Humans in the loop: Community science and machine learning synergies for overcoming herbarium digitization bottlenecks.

Premise: Among the slowest steps in the digitization of natural history collections is converting imaged labels into digital text. We present here a working solution to overcome this long-recognized efficiency bottleneck that leverages synergies between community science efforts and machine learning approaches.

Methods: We present two new semi-automated services.

Maximizing human effort for analyzing scientific images: A case study using digitized herbarium sheets.

Premise: Digitization and imaging of herbarium specimens provides essential historical phenotypic and phenological information about plants. However, the full use of these resources requires high-quality human annotations for downstream use. Here we provide guidance on the design and implementation of image annotation projects for botanical research.

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.

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

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).

Mountaintop Removal Coal Mining and Emergent Cases of Psychological Disorder in Kentucky.

Although mountaintop removal (MTR) coal extraction techniques have been employed in Appalachia for decades, relatively little research has examined its potential psychological impact on people living in close proximity to MTR activity. The current study taps the State Emergency Department Database (Healthcare Cost and Utilization Project, Kentucky State Emergency Department Database, 2008) to examine the relative risk for diagnoses of depressive, substance use, and anxiety disorders originating in areas with and without MTR activity. Logistical regression analyses, controlling for ethnicity, rurality, mean income, and gender, indicated that MTR independently predicts greater risk for depressive (OR 1.

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.

The notes from nature tool for unlocking biodiversity records from museum records through citizen science.

Legacy data from natural history collections contain invaluable and irreplaceable information about biodiversity in the recent past, providing a baseline for detecting change and forecasting the future of biodiversity on a human-dominated planet. However, these data are often not available in formats that facilitate use and synthesis. New approaches are needed to enhance the rates of digitization and data quality improvement.