The Plant Ontology:
An Updated Tool for all Plant Biologists
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 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
www.plantontology.org
Topics for today’s talk
1.  Overview of the Plant Ontology
2.  Recent changes to the PO: new organization, terms
and relations
3.  Demonstration: PO website, accessing ontology files
and association data
4.  Future directions
The Plant Ontology is…
…a controlled vocabulary
•  terms cover
the plant domain
Each term has a:
•  primary name and
synonyms
•  unique ID/url
•  definition vetted by
experts, with
community feedback
The Plant Ontology is…
…a structured vocabulary
cardinal
organ part
plant organ
•  relations
among terms
allow for
reasoning
midvein
PO:0020139
is_a
is_a
vascular leaf
leaf lamina
PO:0020039
part_of
petiole
leaf lamina
midvein
petiole
PO:0020038
The Plant Ontology is…
…a database resource for plant science
Links to associations
from:
•  gene expression
experiments
•  EST and QTL datasets
•  mutant phenotype
screens
Part 2. Recent changes to the PO
l 
Expanded scope
l 
Top-level re-organization
l 
New terms and relations
The PO now covers all green plants:
• angiosperms
• gymnosperms
• pteridophytes
• bryophytes
• green algae
Complete genome sequences
for 25 plant species from JGI
Top level re-organization provides
categories for all anatomical entities:
plant anatomical entity
portion of plant substance
plant cell
plant structure
plant organ
H
portion of
plant tissue
P
collective plant
structure
cardinal organ
part
H
collective organ
part structure
P
is_a
part_of
H
has_part
plant anatomical space
whole plant
vascular
system
rhizoid
ovary
trichome
in vitro plant
structure
embryo plant
structure
Specific changes to accommodate
non-angiosperm plants:
>80 new terms for bryophytes
and pteridophytes:
•  thallus
•  gametophore
•  calyptra
•  seta
•  etc.
New subsets for:
•  angiosperms
•  gymnosperms
•  pteridophytes
•  bryophytes
New whole plant
growth stages:
whole plant
growth stage
sporophyte
phase
gametophyte
phase
protonema
phase
P
P
is_a
part_of
New relations in the PO allow more
accurate expression of biology
•  is_a and part_of
are the backbone
of all anatomical
ontologies
shoot
system
•  has_part allows
the PO to handle
structural variation
among taxa
is_a
reproductive
shoot system
is_a
flower
is_a
•  develops_from
describes shared
developmental
pathways across
all taxa
has_part
inflorescence
develops
_from
infructescence
part_of
perianth
part_of
gynoecium
Part 3. Demonstration
How to:
l 
Navigate the PO website
l 
Access annotations
l 
Download the ontology files
l 
Provide feedback and request new terms
Browse or search the PO web site for
ontology terms or annotations
Use the Search/
browse link
Or do a quick
search from the
home page
Term detail view
To view the term lineage in a graphical
format click on the Graphical View link
Graphical view
Layout can be changed to horizontal
or colors can be changed
View the annotations associated with a term:
Clicking “view annotations”
takes you to the annotations
associated with a terms
Searching for annotations
Searching annotations for
“actin” returns 236 results
Filtering results by “P. patens”
returns 1 result
Downloading annotations
Annotations for individual
terms can be downloaded
as RDF-XML files
Downloading annotation files
through SVN repository
http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/associations/
Downloading the Ontology File
http://palea.cgrb.oregonstate.edu/viewsvn/Poc/tags/live/plant_ontology.obo?view=co
Requesting new term or commenting
on an existing term
Click “Request
PO terms”
Sending feedback
Part 4. Future directions for
the Plant Ontology and
l 
Links to images
l 
Phenotype descriptions for phenomics
and systematics
l 
Web services
Links to images
Plant organs
Plant tissues and cells
Phenotype descriptions using
ontologies
•  for taxonomic descriptions
•  for phenomic applications (crop trails, mutant screening)
PO Web Services
The Plant Ontology is working to make term data
available – via the web, in real-time – to external
software developers for use in their own applications.
Planned services include:
Term Search
Useful for autocomplete features
Term Details
Accession ID's, definitions, and comments
PO Data
Your Application
Acknowledgements:
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