The Plant Ontology: Development of a Reference Ontology for all Plants

1. The Plant Ontology: Development of a Reference Ontology for all Plants 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, CA Barry Smith: OBO Foundry, Department of Philosophy, University at Buffalo, NY www.plantontology.org

2. Vision and Goals of the Plant Ontology: • Develop PO as a reference ontology for plants: • -describeanatomy and development ofallplants • Conform to OBO Foundry Principles of openness, collaborative development and interoperability, etc * • Facilitate annotation of comparative plant genomics data • Interact with other ontologies such as GO, TO, CARO, PATO, etc

3. Challenges in expanding the Plant Ontology to cover 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

4. Phylogenetic diversity can result in inconsistency in nomenclature: Different names are used for the same structure Different structures can have the same name e.g. ‘floret’ Instances of leaf: (PO:0025034) maple leaf pine needle palm frond Asteraceae Poaceae The PO provides consistent terminology for annotation of plant structures and growth and developmental stages across taxa

5. Recent changes to the PO: Two branches or subdomains of the PO are now merged: Plant Anatomy Ontology (PAO) PlantGrowth and Development Stage Ontology (PGDSO)

6. Top level of PAO from CARO plant anatomical entity portion of plant substance plant structure plant anatomical space portion of plant tissue vascular system plant cell plant organ whole plant P H rhizoid collective plant structure cardinal organ part in vitro plant structure ovary collective organ part structure embryo plant structure trichome H is_a part_of has_part P H

7. Relations in the PO allow for an accurate expression of biology has_part allows the PO to handle structural variation among taxa is_a andpart_ofare the backbone of all anatomical ontologies shoot system is_a is_a reproductive shoot system develops_from describes shared developmental pathways across all taxa flower is_a has_part inflorescence part_of develops_from part_of perianth infructescence gynoecium

8. The participates_in relation links an anatomical entity to a plant growth or development stage whole plant growth stage plant structure Example: A sporangium is_aplant organ that produces spores which participates_inasporophyte phase plant organ sporophyte phase participates_in sporangium Describes plant structures that only occur during a specific growth and development stages is_a

9. Ontology structure covers plant domain through general and specific terms General terms for all plants, or homosporous plants Specialized child terms for heterosporous plants, like angiosperms

10. How the PO meets the OBO Foundry criteria: • Opennes- web browser, SVN, wiki • Common shared syntax- OBO and OWL • Unique identifier space: PO:xxxxxxx • Versioning system; #15, May 2011; etc • Orthogonality –yes, improving; e.g. PO-Cell Ontology • Textual definitions- complete

11. OBO Foundry criteria, Cont. • Relations from the OBO Relation Ontology- yes • Documentation- on web and publications • Term request tracker on SourceForge- well utilized • Collaborative Development-recent examples • Plurality of user base – wide adoption, outreach

12. Documentation- on web and publications *Cooper and Walls, et al. The Plant Ontology: A Comparative Plant Sciences Tool for All Plant Taxa, (In preparation) *Ilic et al, 2008. Plant Structure Ontology (PSO) - A morphological and anatomical ontology of flowering plants. In Anatomy Ontologies for Bioinformatics, Springer, 2008, p 27-42. * Avraham et al, 2008. The Plant Ontology Database: a community resource for plant structure and development stages controlled vocabulary and annotations.Nucleic Acid Research, 36(Database issue):D449-D454 * Ilic et al, 2007. The Plant Structure Ontology, a unified vocabulary of anatomy and morphology of a flowering plant.Plant Physiology, 2007, 143: 587-599 * Jaiswal et al, 2005. Plant Ontology (PO): a controlled vocabulary of plant structures and growth stages.Comparative and Functional Genomics, 2005, Volume 6(7-8), 388 - 397

13. Collaborative development ofthe PO: • Recent examples: • Addition of terms for Musa (bananas), Solanaceae (potatos,etc) • Added ~80 new terms in the recent release for the Physcomitrella (Moss)Genome Annotation group

14. Wide range of Users and Collaborators: Cell Ontology Your logo could be here too!

15. The Plant Ontology facilitates comparative plant genomics AtMEE58 Cross-taxa comparisons: I >500,000+ associations for >1300 terms MEE58? plant cell fusiform initial MEE58? AtMEE58 I I I xylem element hydroid axial cell MEE58? AtMEE58 D

16. Annotations allow for data analysis: Annotations may be created based on microarray, EST, QTL, protein, germplasm, phenotype or other data sets, or whole genome sequencing projects. Example microarray data set with PO and GO annotations: PO terms corresponding to synonyms used in the study: * inflorescence (PO:0009049) ** shoot axis (PO:0025029) *** whole plant in the seedling stage (PO:0000003) • Contact us if you are interested in providing and maintaining annotations files for your project Data Image From: Wang, et al. (2010). The Plant Journal, 61.

17. Tool Development: PO web services being developed for the Semantic web: Phenote annotation tool being developed for use by plant scientists

18. Future directions: • Need to expand development of tools to link to other ontologies, e.g. GO, CL • Shortage of plant-specific phenotypic descriptors in PATO • Expanding genomics coverage of PO; e.g. TAIR, SGN, Physcomitrella, MaizeGDB and ….? Thanks!