Gil Nelson

Old Plants, New Tricks: Phenological Research Using Herbarium Specimens

The timing of phenological events, such as leaf-out and flowering, strongly influence plant success and their study is vital to understanding how plants will respond to climate change. Phenological research, however, is often limited by the temporal, geographic, or phylogenetic scope of available data. Hundreds of millions of plant specimens in herbaria worldwide offer a potential solution to this problem, especially as digitization efforts drastically improve access to collections. Herbarium specimens represent snapshots of phenological events and have been reliably used to characterize phenological responses to climate. We review the current state of herbarium-based phenological research, identify potential biases and limitations in the collection, digitization, and interpretation of specimen data, and discuss future opportunities for phenological investigations using herbarium specimens.

Five task clusters that enable efficient and effective digitization of biological collections

Abstract This paper describes and illustrates five major clusters of related tasks (herein referred to as task clusters) that are common to efficient and effective practices in the digitization of biological specimen data and media. Examples of these clusters come from the observation of diverse digitization processes. The staff of iDigBio (The U.S. National Science Foundation’s National Resource for Advancing Digitization of Biological Collections) visited active biological and paleontological collections digitization programs for the purpose of documenting and assessing current digitization practices and tools. These observations identified five task clusters that comprise the digitization process leading up to data publication: (1) pre-digitization curation and staging, (2) specimen image capture, (3) specimen image processing, (4) electronic data capture, and (5) georeferencing locality descriptions. While not all institutions are completing each of these task clusters for each specimen, these clusters describe a composite picture of digitization of biological and paleontological specimens across the programs that were observed. We describe these clusters, three workflow patterns that dominate the implemention of these clusters, and offer a set of workflow recommendations for digitization programs.

Digitization Workflows for Flat Sheets and Packets of Plants, Algae, and Fungi

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 Foundations (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.

Herbarium data: Global biodiversity and societal botanical needs for novel research

Building on centuries of research based on herbarium specimens gathered through time and around the globe, a new era of discovery, synthesis, and prediction using digitized collections data has begun. This paper provides an overview of how aggregated, open access botanical and associated biological, environmental, and ecological data sets, from genes to the ecosystem, can be used to document the impacts of global change on communities, organisms, and society; predict future impacts; and help to drive the remediation of change. Advocacy for botanical collections and their expansion is needed, including ongoing digitization and online publishing. The addition of non‐traditional digitized data fields, user annotation capability, and born‐digital field data collection enables the rapid access of rich, digitally available data sets for research, education, informed decision‐making, and other scholarly and creative activities. Researchers are receiving enormous benefits from data aggregators including the Global Biodiversity Information Facility (GBIF), Integrated Digitized Biocollections (iDigBio), the Atlas of Living Australia (ALA), and the Biodiversity Heritage Library (BHL), but effective collaboration around data infrastructures is needed when working with large and disparate data sets. Tools for data discovery, visualization, analysis, and skills training are increasingly important for inspiring novel research that improves the intrinsic value of physical and digital botanical collections.

Digitization protocol for scoring reproductive phenology from herbarium specimens of seed plants

Premise of the Study Herbarium specimens provide a robust record of historical plant phenology (the timing of seasonal events such as flowering or fruiting). However, the difficulty of aggregating phenological data from specimens arises from a lack of standardized scoring methods and definitions for phenological states across the collections community. Methods and Results To address this problem, we report on a consensus reached by an iDigBio working group of curators, researchers, and data standards experts regarding an efficient scoring protocol and a data‐sharing protocol for reproductive traits available from herbarium specimens of seed plants. The phenological data sets generated can be shared via Darwin Core Archives using the Extended MeasurementOrFact extension. Conclusions Our hope is that curators and others interested in collecting phenological trait data from specimens will use the recommendations presented here in current and future scoring efforts. New tools for scoring specimens are reviewed.

Use of globally unique identifiers (GUIDs) to link herbarium specimen records to physical specimens

With the advent of the U.S. National Science Foundations Advancing Digitization of Biodiversity Collections program and related worldwide digitization initiatives, the rate of herbarium specimen digitization in the United States has expanded exponentially. As the number of electronic herbarium records proliferates, the importance of linking these records to the physical specimens they represent as well as to related records from other sources will intensify. Although a rich and diverse literature has developed over the past decade that addresses the use of specimen identifiers for facilitating linking across the internet, few implementable guidelines or recommended practices for herbaria have been advanced. Here we review this literature with the express purpose of distilling a specific set of recommendations especially tailored to herbarium specimen digitization, curation, and management. We argue that associating globally unique identifiers (GUIDs) with physical herbarium specimens and including these identifiers in all electronic records about those specimens is essential to effective digital data curation. We also address practical applications for ensuring these associations.

