A quick overview of the plant structure development stage branch of the Plant Ontology.

1. Plant Ontology and Cross-Species
Reasoning
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.

2. Plant Ontology
Consortium Members
and Curators
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: rwalls@iplantcollaborative.org
Maria Alejandra Gandolfo: Department of Plant Biology, Cornell University, Ithaca, NY
Ontology Consultants:
Chris Mungall: Gene Ontology, Lawrence Berkeley National Lab, Berkeley, CA
Barry Smith: OBO Foundry, Department of Philosophy, University at Buffalo, NY

3. Plus many others over the years!
http://plantontology.org

4. The Plant Ontology is:
• A structured, controlled vocabulary (ontology)
for plant anatomy, morphology, and
developmental stages
• 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/

5. Green plant diversity
Bowman et al.
(2007), Cell
129:229-234

6. 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
developmental processes.
– Refers to GO:0032502 (developmental process), including
growth, differentiation, and senescence.

7. Upper level plant structure development stages
mirror plant anatomical entity terms

8. Whole plant development stages
Gametophyte development stage also has subclasses for
vegetative, reproductive, dormant, and senescent stages.

9. Development stage boundaries based
on processes

10. Under development:
adding temporal relations
to order stages
= preceded_by

11. Making the PO work across all green plants:
General terms for any species, plus specific
subclasses where needed