The Plant Phenology Ontology (PPO) is a collection of
OBO Foundryontologies that facilitate integration of heterogeneous data about
seed plantphenology from various sources.[1] These data sources include observations networks, such as the
National Ecological Observatory Network[2] (NEON), the
National Phenology Network[3] (NPN), and the
Pan-European Phenology Database[4] (PEP725),
remote sensing,
herbarium specimens, and
citizen science observations. The initial focus during ontology development was to capture phenological data about one plant or a population of plants as observed by a person, and this enabled integration of data across disparate observation network sources.[1] Because phenological scorings vary in their methods and reporting, this allows these data to be aggregated and compared. Changes in plant phenology can be linked to different climate factors depending on the species, such
precipitation or
growing degree days.[5] Aggregated data about the timing of plant life cycle stages at different places and times can provide information about
spatiotemporal patterns within and among species, and potentially offer insight into how plants may change or shift their life cycles in response to
climate change.[6] These shifts can have implications for
agriculture and various
biodiversity research avenues, such as shifts in
pollinator and host life cycles.[7][8][9]
General structure
The structure of the Plant Phenology Ontology relies on integrated terms from other ontologies, notably the
Basic Formal Ontology,[10] the
Plant Ontology,[11] the
Information Artifact Ontology,[12] and the
Biological Collections Ontology.[13] The basic structure of the PPO models the 'observing process' (BCO:0000003), which has an input of a 'whole plant' (PO:0000003) and an output of a 'measurement datum' (IAO:0000109). The value of the 'measurement datum' is determined by what was observed or not observed on the plant. Measurement data in the PPO are numbers of upper counts and lower counts for some 'plant structure' (PO:0009011) on the observed plant. When the upper and lower counts both equal zero, an absence is inferred for that trait by the ontology using the
HermiT reasoner.[1][14] Plant Ontology
anatomy terms were used to enable the ontology to infer the presence or absence of hierarchical phenological traits using the reasoner. For example, if
pollen-releasing
flower heads are observed to be present (PPO:0002340) with an upper count of five and lower count of five (meaning there are exactly five pollen-releasing flower heads on the observed plant), the reasoned ontology can also infer that
floral structures are present (PPO:0002026) on the plant.[1]
Recent developments
Because most observation networks were only established in the early 2000s,[4][15][16] they contain a wealth of plant phenological data for the 21st century, but do not offer insight into historical baselines. Herbarium specimens inherently capture the phenological traits of a plant in a specific location at a specific time.[17][18][19] Because some herbarium collections date back to the 17th century,[20] herbarium specimens represent an enormous amount of historical phenology data. These data would enable researchers to address new questions about how much the current
climate has shifted from historical baselines.
Efforts have been made to expand the scope of the ontology to include observations made on herbarium specimens.[17] Because the backbone of the existing PPO is built around the concept of whole plants, new logic had to be added to enable reasoning over data from parts of plants, because this is usually, though not always, what is captured by an herbarium specimen. The concept of 'portion of a plant' was added to the ontology, and a new relationship 'is or was part of' was added to describe how a 'portion of a plant' relates to a 'whole plant'.[17] The
new PPO release allows integration of phenology data from herbarium specimens, provided that observations or phenological scorings for the specimens already exist.
Global Plant Phenology Data Portal
The
Global Plant Phenology Data Portal is an
interface that allows users to see data that have been ingested by the PPO.[1][17] It provides a way for those unfamiliar with the ontology to search for and download plant phenology data of interest. It has also served as a
proof of concept during ontology development, and as a means of checking these data.
^
abTempl, Barbara; Koch, Elisabeth; Bolmgren, Kjell; Ungersböck, Markus; Paul, Anita; Scheifinger, Helfried; Rutishauser, This; Busto, Montserrat; Chmielewski, Frank-M. (2018). "Pan European Phenological database (PEP725): a single point of access for European data". International Journal of Biometeorology. 62 (6): 1109–1113.
Bibcode:
2018IJBm...62.1109T.
doi:
10.1007/s00484-018-1512-8.
ISSN1432-1254.
PMID29455297.
S2CID3379514.
^Chuine, Isabelle; de Cortazar-Atauri, Iñaki Garcia; Kramer, Koen; Hänninen, Heikki (2013), Schwartz, Mark D. (ed.), "Plant Development Models", Phenology: An Integrative Environmental Science, Springer Netherlands, pp. 275–293,
doi:
10.1007/978-94-007-6925-0_15,
ISBN9789400769250
^Cleland, E; Chuine, I; Menzel, A; Mooney, H; Schwartz, M (2007). "Shifting plant phenology in response to global change". Trends in Ecology & Evolution. 22 (7): 357–365.
doi:
10.1016/j.tree.2007.04.003.
PMID17478009.
^Memmott, Jane; Craze, Paul G.; Waser, Nickolas M.; Price, Mary V. (2007). "Global warming and the disruption of plant–pollinator interactions". Ecology Letters. 10 (8): 710–717.
doi:
10.1111/j.1461-0248.2007.01061.x.
ISSN1461-0248.
PMID17594426.
^Ceusters, Werner (2012). "IOS Press Ebooks - An Information Artifact Ontology Perspective on Data Collections and Associated Representational Artifacts". Studies in Health Technology and Informatics. 180 (Quality of Life through Quality of Information).
doi:
10.3233/978-1-61499-101-4-68.