Plant Phenology Ontology

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The Plant Phenology Ontology (PPO) is a collection of OBO Foundry ontologies that facilitate integration of heterogeneous data about seed plant phenology 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[edit]

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[edit]

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[edit]

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.

References[edit]

  1. ^ a b c d e Stucky, Brian J.; Guralnick, Rob; Deck, John; Denny, Ellen G.; Bolmgren, Kjell; Walls, Ramona (2018-05-01). "The Plant Phenology Ontology: A New Informatics Resource for Large-Scale Integration of Plant Phenology Data". Frontiers in Plant Science. 9: 517. Bibcode:2018EGUGA..2017614S. doi:10.3389/fpls.2018.00517. ISSN 1664-462X. PMC 5938398. PMID 29765382.
  2. ^ Keller, Michael; Schimel, David S.; Hargrove, William W.; Hoffman, Forrest M. (2008). "A continental strategy for the National Ecological Observatory Network". Frontiers in Ecology and the Environment. 6 (5): 282–284. doi:10.1890/1540-9295(2008)6[282:ACSFTN]2.0.CO;2. ISSN 1540-9309.
  3. ^ Betancourt, Julio L.; Schwartz, Mark D.; Breshears, David D.; Cayan, Daniel R.; Dettinger, Michael D.; Inouye, David W.; Post, Eric; Reed, Bradley C. (2005). "Implementing a U.S. National Phenology Network". Eos, Transactions American Geophysical Union. 86 (51): 539. Bibcode:2005EOSTr..86..539B. doi:10.1029/2005EO510005. ISSN 2324-9250.
  4. ^ a b Templ, 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. ISSN 1432-1254. PMID 29455297. S2CID 3379514.
  5. ^ 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, ISBN 9789400769250
  6. ^ 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. PMID 17478009.
  7. ^ Winfree, Rachael; Kornbluth, Sarah; Colla, Sheila; Danforth, Bryan N.; Wagner, David; Ascher, John S.; Bartomeus, Ignasi (2011-12-20). "Climate-associated phenological advances in bee pollinators and bee-pollinated plants". Proceedings of the National Academy of Sciences. 108 (51): 20645–20649. Bibcode:2011PNAS..10820645B. doi:10.1073/pnas.1115559108. ISSN 0027-8424. PMC 3251156. PMID 22143794.
  8. ^ Burkle, L. A.; Marlin, J. C.; Knight, T. M. (2013-03-29). "Plant-Pollinator Interactions over 120 Years: Loss of Species, Co-Occurrence, and Function". Science. 339 (6127): 1611–1615. Bibcode:2013Sci...339.1611B. doi:10.1126/science.1232728. ISSN 0036-8075. PMID 23449999. S2CID 14660808.
  9. ^ 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. ISSN 1461-0248. PMID 17594426.
  10. ^ Arp, Robert; Smith, Barry; Spear, Andrew D. (2015-08-24). Building Ontologies With Basic Formal Ontology. The MIT Press. doi:10.7551/mitpress/9780262527811.001.0001. ISBN 9780262527811.
  11. ^ Walls, Ramona L.; Athreya, Balaji; Cooper, Laurel; Elser, Justin; Gandolfo, Maria A.; Jaiswal, Pankaj; Mungall, Christopher J.; Preece, Justin; Rensing, Stefan (2012). "Ontologies as integrative tools for plant science". American Journal of Botany. 99 (8): 1263–1275. doi:10.3732/ajb.1200222. ISSN 1537-2197. PMC 3492881. PMID 22847540.
  12. ^ 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.
  13. ^ Wooley, John; Whitacre, Jamie; Wieczorek, John; Thomer, Andrea; Stucky, Brian J.; Smith, Barry; Schildhauer, Mark; Tuama, Éamonn Ó; Morrison, Norman (2014-03-03). "Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies". PLOS ONE. 9 (3): e89606. Bibcode:2014PLoSO...989606W. doi:10.1371/journal.pone.0089606. ISSN 1932-6203. PMC 3940615. PMID 24595056.
  14. ^ Glimm, Birte; Horrocks, Ian; Motik, Boris; Stoilos, Giorgos; Wang, Zhe (2014-10-01). "HermiT: An OWL 2 Reasoner". Journal of Automated Reasoning. 53 (3): 245–269. doi:10.1007/s10817-014-9305-1. hdl:10072/66648. ISSN 1573-0670. S2CID 15513227.
  15. ^ "Our History | USA National Phenology Network". www.usanpn.org. Retrieved 2019-02-09.
  16. ^ "History | NSF NEON | Open Data to Understand our Ecosystems". www.neonscience.org. Retrieved 2019-02-09.
  17. ^ a b c d Brenskelle, Laura; Stucky, Brian; Deck, John; Walls, Ramona; Guralnick, Robert (2019). "Integrating herbarium specimen observations into global phenology data systems". Applications in Plant Sciences. 7 (3): e01231. doi:10.1002/aps3.1231. PMC 6426164. PMID 30937223.
  18. ^ Jones, Casey A.; Daehler, Curtis C. (2018-04-03). "Herbarium specimens can reveal impacts of climate change on plant phenology; a review of methods and applications". PeerJ. 6: e4576. doi:10.7717/peerj.4576. ISSN 2167-8359. PMC 5888139. PMID 29632745.
  19. ^ Yost, Jennifer M.; Sweeney, Patrick W.; Gilbert, Ed; Nelson, Gil; Guralnick, Robert; Gallinat, Amanda S.; Ellwood, Elizabeth R.; Rossington, Natalie; Willis, Charles G. (2018). "Digitization protocol for scoring reproductive phenology from herbarium specimens of seed plants". Applications in Plant Sciences. 6 (2): e1022. doi:10.1002/aps3.1022. ISSN 2168-0450. PMC 5851559. PMID 29732253.
  20. ^ Müller-Wille, Staffan (2006-06-01). "Linnaeus' herbarium cabinet: a piece of furniture and its function". Endeavour. 30 (2): 60–64. doi:10.1016/j.endeavour.2006.03.001. ISSN 0160-9327. PMID 16600379.

External links[edit]

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