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

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

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

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  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. 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: 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.

  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. Top level re-organization of the Plant Anatomy Ontology: plant anatomical entity plant structure portion of plant substance plant anatomical space Was: Release# 0409 (12) - April 2009 trichome embryonic plant structure in vitro plant structure ovary whole plant plant cell plant organ cardinal organ part portion of plant tissue vascular system collective plant structure collective organ part structure is_a part_of has_part New: plant structure Version 15, May 2011 whole plant plant cell tissue gametophyte sporophyte in vitro cultured cell, tissue and organ organ • 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 plant anatomical entity portion of plant substance plant structure plant anatomical space portion of plant tissue vascular system plant cell plant organ whole plant H P rhizoid collective plant structure cardinal organ part in vitro plant structure ovary H embryonic plant structure collective organ part structure trichome is_a part_of has_part P H

  7. Vision for Plant Ontology: • Encompassallplants • 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 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

  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

  11. Participants and Collaborators: Your logo could be here too!

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