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Plant Ontology Consortium plantontology

Plant Ontology Consortium www.plantontology.org. In this presentation:. Why develop “Plant Ontology (PO)”? What is PO? How is PO designed and structured? Annotations to PO Who is using PO? How to use PO in your research? How to request your PO term?. Why develop PO?.

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Plant Ontology Consortium plantontology

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  1. Plant Ontology Consortiumwww.plantontology.org

  2. In this presentation: • Why develop “Plant Ontology (PO)”? • What is PO? • How is PO designed and structured? • Annotations to PO • Who is using PO? • How to use PO in your research? • How to request your PO term?

  3. Why develop PO? • More and more plants genome are getting sequenced • More and more datatypes are involved • More and more databases are developed

  4. We need controlled vocabulary A set of defined terms to describe knowledge of a specific domain • Avoid ambiguity - conducting a search in a database that use controlled vocabulary is efficient and precise • User can make a meaningful cross-species query across databases

  5. They are all “Fruit”The seed-bearing structure in angiosperms, formed from the ovary after flowering Rice grain/caryopsis Maize kernel Berry Arabidopsis silique Peapod

  6. What is “ Plant Ontology “ ? • PO is an arrangement of controlled vocabularies - plant anatomical, morphological structures - plant growth and developmental stages • Based on internationally published/accepted terminology and their definitions • Recognized by computers • A tool for annotation of gene expression patterns and phenotypes of germplasms across angiosperms

  7. What is in a PO term?

  8. Rationale on creating a term to describe plant structure • Botanical terms - anatomy and morphology • Derivation - origin of plant parts and cell lineage; spatial/positional organization of tissues, organs and organ systems (mainly for annotation purpose) • Avoids subcellular structure (GO has it) • Avoids attributes (qualifiers) of anatomical terms • Use synonym fields to cover various instances, types and terms with attributes

  9. How is PO structured? (graphical view) Similar to GO, the PO is organized into a hierarchical network called the Directed Acyclic Graph (DAG)

  10. How is PO structured? (tree view via AmiGo)

  11. Use “Sensu”(in the sense of; restricted to) FLORET www.vplants.org

  12. True Path Rule The path from any node (term) all the way to the top node of the tree must be biologically correct. flower (generic) Solution: add floret as instance of flower and add an instance of a maize floret flower (generic) floret is_a lemma floret (sensu Poaceae) part_of is_a lemma part_of

  13. Annotation using PO Objects for annotation: Genes, Gene products, such as transcripts, proteins, ESTs, cDNA, QTLs, mutants, germplasm, phenotypes, microarray data ……etc Example: Annotations to a plant structure term: pericarp (PO:0009084) in the POC database

  14. Visit www.plantontology.org

  15. Search “pericarp”

  16. Search result click

  17. Description of “pericarp” scroll

  18. Gene Product associations click

  19. Ch1 from MaizaGDB

  20. CYP707A1 from TAIR click

  21. Annotation details

  22. QTL “AQGD029” in Gramene

  23. Get detailed View check check click

  24. Detailed view

  25. Who use PO? TAIR http://www.arabidopsis.org Gramene http://www.gramene.org

  26. Who use PO? NASC http://arabidopsis.info SGN http://www.sgn.cornell.edu

  27. Who use PO? BRENDA http://www.brenda.uni-koeln.de/ Genevestigator https://www.genevestigator.ethz.ch/

  28. There are more, Yours is here!

  29. How to apply PO in your research? • Find appropriate PO terms for your species of interest; if no term, request it! • Curate your objects using PO • Start making cross-species querying • Submit your annotation to POC or species-specific databases

  30. Submit your PO term request!

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