The Plant Ontology: Development of a Reference

Ontology for all Plants

www.plantontology.org

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

Maria A. 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

Challenges in expanding the Plant Ontology to covers all plants:

Diversity in anatomy, morphology, life cycles, growth patterns

Seed plants(Angiosperms and

Gymnosperms)

Pteridophytes(Ferns and Lycopods)

Bryophytes(Mosses, Hornworts and

Liverworts)

Algae

Bowman et al, Cell, 2007

Phylogenetic diversity can result in inconsistency in nomenclature:

Instances of leaf: (PO:0025034)

maple leaf palm frond pine needle

Different names are used for the same structure

The PO provides consistent terminology for annotation of plant structures and growth and developmental stages.

Different structures can have the same name e.g. ‘floret’

Asteraceae Poaceae

Plant Ontology

• Two branches: Plant Anatomical Entity and Growth and Development• Every term has definition• Every term has is_a relationship as mandated to have single inheritance (some

terms may have dual parentage for enriched biological reasoning)• Use multiple relationship types

• is_a, part_of, has_part, adjacent_to, develops_from, derived_from, participates_in

plant structure

organ

tissue

whole plant

plant cell

in vitro cultured cell, tissue and organ

sporophyte

gametophyte

is_a

part_of

has_part

plant anatomical entity

plant anatomical space

plant structure

portion of plant substance

plant organ

portion of plant tissue

whole plant

plant cell

cardinal organ part

collective plant structure

collective organ part structure

vascular system

trichome

ovary

embryonic plant structure

in vitro plant structure

Top level re-organization of the Plant Anatomy Ontology:

Version 15, May 2011

Was:

New:

Release# 0409 (12) - April 2009

• New or renamed top-level terms provide is_a parents for terms from all taxa• Extensive revision of the second and third level child terms (not shown)

Top level of PAO from CARO

is_apart_ofhas_partH

P

plant anatomical entity

plant anatomical spaceplant structureportion of plant substance

plant organ portion of plant tissue

whole plantplant cell

cardinal organ part

collective plant structure

collective organ part structure

trichome embryonic plant structure

in vitro plant structure

rhizoid

H

H

P

vascular system

ovary

Vision for Plant Ontology:• Encompass all plants• Facilitate consistency in:

• Annotation of comparative genomics data• Cross-database queries

• Develop PO as a reference ontology for plants:• Provide mappings to other ontologies in use by plant

databases• Create cross-products to other ontologies such as PATO to

describe phenotypic characters

The Plant Ontology facilitates comparative plant genomics

>500,000 associations for >1300 termsMEE58?AtMEE58

AtMEE58

hydroidxylem element

I I

plant cell

axial cell

fusiform initial

MEE58?

MEE58?D

I

AtMEE58

I

Cross-taxa comparisons:

Tools:• Developing the ontology using OBO-Edit• Ontology is displayed on our website using AmiGO• OWL version of the ontology

• Protégé• Semantic web via SSWAP (Simple Semantic Web

Architecture and Protocol )• Phenote annotation tool being developed for use by

plant scientists

Challenges and/or Roadblocks• Need to expand development of tools to link to other

ontologies, e.g. GO, CL• Shortage of plant-specific phenotypic descriptors in PATO• Other species-specific vocabularies should use cross

references to PO terms• Working with new sources of annotations to expand

genomics coverage of PO; e.g. Physcomitrella

Participants and Collaborators:

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