1. The Plant Ontology: Development of a Reference Ontology for all Plants www.plantontology.org 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

2. Challenges in expanding the Plant Ontology to covers 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

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

4. Plant Ontology Two branches: Plant Anatomical Entity and Growth and Development Every term has definition Every term has is_a relationship as mandated to have single inheritance (some terms may have dual parentage for enriched biological reasoning) Use multiple relationship types is_a, part_of, has_part, adjacent_to, develops_from, derived_from, participates_in

5. plant structure organtissuewhole plantplant cellin vitro cultured cell, tissue and organsporophytegametophyte is_a part_of has_part plant anatomical entity plant anatomical spaceplant structureportion of plant substance plant organportion of plant tissue whole plant plant cellcardinal organ part collective plant structurecollective organ part structure vascular system trichome ovary embryonic plant structurein vitro plant structure Top level re-organization of the Plant Anatomy Ontology: Version 15, May 2011 Was: New: Release# 0409 (12) - April 2009 New or renamed top-level terms provide is_a parents for terms from all taxa Extensive revision of the second and third level child terms (not shown)

6. 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 embryonic plant structure in vitro plant structure rhizoid H H P vascular system ovary

7. Vision for Plant Ontology: Encompass all plants Facilitate consistency in: Annotation of comparative genomics data Cross-database queries Develop PO as a reference ontology for plants: Provide mappings to other ontologies in use by plant databases Create cross-products to other ontologies such as PATO to describe phenotypic characters

8. 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:

9. Tools: Developing the ontology using OBO-Edit Ontology is displayed on our website using AmiGO OWL version of the ontology Protégé Semantic web via SSWAP (Simple Semantic Web Architecture and Protocol ) Phenote annotation tool being developed for use by plant scientists

10. Challenges and/or Roadblocks Need to expand development of tools to link to other ontologies, e.g. GO, CL Shortage of plant-specific phenotypic descriptors in PATO Other species-specific vocabularies should use cross references to PO terms Working with new sources of annotations to expand genomics coverage of PO; e.g. Physcomitrella

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