Ontology Card

Domain	Agriculture
Category	Plant Anatomy, Morphology, Growth and Development
Current Version	None
Last Updated	None
Creator	None
License	Creative Commons 4.0
Format	owl
Download	Download Plant Ontology (PO)

Plant Ontology (PO)

The Plant Ontology (PO) is a structured vocabulary and ontology resource that links plant anatomy, morphology, growth, and development to plant genomics and phenomics data [1] [2]. Developed as a community resource, PO provides a framework for describing plant structures and developmental stages across plant species [1] [3]. The ontology integrates anatomical and developmental terms that can be associated with plant genes and phenotypes, enabling researchers to annotate data and support comparative genomics and comparative plant biology [2] [3]. PO is designed to facilitate data integration and interoperability in plant science research [1] [2]. With its hierarchical organization of plant structures and developmental stages, including whole plants, organs, tissues, and cell types, PO supports applications such as literature curation, genome annotation, and phenotypic data annotation [2]. The ontology is under active development and is integrated with the Planteome project and other biological ontologies to support semantic compatibility in the plant science community [1] [4].

Example Usage: Annotate a plant genomics or phenomics dataset with PO terms for plant structures and developmental stages, such as leaf, root, flower, seed, or senescent stage, to enable standardized annotation, cross-species comparison, and integration with plant science databases and analysis platforms [1] [2].

Metrics & Statistics

Graph

Graph Statistics

Total Nodes	20790
Total Edges	60638
Root Nodes	5936
Leaf Nodes	11639

Coverage

Knowledge Coverage Statistics

Classes	1874
Individuals	0
Properties	13

Hierarchy

Hierarchical Metrics

Maximum Depth	5
Minimum Depth	0
Average Depth	1.07
Depth Variance	0.72

Breadth

Breadth Metrics

Maximum Breadth	8034
Minimum Breadth	82
Average Breadth	3462.50
Breadth Variance	11752362.58

LLMs4OL

LLMs4OL Dataset Statistics

Term Types	0
Taxonomic Relations	2863
Non-taxonomic Relations	36
Average Terms per Type	0.00

Usage Example

Use the following code to import this ontology programmatically:

from ontolearner.ontology import PO

ontology = PO()
ontology.load("path/to/PO-ontology.owl")

# Extract datasets
data = ontology.extract()

# Access specific relations
term_types = data.term_typings
taxonomic_relations = data.type_taxonomies
non_taxonomic_relations = data.type_non_taxonomic_relations

References

[1] (1,2,3,4,5)

OBO Foundry. n.d. “Plant Ontology (PO).” Available at: https://obofoundry.org/ontology/po.html

[2] (1,2,3,4,5)

Cooper, L., Walls, R. L., Elser, J., Gandolfo, M. A., Stevenson, D. W., Smith, B., Preece, J., Athreya, B., Mungall, C. J., and Rensing, S. A. 2013. “The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses.” Plant and Cell Physiology 54(2): e1. doi:10.1093/pcp/pcs163 Available at: https://pmc.ncbi.nlm.nih.gov/articles/PMC3583023/

[3] (1,2)

Walls, R. L., Cooper, L., Elser, J., Gandolfo, M. A., Mungall, C. J., Smith, B., Stevenson, D. W., and Jaiswal, P. 2019. “The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species.” Frontiers in Plant Science 10:631. doi:10.3389/fpls.2019.00631 Available at: https://pmc.ncbi.nlm.nih.gov/articles/PMC6558174/

[4]

Cooper, L., Elser, J., Laporte, M.-A., Arnaud, E., and Jaiswal, P. 2024. “Planteome 2024 Update: Reference Ontologies and Knowledgebase for Plant Biology.” Nucleic Acids Research 52(D1): D1548-D1555. doi:10.1093/nar/gkad1028 Available at: https://pmc.ncbi.nlm.nih.gov/articles/PMC10767901/