investigator (PI): Mare Nazaire (NSF Award #2223877)
Arizona State University
Principal Investigator (PI): Nico M. Franz (NSF Award #2223878)
Missouri Botanical Garden (MO)
Principal Investigator (PI): Alexander Linan (NSF Award #2223879)
Harvard University (GH)
Principal Investigator (PI): Elena Kramer (NSF Award #2223880)
New York Botanical Garden (NY)
Principal Investigator (PI): Nicole Tarnowsky (NSF Award #2223881)
Academy of Natural Sciences of Drexel University (PH)
Subaward Principal Investigator (Sub PI): Tatyana Livshultz (NSF Award #2223875)
Carnegie Museum of Natural History (CM)
Subaward Principal Investigator (Sub PI): Bonnie L. Isaac (NSF Award #2223875)
Field Museum of Natural History (F)
Subaward Principal Investigator (Sub PI): Maria Lucia Kawasaki (NSF Award #2223875)
Purdue University (PUL)
Subaward Principal Investigator (Sub PI): D. Rabern Simmons (NSF Award #2223875)
University of Minnesota (MIN)
Subaward Principal Investigator (Sub PI): Timothy Whitfeld (NSF Award #2223875)
Yale University (YU)
Subaward Principal Investigator (Sub PI): Patrick Sweeney (NSF Award #2223875)
Bringham and Young University (BRY)
Contact: Robert Johnson
Brown University (BRU)
Contact: Rebecca Y. Kartzinel
Cornell University(BH)
Contact: Kevin C. Nixon
Louisiana State University (LSU)
Contacts: Laura Lagomarsino and Jennifer Kluse
National Museum of Natural History (US)
Contacts: Sylvia Orli and Eric Schuettpelz
Philecology Herbarium at the Botanical Research Institute of Texas (BRIT)
Contacts: Peter Fritsch and Tiana F. Rehman
Pittsburg State University (KSP)
Contact: Neil Snow
University of Arizona (ARIZ)
Contact: Michelle McMahon
University of California, Davis (DAV)
Contacts: Alison Colwell and Daniel Potter
University of Utah (UT)
Contact: Mitchell J. Power
Centre for Plant Medicine Research (CPMR), Mampong-Akuapem, Ghana
Contact: Alex Asase (Georeferencing Team Lead)
Center of Excellence in Biodiversity and Natural Resource Management at University of Rwanda, Kigali, Rwanda
Contact: Beth A. Kaplin (Georeferencing Team Lead)
L’Herbier National du Gabon, Libreville, Gabon
Contact: Nestor Engone Obiang (Georeferencing Team Lead)
Malawi University of Science and Technology, Limbe, Malawi
Contact: Tiwonge Mzumara-Gawa (Georeferencing Team Lead)
Georeferencing Coordinators
Contact: John Wieczorek, Rauthiflor LLC, Bariloche, Argentina
Contact: Paula Zermoglio, Instituto de Investigaciones en Recursos Naturales, Agroecología y Desarrollo Rural (IRNAD)
Protocols & Workflows
The Missouri Botanical Garden team initiated contact with Cyrille Chatelain from Geneva, responsible for the African Plant Database (APD), and Chatelain provided a copy of the APD for the project. The University of Minnesota team (Tim Whitfeld and George Weiblen) then quality-controlled the APD dataset, and created a clean and effective version thereof, for use by the project, which has the dual advantage of creating a controlled vocabulary for each institutional dataset, and of moving all project datasets to a common taxonomic authority.
Details of taxonomy list:
458 families, 6666 genera, 38193 species (accepted names), 43960 species synonyms, 5466 subspecies (accepted names), 1256 subspecies synonyms, 3714 varieties (accepted names), 6768 variety synonyms, 166 forms (accepted names), and 464 form synonyms for consistency among project partners on this project. Csv file in UTF-8.
