OSR - Phenology

A Task Group of the Observation and Specimen Records (OSR) Interest Group

task group

Plant Phenology Task Group Charter

A Task Group of the Observation and Specimen Records (OSR) Interest Group

Convenors

Core members

  • Pierre Bonnet
  • Libby Ellwood
  • Dag Endresen
  • Ed Gilbert
  • Rob Guralnick
  • James Macklin
  • Gil Nelson
  • Anabela Plos
  • Brian Stucky
  • Patrick Sweeney
  • John Wieczorek

Motivation

Phenological data are increasingly being used to examine the effects of climate change and other drivers of biological change. Phenological observation networks, historical phenological surveys, and biodiversity specimens have arisen as important sources of phenological data. However, fields for phenological data are not expressly identified in the Darwin Core, and phenological data have variously been stored in the DwC fields occurrenceRemarks, reproductiveCondition, verbatimAttributes, and others, making phenological data difficult to access, aggregate, and analyze at scale across data sources. The California Phenology Network has hitherto used the Measurement Or Fact extension to serve phenological data and thereby capture important metadata about phenological scorings. Still, these data have seen relatively little use by researchers because they are difficult to discover both via GBIF and their data portal. Phenological data are, in practice, lost within such extensions since they aren’t well-explored by the data-using community.

The Plant Phenology Task Group aims to develop a plant phenology extension for the Darwin Core. We will create fields into which plant phenological data can be entered and recommend a standardized vocabulary for use in these fields, drawing heavily from the Plant Phenology Ontology. This task group is focused first on phenological data associated with flowering plants, but the standards will be developed such that phenological data associated with gymnosperms and nonvascular plant groups can be addressed in the future.

Stakeholders

There is a substantial community of researchers who use phenological data, including that derived from specimens, to investigate regional and global change (see Willis et al. 2017, Trends in Ecology and Evolution). With the increased availability of digitized specimen data and other phenological data (e.g., from the USA-NPN, SWE-NPN), researchers are beginning to integrate data from different sources and investigate questions at both broad scales (e.g., Park & Mazer 2018, Global Change Biology) and to greater detail at fine scales (e.g., Pearson et al. 2021, Madroño).

Shifts in phenological events impact agriculture by changing overlap with pollinators, pests, pathogens, competitors, and adverse climatic conditions, thereby influencing crop yields (Fatima et al. 2020). Understanding how phenology will shift with a changing climate is therefore critical to feeding the growing human population. The phenological standards developed by this task group will integrate with the BBCH-scale--widely used in agricultural research--and can therefore be integrated into current phenological research in agriculture.

Phenology is increasingly being considered in conservation applications (e.g., Morellato et al. 2016). Phenology can impact community dynamics, the success of invasive species, associations with other plant and animal species, and other variables important to informed conservation and management. Readily available phenological data is important for supporting biodiversity at local to global scales.

Lastly, the study of phenological patterns using biodiversity data lends well to education and community science applications, as evidenced by the success of initiatives including GLOBE, the USA-NPN, NatureWatch, Nature’s Calendar, RitmeNatura, Project Budburst, the California Phenology Project, and many others. Creating data standards for phenological data in the Darwin Core will improve our ability to harmonize across datasets like those produced by these community science programs. Data standards will also allow greater findability and access of phenological data for educational use, such as course-based undergraduate research experiences (e.g., https://qubeshub.org/publications/1956/3) and modules developed by the Biodiversity Literacy and Undergraduate Education program.

Goals, outputs, and outcomes

  1. Determine whether Darwin Core must be amended to accommodate phenological trait data.
  2. Establish a draft Darwin Core extension (if a new extension is identified as the best route forward) for phenological data with feedback from users.
  3. Identify Plant Phenology Ontology terms to be used as a standardized vocabulary for the extension/standards.
  4. Pilot implementation of the extension/standards using the CCH2 data portal and another non-Symbiota data publisher.
  5. (If extension) Serve the extension from GBIF’s registry of extensions.
  6. Advocate for the use of standardized phenological vocabulary and the new phenology standards.

Strategy

  1. Determine whether Darwin Core must be amended to accommodate phenological trait data.
  2. Establish a draft Darwin Core extension (if a new extension is identified as the best route forward) for phenological data with feedback from users.
  3. Identify Plant Phenology Ontology terms to be used as a standardized vocabulary for the extension/standards.
  4. Pilot implementation of the extension/standards using the CCH2 data portal and another non-Symbiota data publisher.
  5. (If extension) Serve the extension from GBIF’s registry of extensions.
  6. Advocate for the use of standardized phenological vocabulary and the new phenology standards.

The Task Group will communicate and document its work primarily online and conduct online meetings. Collaborative progress will be made using Google Drive and Google Docs. Ultimately, the Task Group will submit its proposals to TDWG’s journal BISS and follow the TDWG Vocabulary Maintenance Standard to get these proposals adopted.

History/Context

In 2018, core members Stucky, Guralnick, and Walls (among others) developed a draft Plant Phenology Ontology to scale-up integration of plant phenological data among disparate data sources. Brenskelle et al. (2019) extended the Plant Phenology Ontology to integrate herbarium specimen-based phenological data. Concurrently, convener Yost, core members Gilbert and Pearson, and others developed a phenological scoring schema (Yost et al. 2018, APPS) and phenological attribute scoring tool in the Consortium of California Herbaria Symbiota portal, the CCH2. The phenological data from this schema and tool are currently exported as a DwC measurementOrFact file, which is neither intuitive for users nor easily accessible through global aggregators.

Summary

Phenological data are increasingly being used to examine the effects of climate change and other drivers of biological change, and biodiversity specimens have arisen as an important source of phenological data. However, phenological data have not been captured in standardized fields or using a standardized vocabulary, making the data difficult to access, aggregate, and analyze at scale across data sources. The Specimen Phenology Task Group is developing a phenology extension for the Darwin Core. We will create fields into which phenological data can be entered and recommend a standardized vocabulary from the Plant Phenology Ontology for use in these fields. This task group is focused first on phenological data associated with flowering plants, but the standards will be developed such that phenological data associated with gymnosperms and nonvascular non-plant and other taxonomic plant groups can be addressed in the future.

Get Involved

Email conveners Jenn Yost and Katie Pearson to participate, contribute, and/or join our listserv. To contribute or comment on our developing standards, visit and "Watch" our GitHub repository.

Resources

  • Plant phenology ontology - http://www.obofoundry.org/ontology/ppo.html
  • Yost et al. 2018. APPS - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5851559/
  • Brenskelle et al. 2019 - https://pubmed.ncbi.nlm.nih.gov/30937223/