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

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

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

Phylogenetic diversity can result in inconsistency in nomenclature: Instances of leaf: (PO: ) 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

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

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

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

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

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

How the PO meets the OBO Foundry criteria: 1.Opennes- web browser, SVN, wiki 2. Common shared syntax- OBO and OWL 3. Unique identifier space: PO:xxxxxxx 4.Versioning system; #15, May 2011; etc 5.Orthogonality –yes, improving; e.g. PO-Cell Ontology 6.Textual definitions- complete

OBO Foundry criteria, Cont. 7.Relations from the OBO Relation Ontology- yes 8.Documentation- on web and publications 9.Term request tracker on SourceForge- well utilized 10. Collaborative Development- recent examples 11. Plurality of user base – wide adoption, outreach

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, Plant Structure Ontology (PSO) - A morphological and anatomical ontology of flowering plants. In Anatomy Ontologies for Bioinformatics, Springer, 2008, p * Avraham et al, The Plant Ontology Database: a community resource for plant structure and development stages controlled vocabulary and annotations. Nucleic Acid Research, 36(Database issue):D449- D454Nucleic Acid Research * Ilic et al, The Plant Structure Ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiology, 2007, 143: Plant Physiology * Jaiswal et al, Plant Ontology (PO): a controlled vocabulary of plant structures and growth stages. Comparative and Functional Genomics, 2005, Volume 6(7-8), Comparative and Functional Genomics

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

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

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

Annotations allow for data analysis: Data Image From: Wang, et al. (2010). The Plant Journal, 61. 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: Contact us if you are interested in providing and maintaining annotations files for your project PO terms corresponding to synonyms used in the study: * inflorescence (PO: ) ** shoot axis (PO: ) *** whole plant in the seedling stage (PO: )

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

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!