Publications
von Konrat M, Rodriguez Y, Bailey C, Gwilliam III GF, Christian C, Aguero B, Ahn J, Albion Z, Allen J, Bailey C, Blake E, Blake W, Blake G, Briscoe L, Budke J, Campbell T, Chansler M, Clark D, Delapena R, Denslow M, Ellis S, Ellwood E, Ens B, Evans N, Fabian A, Gaswick W, Golembiewski K, Grant S, Hansen K, Janney B, Jones J, Kachian Z, Kawasaki L, Leek O, Kellum K, Maier C, Mast A, Martinec J, Mayer P, Mladek M, Nadhifah A, Neefus C, Nodulman M, Oliver M, Overberg K, Peterson AT, Qazi-Lampert A, Rothfels C, Salm R, Schreiner D, Schreiner M, Tepe EJ, Turcatel M, Vega A, Wade H, Weinand D, Webbink K, Widhelm T, Zwingelberg M (2024) From Spectators to Stewards: Transforming Public Involvement in Natural History Collections. ARPHA Preprints. https://doi.org/10.3897/arphapreprints.e132939
Professional Presentations
Barberá, Patricia; Asase, Alex; Borokini, Israel T.; Colwell, Alison; Davis, Charles C.; Franz, Nico M.; Fritsch, Peter; Gilbert, Edward; Isaac, Bonnie L.; Johnson, Robert; Kaplin, Beth A.; Kartzinel, Rebecca Y.; Kawasaki, Maria Lucia; Kennedy, Jonathan; Kluse, Jennifer; Kramer, Elena M.; Lagomarsino, Laura; Livshultz, Tatyana; Lowry, Porter P.; McMahon, Michelle; Mishler, Brent D.; Mzumara, Tiwonge I.; Nazaire, Mare; Nixon, Kevin C.; Engone Obiang, Nestor; Orli, Sylvia; Pearson, Katelin; Peterson, A. Townsend; Potter, Daniel; Power, Mitchell J.; Rehman, Tiana F.; Schmidt, Heidi; Simmons, D. Rabern; Schmull, Michaela; Schuettpelz, Eric; Smith, Chelsea R.; Snow, Neil; Sweeney, Patrick W.; Tarnowsky, Nicole; Teisher, Jordan K. ; Weiblen, George D.; Whitfeld, Timothy J.S.;Wieczorek, John; and Zermoglio, Paula (2024). Digitization and Enrichment of U.S. Herbarium Data from Tropical Africa to Enable Urgent Quantitative Conservation Assessments. XX International Botanical Congress (IBC 2024), as part of the symposium titled, African Taxonomy: A Collaborative Effort Towards Biodiversity Conservation. Madrid, Spain.
Nazaire, Mare (2023). Enriching the Internship Experience Through Digitization of the RSA Herbarium. Society for the Preservation of Natural History Collections (SPNHC) 2023. San Francisco, California.
Peterson, A. Townsend (2022). Digitization and Enrichment of U.S. Herbarium Data from Tropical Africa to Enable Urgent Quantitative Conservation Assessments. 2022 Biodiversity Digitization Conference (BioDigiCon). Virtual.
Peterson, A. Townsend (2024). Managing Biodiversity Data in the Blockchain: Full Tracking of All Data Transactions Through Time in Managing Systematic Collections. iDigBio Digital Data 2024: Synthesizing & Harmonizing Data for Integrated Biodiversity Research. Lawrence, Kansas.
Simmons, D. Rabern; Bunch, Sidney M.; Reyes, Bryan; and Aime, M. Catherine (2024). Conference poster: African Plants in the Purdue University Herbaria Arthur (PUR) and Kriebel (PUL) Collections. Indiana Academy of Science annual meeting. Indianapolis, Indiana.
Simmons, D. Rabern; Bunch, Sidney M.; Reyes, Bryan; and Aime, M. Catherine (2024). Conference poster: Digitization of the African plants of the Arthur Fungarium (PUR) and Kriebel Herbarium (PUL) at Purdue University. 2024 American Society of Plant Biologists, Midwest Section Meeting. West Lafayette, Indiana.
Other project documentation
Recordings of each live class and Q&A session of the African Plants Georeferencing Train the Trainers Workshop shared on YouTube at https://tinyurl.com/AfricanPlantsGeorefCourseYT, as presented to the georeferencing teams in Ghana, Gabon, Rwanda, and Malawi for this project by the georeferencing coordinators, Paula Zermoglio and John Wieczorek
Adventures in the Herbarium: Preserving African Plants (Episodes 1 & 2), two podcasts prepared by the Summer interns from Education Department at the Field Museum, shared on https://rss.com/podcasts/teenstudio/
Desalvio, Serina. (2024, July 8). Missouri Botanical Garden: AI used to learn how trees move. St. Louis Post-Dispatch, Vol. 146, No. 190.