1. The Plant Ontology A Resource for Plant Genomics www.plantontology.org Laurel Cooper Department of Botany and Plant Pathology Oregon State University, Corvallis, OR

2. The Plant Ontology - A Collaborative Effort Cell Ontology

3. 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

4. …a controlled vocabulary The 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

5. 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

6. 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

7. Nine types of Relations in the PO:

8. …a database resource for plant science The 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

9. 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)

11. PO annotations of source tissue and growth stages 11 Sekhon 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 12

13. View Annotations in PO (Gene products) Click to view the annotation details

14. Embryo Endosperm Primary Root Anther Leaf MaizeCyc Metabolic Pathway Analysis using PO Annotations -500 0 500 Primary Root [R] A 22 L 40 R 23 E 12 D 14 DR 2 DL 10 DLR 2 EL 11 2 EDL AEL 10 AL 4 6 EDLR EDR 1 ED 2 3 AED 12 AE AEDR 2 26 AEDLR 9 AEDL ADL 9 AD 1 ADR 2 9 AR 18 ALR 15 LR AELR 17 13 ADLR AER 1 5 ELR 3 ER Leaf [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:0009009 PO:0009089 Source: MaizeCyc project Sekhon et al. (2011) Plant J 66:552-563

15. The PO as a teaching tool: Images Tree View

16. 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

17. Example- Leaf Anatomy- cell types http://en.wikipedia.org/wiki/File:Leaf_anatomy.svg

18. PO Web Services Plant 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 application Request terms by keyword:

19. Desktop Application for Annotation of Image Segments using Ontologies (AISO) Sections of the images are annotated with PO terms: anther petal sepal Links out to PO database and annotations

20. 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, CA Barry Smith : OBO Foundry, Department of Philosophy, University at Buffalo, NY Ramona L. Walls- former curator, now at iPlant