The Plant Ontology A Resource for Plant Genomics

The Plant OntologyA Resource for Plant Genomics

www.plantontology.org

Laurel CooperDepartment of Botany and Plant PathologyOregon State University, Corvallis, OR

The Plant Ontology- A Collaborative Effort

Cell Ontology

Ontologies for Plant Sciences:

Plant Ontology

Plant Trait Ontology

Gene Ontology

Phenotypic Quality Ontology

http://www.obofoundry.org/ http://bioportal.bioontology.org/

Chemical Entities of Biological Interest

…a controlled vocabularyThe Plant Ontology is…

Each term has:

• primary name and synonyms

• unique PO ID and url

• definition vetted by experts, with community feedback

• two aspects

• terms cover the plant domain

is_a

is_a

Organization of Plant Anatomy Branch

Relations in the PO:

• is_a and part_of are the backbone of all anatomical ontologies

• has_part allows the PO to describe structural variation among taxa

New terms to describe multi-tissue plant structures released July 2012

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 across taxa

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

Asteraceae Poaceae

Nine types of Relations in the PO:

…a database resource for plant scienceThe Plant Ontology is…

Links to associations from:

• gene expression experiments

• EST and QTL datasets

• mutant phenotype screens

Release #19, Dec. 2012~2.26 million associations for 1509 PO terms covering 23 species

Collaborative development of the PO: descriptors and annotations

Recent Examples: • Oryza sativa, Japonica group -  Added ~74,000 associations based a study

involving 33 laser microdissection and 143 spatiotemporal microarrays (Aya et al, 2011. PLoS ONE 6: e261) 

• Vitis vinifera:  Added ~ 3,400 associations to PO terms based Grapevine Expression Atlas microarray (Fasoli, et al 2012, The Plant Cell Online. doi: 10.1105/tpc.112.100230)

• ~80 new anatomy terms for the Physcomitrella- Moss Computational Biology Resource and added ~ 82,000 new annotations to Moss genomics data (Jan 2012)

• Addition of 1.5 million associations between Zea mays (maize) gene models and Plant Ontology terms (October 2011)

PO annotations of source tissue and growth stages

11Sekhon et al. (2011) Plant J 66:552-563

~1.5 million associations between Plant Ontology terms and ~35,000 Zea mays gene models from the sequencing of the Maize genome (Oct 2011)

12

Browse and Search for Annotations on PO Database

View Annotations in PO (Gene products)

Click to view the annotation details

Embr

yo

Endo

sper

m

Prim

ary

Root

Anth

er

Leaf

MaizeCyc Metabolic Pathway Analysis using PO Annotations-500 0 500

Primary Root [R]A 22

L 40

R 23

E12D 14

DR 2

DL 10DLR 2

EL11

2 EDL

AEL 10AL 4

6 EDLR

EDR 1

ED 23 AED

12 AEAEDR 2

26 AEDLR

9 AEDL

ADL 9

AD 1ADR 2 9 AR

18 ALR

15 LR

AELR 17

13 ADLR

AER 1

5 ELR3 ERLeaf [L]

Anther [A]

Embryo [E]Endosperm [D]

(# of pathways)A = anther (159)E = embryo (122)D = endosperm (106)L = leaf (199)R = root (145)

PO:0009066

PO:0009025

PO:0020127

PO:0009009PO:0009089

Source: MaizeCyc projectSekhon et al. (2011) Plant J 66:552-563

The PO as a teaching tool: Images

Tree View

The Plant Cell branch of the PO- an example of inter-ontology cooperation

• PO encompasses whole plant cells and references the GO definition of cell

• Plant cell components are described by the GO cellular component ontology

• Formerly duplicated by the Cell Type Ontology, but those have been obsoleted with a redirection to see the PO terms

Example- Leaf Anatomy- cell types

http://en.wikipedia.org/wiki/File:Leaf_anatomy.svg

PO Web ServicesPlant Ontology terms, synonyms, and definitions are now available via RESTful* web services

* REST: Representational State Transfer (an architecture for web-based data communication)† Web service results are encoded in JSON, a lightweight data-interchange format

Detailed documentation for application developers is available on the PO web site

…and use the real-time results† in your applicationRequest terms by keyword:

Desktop Application for Annotation of Image Segments using Ontologies (AISO)

Sections of the images are annotated with PO terms:• anther• petal• sepalLinks out to PO database and annotations

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

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

Ramona L. Walls- former curator, now at iPlant