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The Plant Ontology A Resource for Plant Genomics

The Plant Ontology A Resource for Plant Genomics. Laurel Cooper Department of Botany and Plant Pathology Oregon State University, Corvallis, OR. www.plantontology.org. The Plant Ontology - A Collaborative Effort. Cell Ontology. Ontologies for Plant Sciences:. Gene Ontology.

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The Plant Ontology A Resource for Plant Genomics

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

  2. The Plant Ontology- A Collaborative Effort Cell Ontology

  3. Ontologies for Plant Sciences: Gene Ontology Plant Ontology Plant Trait Ontology Chemical Entities of Biological Interest Phenotypic QualityOntology http://bioportal.bioontology.org/ http://www.obofoundry.org/

  4. The Plant Ontology is… …a controlled vocabulary • two aspects • terms cover the plant domain • Each term has: • primary name and synonyms • unique PO ID and url • definition vetted by experts, with community feedback

  5. Organization of Plant Anatomy Branch is_a • Relations in the PO: • is_a andpart_ofare the backbone of all anatomical ontologies • has_part allows the PO to describe structural variation among taxa is_a New terms to describe multi-tissue plant structures released July 2012

  6. 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

  7. Nine types of Relations in the PO:

  8. The Plant Ontology is… …a database resource for plant science • 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 microdissectionand 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)

  10. PO annotations of source tissue and growth stages ~1.5 million associations between Plant Ontology terms and ~35,000 Zea mays gene models from the sequencing of the Maize genome (Oct 2011) Sekhon et al. (2011) Plant J 66:552-563

  11. Browse and Search for Annotations on PO Database

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

  13. MaizeCyc Metabolic Pathway Analysis using PO Annotations Embryo [E] Endosperm [D] Embryo Endosperm Primary Root Anther Leaf PO:0009009 PO:0009089 D 14 E12 ED2 3 AED 12 AE EDR 1 AEDR 2 DR 2 AER1 Leaf [L] DLR 2 3 ER 6 EDLR DL 10 AELR 17 5 ELR PO:0009025 26 AEDLR 2 EDL 15LR L40 18ALR EL11 9AEDL (# of pathways) A = anther (159) E = embryo (122) D = endosperm (106) L = leaf (199) R = root (145) 13 ADLR AEL10 ADL9 AL 4 ADR2 R 23 9AR AD1 -500 0 500 Primary Root [R] Anther [A] Sekhon et al. (2011) Plant J 66:552-563 PO:0020127 A 22 PO:0009066 Source: MaizeCyc project

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

  15. 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

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

  17. Request terms by keyword: …and use the real-time results† in your application PO Web Services Plant Ontology terms, synonyms, and definitions are now available via RESTful* web services Detailed documentation for application developers is available on the PO web site * REST: Representational State Transfer (an architecture for web-based data communication)† Web service results are encoded in JSON, a lightweight data-interchange format

  18. 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

  19. 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

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