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.

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, ORRamona L. Walls* and Dennis W. Stevenson: The New York Botanical Garden, Bronx, NY*current address: rwalls@iplantcollaborative.orgMaria Alejandra Gandolfo: Department of Plant Biology, Cornell University, Ithaca, NY

Ontology Consultants:Chris Mungall: Gene Ontology, Lawrence Berkeley National Lab, Berkeley, CABarry Smith: OBO Foundry, Department of Philosophy, University at Buffalo, NY

Plus many others over the years!

http://plantontology.org

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/

Bowman et al. (2007), Cell 129:229-234

Green plant diversity

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.

Upper level plant structure development stages mirror plant anatomical entity terms

Whole plant development stages

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

Development stage boundaries based on processes

Under development: adding temporal relations to order stages

= preceded_by

Making the PO work across all green plants: General terms for any species, plus specific

subclasses where needed