Digitization workflows for flat sheets and packets of plants, algae, and fungi

Gil Nelson¹, Patrick Sweeney², Lisa E Wallace³, Richard K Rabeler⁴, Dorothy Allard⁵, Herrick Brown⁶, J Richard Carter⁷, Michael W Denslow⁸, Elizabeth R Ellwood⁹, Charlotte C Germain-Aubrey¹⁰, Ed Gilbert¹¹, Emily Gillespie¹², Leslie R Goertzen¹³, Ben Legler¹⁴, D Blaine Marchant¹⁵, Travis D Marsico¹⁶, Ashley B Morris¹⁷, Zack Murrell⁸, Mare Nazaire¹⁸, Chris Neefus¹⁹, Shanna Oberreiter²⁰, Deborah Paul¹, Brad R Ruhfel²¹, Thomas Sasek²², Joey Shaw²³, Pamela S Soltis¹⁰, Kimberly Watson²⁴, Andrea Weeks²⁵, Austin R Mast⁹

Affiliations

¹ Integrated Digitized Biocollections (iDigBio), Florida State University, Tallahassee, Florida 32306-2100 USA.
² Peabody Museum of Natural History, Yale University, New Haven, Connecticut, USA.
³ Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA.
⁴ University of Michigan Herbarium-EEB, Ann Arbor, Michigan, USA.
⁵ Department of Plant Biology, University of Vermont, Burlington, Vermont, USA.
⁶ Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA.
⁷ Biology Department, Valdosta State University, Valdosta, Georgia, USA.
⁸ Department of Biology, Appalachian State University, Boone, North Carolina, USA.
⁹ Department of Biological Science, Florida State University, Tallahassee, Florida, USA.
¹⁰ Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA.
¹¹ School of Life Sciences, Arizona State University, Tempe, Arizona, USA.
¹² Department of Biological Sciences, Marshall University, Huntington, West Virginia, USA.
¹³ Department of Biological Sciences, Auburn University, Auburn, Alabama, USA.
¹⁴ Burke Museum, University of Washington, Seattle, Washington, USA.
¹⁵ Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA ; Department of Biology, University of Florida, Gainesville, Florida, USA.
¹⁶ Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, USA.
¹⁷ Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA.
¹⁸ Rancho Santa Ana Botanic Garden, Claremont, California, USA.
¹⁹ Department of Biological Sciences, University of New Hampshire, Durham, New Hampshire, USA.
²⁰ University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
²¹ Department of Biological Sciences, Eastern Kentucky University, Richmond, Kentucky, USA.
²² Department of Biology, University of Louisiana at Monroe, Monroe, Louisiana, USA.
²³ Biological and Environmental Sciences, University of Tennessee, Chattanooga, Tennessee, USA.
²⁴ William and Lynda Steere Herbarium, The New York Botanical Garden, Bronx, New York, USA.
²⁵ Department of Biology and the Ted R. Bradley Herbarium, George Mason University, Fairfax, Virginia, USA.

PMID: 26421256
PMCID: PMC4578381
DOI: 10.3732/apps.1500065

Digitization workflows for flat sheets and packets of plants, algae, and fungi

Gil Nelson et al. Appl Plant Sci. 2015.

. 2015 Sep 10;3(9):apps.1500065.

doi: 10.3732/apps.1500065. eCollection 2015 Sep.

Authors

Affiliations

¹ Integrated Digitized Biocollections (iDigBio), Florida State University, Tallahassee, Florida 32306-2100 USA.
² Peabody Museum of Natural History, Yale University, New Haven, Connecticut, USA.
³ Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA.
⁴ University of Michigan Herbarium-EEB, Ann Arbor, Michigan, USA.
⁵ Department of Plant Biology, University of Vermont, Burlington, Vermont, USA.
⁶ Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA.
⁷ Biology Department, Valdosta State University, Valdosta, Georgia, USA.
⁸ Department of Biology, Appalachian State University, Boone, North Carolina, USA.
⁹ Department of Biological Science, Florida State University, Tallahassee, Florida, USA.
¹⁰ Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA.
¹¹ School of Life Sciences, Arizona State University, Tempe, Arizona, USA.
¹² Department of Biological Sciences, Marshall University, Huntington, West Virginia, USA.
¹³ Department of Biological Sciences, Auburn University, Auburn, Alabama, USA.
¹⁴ Burke Museum, University of Washington, Seattle, Washington, USA.
¹⁵ Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA ; Department of Biology, University of Florida, Gainesville, Florida, USA.
¹⁶ Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, USA.
¹⁷ Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA.
¹⁸ Rancho Santa Ana Botanic Garden, Claremont, California, USA.
¹⁹ Department of Biological Sciences, University of New Hampshire, Durham, New Hampshire, USA.
²⁰ University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
²¹ Department of Biological Sciences, Eastern Kentucky University, Richmond, Kentucky, USA.
²² Department of Biology, University of Louisiana at Monroe, Monroe, Louisiana, USA.
²³ Biological and Environmental Sciences, University of Tennessee, Chattanooga, Tennessee, USA.
²⁴ William and Lynda Steere Herbarium, The New York Botanical Garden, Bronx, New York, USA.
²⁵ Department of Biology and the Ted R. Bradley Herbarium, George Mason University, Fairfax, Virginia, USA.

PMID: 26421256
PMCID: PMC4578381
DOI: 10.3732/apps.1500065

Abstract

Effective workflows are essential components in the digitization of biodiversity specimen collections. To date, no comprehensive, community-vetted workflows have been published for digitizing flat sheets and packets of plants, algae, and fungi, even though latest estimates suggest that only 33% of herbarium specimens have been digitally transcribed, 54% of herbaria use a specimen database, and 24% are imaging specimens. In 2012, iDigBio, the U.S. National Science Foundation's (NSF) coordinating center and national resource for the digitization of public, nonfederal U.S. collections, launched several working groups to address this deficiency. Here, we report the development of 14 workflow modules with 7-36 tasks each. These workflows represent the combined work of approximately 35 curators, directors, and collections managers representing more than 30 herbaria, including 15 NSF-supported plant-related Thematic Collections Networks and collaboratives. The workflows are provided for download as Portable Document Format (PDF) and Microsoft Word files. Customization of these workflows for specific institutional implementation is encouraged.

Keywords: citizen science; digital imaging; digitization; herbarium; specimen database; workflow.

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Figures

**Fig. 1.**
Example object-to-data-to-image workflow. This workflow captures data directly from labels on physical specimens. Images of specimens may or may not be captured. Barcodes are usually applied inline or as an iterative step through which dozens or hundreds of barcodes are affixed, immediately preceding data entry. Pre-digitization curation, including nomenclatural annotations and specimen organization, is usually important in this workflow. The need for specimen conservation may be discovered and remedied as physical specimens are passed to data entry technicians or following the specimen handling associated with imaging procedures.

**Fig. 2.**
Example object-to-image-to-data workflow. This workflow captures specimen images and uses these images as the basis for data capture. Barcodes are sometimes applied inline as the step immediately previous to imaging (shown optionally) and other times through an iterative process during which several dozen or several hundred barcodes are applied. Nomenclatural annotation during pre-digitization ensures synchronization of name-on-folder with name-on-specimen. The need for specimen conservation may be discovered and remedied before or after imaging.

See this image and copyright information in PMC

References

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Digitization workflows for flat sheets and packets of plants, algae, and fungi

Affiliations

Digitization workflows for flat sheets and packets of plants, algae, and fungi

Authors

Affiliations

Abstract

Figures

References

LinkOut - more resources

Full Text Sources

Other Literature Sources