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. 2019 Mar 7;7(3):e01231.
doi: 10.1002/aps3.1231. eCollection 2019 Mar.

Integrating herbarium specimen observations into global phenology data systems

Laura Brenskelle  1 , Brian J Stucky  1 , John Deck  2 , Ramona Walls  3 , Rob P Guralnick  1
Affiliations

Integrating herbarium specimen observations into global phenology data systems

Laura Brenskelle et al. Appl Plant Sci. .

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.

Keywords: data integration; herbarium specimens; knowledge representation; ontology; plant phenology.

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Figures

Figure 1
Figure 1
An example of the PPO's model for a phenology observation of a herbarium specimen (or any other ‘portion of a plant’), on the left, and how that observation can be linked to data about a ‘whole plant’, on the right. This figure shows the key new class, ‘portion of a plant’, and three of the new object properties (‘is or was part of’, ‘generated from’, and ‘quality datum of’).
Figure 2
Figure 2
A screenshot of search results for Prunus serotina observations of open flowers present on https://www.plantphenology.org. Note the inclusion of record counts for herbarium specimens shown at the top of the figure.
Figure 3
Figure 3
An effect plot showing a trend toward earlier flowering over more than a century, when accounting for latitude.
See this image and copyright information in PMC

References

    1. Anderson, J. T. , Inouye D. W., McKinney A. M., Colautti R. I., and Mitchell‐Olds T.. 2012. Phenotypic plasticity and adaptive evolution contribute to advancing flowering phenology in response to climate change. Proceedings of the Royal Society B. Biological Sciences 279: 3843–3852. - PMC - PubMed
    1. Bertin, R. I. 2008. Plant phenology and distribution in relation to recent climate change. Journal of the Torrey Botanical Society 135: 126–146.
    1. Ceusters, W. 2012. An information artifact ontology perspective on data collections and associated representational artifacts. Studies in Health Technology and Informatics 180: 68–72. - PubMed
    1. Chmielewski, F.‐M. , Müller A., and Bruns E.. 2004. Climate changes and trends in phenology of fruit trees and field crops in Germany, 1961–2000. Agricultural and Forest Meteorology 121: 69–78.
    1. Chuine, I. , and Régnière J.. 2017. Process‐based models of phenology for plants and animals. Annual Review of Ecology, Evolution, and Systematics 48: 159–182.