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The Plant Ontology A Resource for Plant Genomics. Laurel Cooper Department of Botany and Plant Pathology Oregon State University, Corvallis, OR. www.plantontology.org. The Plant Ontology - A Collaborative Effort. Cell Ontology. Ontologies for Plant Sciences:. Gene Ontology. - PowerPoint PPT Presentation
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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