Plant Ontology and Cross-Species
How the PO defines developmental
stage terms to be used across all
green plant species
This is a sub-set of a talk originally presented at the Phenotype RCN monthly community call.
Laurel D. Cooper, Justin Elser, Justin Preece, and Pankaj Jaiswal: Department of Botany
and Plant Pathology, Oregon State University, Corvallis, OR
Ramona L. Walls* and Dennis W. Stevenson: The New York Botanical Garden, Bronx, NY
*current address: firstname.lastname@example.org
Maria Alejandra Gandolfo: Department of Plant Biology, Cornell University, Ithaca, NY
Chris Mungall: Gene Ontology, Lawrence Berkeley National Lab, Berkeley, CA
Barry Smith: OBO Foundry, Department of Philosophy, University at Buffalo, NY
Plus many others over the years!
The Plant Ontology is:
• A structured, controlled vocabulary (ontology)
for plant anatomy, morphology, and
• A resource for data annotators
• A database of associations between PO terms
and genes, gene models, proteins, RNAs,
germplasms, and QTLs
• A web portal: http://plantontology.org/
Green plant diversity
Bowman et al.
Two main branches of the PO
• plant anatomical entity (PO:0025131): An anatomical
entity that is or was part of a plant.
– CARO:0000000 (anatomical entity) is defined as: Biological
entity that is either an individual member of a biological
species or constitutes the structural organization of an
individual member of a biological species.
• plant structure development stage (PO:0009012): A
stage in the life of a plant structure (PO:0009011)
during which the plant structure undergoes
– Refers to GO:0032502 (developmental process), including
growth, differentiation, and senescence.