Patrick W. Sweeney

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.

Nomenclatural Notes on Garcinia (Clusiaceae) from Madagascar and The Comoros

ABSTRACT New results from phylogenetic analyses utilizing chloroplast and nuclear DNA markers agree with morphology in support of the unification of all of Rheedia L. and part of Ochrocarpos Thouars with Garcinia L. and show that species occurring in Madagascar and the Comoros fall into four separate lineages, which are designated here as informal species groups. An examination of Garcinia from these areas results in the recognition of 32 currently described species, all but one of which are endemic. The widespread African species, G. livingstonei T. Anderson, is noted for the first time to occur in Mayotte. Eleven new combinations are published here: G. ambrensis (H. Perrier) P. Sweeney & Z. S. Rogers, G. anjouanensis (H. Perrier) P. Sweeney & Z. S. Rogers, G. arenicola (Jumelle & H. Perrier) P. Sweeney & Z. S. Rogers, G. calcicola (Jumelle & H. Perrier) P. Sweeney & Z. S. Rogers, G. dalleizettei (H. Perrier) P. Sweeney & Z. S. Rogers, G. mangorensis (R. Viguier & Humbert) P. Sweeney & Z. S. Rogers, G. multifida (H. Perrier) P. Sweeney & Z. S. Rogers, G. parvula (H. Perrier) P. Sweeney & Z. S. Rogers, G. thouvenotii (H. Perrier) P. Sweeney & Z. S. Rogers, G. tsaratananensis (H. Perrier) P. Sweeney & Z. S. Rogers), and G. urschii (H. Perrier) P. Sweeney & Z. S. Rogers. Three new names, G. dauphinensis P. Sweeney & Z. S. Rogers, G. megistophylla P. Sweeney & Z. S. Rogers, and G. tsimatimia P. Sweeney & Z. S. Rogers, are provided for O. parvifolius Scott-Elliot, R. megaphylla H. Perrier, and R. pedicellata (Jumelle & H. Perrier) H. Perrier, respectively. Lectotypes are designated for 12 names: G. crassiflora Jumelle & H. Perrier, G. disepala Vesque, G. melleri Baker, G. polyphlebia Baker, G. verrucosa Jumelle & H. Perrier, O. ambrensis H. Perrier, O. macrophyllus O. Hoffmann, O. parvifolius, O. parvulus H. Perrier, O. tsaratananae H. Perrier, R. arenicola Jumelle & H. Perrier, and R. calcicola Jumelle & H. Perrier.

Worldwide Engagement for Digitizing Biocollections (WeDigBio): The Biocollections Community's Citizen-Science Space on the Calendar

Abstract The digitization of biocollections is a critical task with direct implications for the global community who use the data for research and education. Recent innovations to involve citizen scientists in digitization increase awareness of the value of biodiversity specimens; advance science, technology, engineering, and math literacy; and build sustainability for digitization. In support of these activities, we launched the first global citizen-science event focused on the digitization of biodiversity specimens: Worldwide Engagement for Digitizing Biocollections (WeDigBio). During the inaugural 2015 event, 21 sites hosted events where citizen scientists transcribed specimen labels via online platforms (DigiVol, Les Herbonautes, Notes from Nature, the Smithsonian Institutions Transcription Center, and Symbiota). Many citizen scientists also contributed off-site. In total, thousands of citizen scientists around the world completed over 50,000 transcription tasks. Here, we present the process of organizing an international citizen-science event, an analysis of the events effectiveness, and future directions—content now foundational to the growing WeDigBio event.

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.

Large-scale digitization of herbarium specimens: Development and usage of an automated, high-throughput conveyor system

The billions of specimens housed in natural science collections provide a tremendous source of under-utilized data that are useful for scientific research, conservation, commerce, and education. Digitization and mobilization of specimen data and images promises to greatly accelerate their utilization. While digitization of natural science collection specimens has been occurring for decades, the vast majority of specimens remain un-digitized. If the digitization task is to be completed in the near future, innovative, high-throughput approaches are needed. To create a dataset for the study of global change in New England, we designed and implemented an industrial-scale, conveyor-based digitization workflow for herbarium specimen sheets. The workflow is a variation of an object-to-image-to-data workflow that prioritizes imaging and the capture of storage container-level data. The workflow utilizes a novel conveyor system developed specifically for the task of imaging flattened herbarium specimens. Using our workflow, we imaged and transcribed specimen-level data for almost 350,000 specimens over a 131-week period; an additional 56 weeks was required for storage container-level data capture. Our project has demonstrated that it is possible to capture both an image of a specimen and a core database record in 35 seconds per herbarium sheet (for intervals between images of 30 minutes or less) plus some additional overhead for container-level data capture. This rate was in line with the pre-project expectations for our approach. Our throughput rates are comparable with some other similar, highthroughput approaches focused on digitizing herbarium sheets and is as much as three times faster than rates achieved with more conventional non-automated approaches used during the project. We report on challenges encountered during development and use of our system and discuss ways in which our workflow could be improved. The conveyor apparatus software, database schema, configuration files, hardware list, and conveyor schematics are available for download on GitHub.