Integrating herbarium specimen observations into global phenology data systems

Abstract

Premise of the Study The Plant Phenology Ontology ( PPO ) was originally developed to integrate phenology observations of whole plants across different global observation networks. Here we describe a new release of the PPO and associated data pipelines that supports integration of phenology observations from herbarium specimens, which provide historical and modern phenology data. Methods and Results Critical changes to the PPO include key terms that describe how measurements from parts of plants, which are captured in most imaged herbarium specimens, relate to whole plants. We provide proof of concept for ingesting annotations from imaged herbarium sheets of Prunus serotina , the common black cherry. We then provide an example analysis of changes in flowering timing over the past 125 years, demonstrating the value of integrating herbarium and observational phenology data sets. Conclusions These conceptual and technical advances will support the addition of phenology data from herbaria, but also could be expanded upon to facilitate the inclusion of data from photograph‐based citizen science platforms. With the incorporation of herbarium phenology data, new historical baseline data will strengthen the capability to monitor, model, and forecast plant phenology changes.

Toward a large‐scale and deep phenological stage annotation of herbarium specimens: Case studies from temperate, tropical, and equatorial floras

“…Furthermore, as multimedia data streams are now much more easily produced by, e.g., drones equipped with cameras, such automated tasks could offer new opportunities for production of large volumes of phenological data. The adoption of these automated techniques by collection managers, particularly within the framework of the established Plant Phenology Ontology (Brenskelle et al, 2019), could make it possible to (1) pre-annotate large volumes of herbarium specimens that have not yet been annotated, which could then be revised by collaborative approaches; (2) have a standardized methodology that avoids bias related to expertise and perception variability of annotators; (3) use pre-annotated herbarium specimens for phenological studies at large scales that would not be possible with human investment alone; and (4) identify and correct annotation mistakes made by human annotators.…”

Testing Hopkins’ Bioclimatic Law with PhenoCam data

“…() demonstrates that for most ecosystem types camera‐ and satellite‐derived phenometrics are in close agreement, giving confidence in the use of remotely sensed data for validation. Phenological models could also be validated against transition dates estimated from herbarium samples collected years or decades earlier (Brenskelle et al., ; Pearson, ), enabling robust validation of hindcasting skill. Public release and documentation of software packages to facilitate phenological modeling (Hufkens et al., ; Park et al., ) should further contribute to advancing understanding of the controls on vegetation phenology.…”

Emerging frontiers in phenological research

“…Fortunately, a standardized, relational vocabulary is being developed in the Plant Phenology Ontology (PPO), which enables integration of phenological data across platforms, data sources, and species (Stucky et al, 2018). Brenskelle et al (2019) describe important updates to the PPO that will allow data from herbarium-based studies to be represented more accurately by including descriptive terms for how measurements of plant parts relate to full plants-a relationship that was previously unaddressed in this standardized vocabulary.…”

“…Brenskelle et al. () describe important updates to the PPO that will allow data from herbarium‐based studies to be represented more accurately by including descriptive terms for how measurements of plant parts relate to full plants—a relationship that was previously unaddressed in this standardized vocabulary.…”