Green digitization: Online botanical collections data answering real-world questions

Recent advances in digital technology, coupled with rapidly increasing interest in the creation and dissemination of digitized specimen data for use in broadscale research by botanists and other organismal scientists, have encouraged the development of a variety of new research opportunities in the botanical sciences (e.g., Page et al., 2015; Soltis, 2017). It is now increasingly possible to collect, use, reuse, and share data more easily and effectively. With the advent of the U.S. National Science Foundation’s Advancing Digitization of Biodiversity Collections initiative and the establishment of iDigBio (Integrated Digitized Biocollections; www.idigbio.org) as the national resource for specimen digitization and digital data mobilization, researchers now have access to ever larger and varied digital data sets for visualization, analysis, and modeling and have new opportunities for adopting “big data” strategies for facilitating discovery. The iDigBio portal alone now includes nearly 20 million botanical specimen records, a figure that is growing rapidly as new institutions share their data. In this special issue of Applications in Plant Sciences, which is based on symposium presentations at Botany 2017 (the annual meeting of the Botanical Society of America and affiliated societies) and the XIX International Botanical Congress, authors present a broad array of examples of the latest developments in botanical biodiversity research using digitized specimen data, including in the fields of genomics, conservation assessment, ecology, phenology, and taxonomic revisions. The papers present current trends in the proactive digitization of specimen data that occurs during the collecting and vouchering of specimens and field data; the tools, skills, and strategies needed for linking and visualizing botanical data; and innovative methods for digital discovery. This collection also highlights how digital data are being used in research that expands our understanding and conservation of plant diversity and the environment. Although the source data for the papers in this collection are herbarium specimens, the topics extend well beyond systematics. Broadly integrative plant biologists will be interested in new approaches to using and reusing specimen data—whether locality information for modeling or images for analysis of morphology and/or functional traits. More importantly, digitized herbarium data become even more valuable when linked to other data sources, such as environmental or genetic data. In fact, emerging cyberinfrastructure and new data sources provide unparalleled opportunities for mobilizing and integrating massive amounts of information from organismal biology, ecology, genetics, climatology, and other disciplines. Particularly powerful is the integration of phylogenies with specimen data, enabling analyses of phylogenetic diversity in a spatiotemporal context, the evolution of niche space, and more. Such datadriven synthetic analyses may generate unexpected patterns, yielding new hypotheses for further study. However, a major challenge is the heterogeneous nature of complex data, and new methods are needed to link these divergent data types. Ongoing efforts to link and analyze diverse data are yielding new perspectives on a range of ecological problems. Integration of plant phylogeny, distributions, traits, and ultimately genetics is permitting new

THE EPANDDA PROJECT: LINKING THE PALEOBIOLOGY DATABASE, IDIGBIO, AND IDIGPALEO FOR BIOLOGICAL AND PALEONTOLOGICAL RESEARCH, COLLECTIONS MANAGEMENT, AND OUTREACH

There are several online paleontological resources that serve a diversity of needs: the Paleobiology Database (PaleoBioDB), a database of fossil occurrences built largely from the primary scientific literature; iDigBio, the national hub for neontological and paleontological specimen data; and iDigPaleo, a specimen-based website built for educational use. While each resource is useful on its own, aggregating data from them is laborious and problematic, as the connectivity between modern and fossil, and specimen and literature-based, resources does not currently exist. Funded by the NSF EarthCube initiative (ICER 1821039), the enhancing Paleontological and Neontological Data Discovery API (ePANDDA) project is using application programming interfaces (APIs) to integrate the paleontological and neontological resources of these three sites. The ePANDDA API ‡ § | ¶ § # ¤

Digitization workflows for paleontology collections

The development of digitization workflows is an essential part of any formalized large-scale digitization program. Paleontological collections literature has addressed the need for, and utility of, digitized collections for nearly four decades, but no modern, community-vetted set of digitization workflows to accomplish this goal has been widely adopted. With the advent of the U.S. National Science Foundation’s (NSF) Advancing the Digitization of Biodiversity Collections (ADBC) program in 2011, iDigBio, NSF’s national coordinating center for facilitating digitization, in collaboration with broad community representation from numerous institutions, launched a series of working groups to address workflow development across all major preparation types. Workflow modules have been developed for pre-digitization curation, data entry, imaging objects (catalogs, field notes and other materials not stored with specimens, labels, twoand three-dimensionally preserved specimens), image processing, and proactive digitization. Modules and the tasks they include may be implemented in any order and customized for specific configurations and institutional parameters. The workflows are made publicly available for download and customization at GitHub and via the iDigBio documentation pages. A review of platforms for electronic data publishing through online aggregators, a crucial step in any digitization program, is also provided. Talia S. Karim. University of Colorado Museum of Natural History, Boulder, Colorado 80503, USA. talia.karim@colorado.edu Roger Burkhalter. Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Avenue, Norman, Oklahoma 73072, USA. rjb@ou.edu Úna C. Farrell. Department of Geological Sciences, Stanford University, 450 Serra Mall, Stanford, California 94305, USA. ufarrell@stanford.edu Ann Molineux. Non-vertebrate Paleontology Lab, University of Texas, 10100 Burnet Road, Austin, Texas 78758, USA. annm@austin.utexas.edu Gil Nelson. Department of Biological Sciences, Florida State University, Tallahassee, Florida 32303, USA. gnelson@bio.fsu.edu Jessica Utrup. Yale University, Peabody Museum of Natural History, Division of Invertebrate Paleontology, 170 Whitney Avenue, PO Box 208118, New Haven, Connecticut 06520, USA. jessica.utrup@yale.edu Susan H. Butts. Yale University, Peabody Museum of Natural History, Division of Invertebrate Paleontology, 170 Whitney Avenue, PO Box 208118, New Haven, Connecticut 06520, USA. susan.butts@yale.edu Karim, Talia S., Burkhalter, Roger, Farrell, Úna C., Molineux, Ann, Nelson, Gil, and Butts, Susan H. 2016. Digitization workflows for paleontology collections. Palaeontologia Electronica 19.3.4T: 1-14 palaeo-electronica.org/content/2016/1569-digitization-workflows Copyright: Paleontological Society October 2016 KARIM ET AL.: DIGITIZATION WORKFLOWS