Po development stages jan2014

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A quick overview of the plant structure development stage branch of the Plant Ontology.

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Po development stages jan2014

  1. 1. Plant Ontology and Cross-Species Reasoning How the PO defines developmental stage terms to be used across all green plant species This is a sub-set of a talk originally presented at the Phenotype RCN monthly community call.
  2. 2. 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 *current address: rwalls@iplantcollaborative.org Maria Alejandra 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
  3. 3. Plus many others over the years! http://plantontology.org
  4. 4. The Plant Ontology is: • A structured, controlled vocabulary (ontology) for plant anatomy, morphology, and developmental stages • A resource for data annotators • A database of associations between PO terms and genes, gene models, proteins, RNAs, germplasms, and QTLs • A web portal: http://plantontology.org/
  5. 5. Green plant diversity Bowman et al. (2007), Cell 129:229-234
  6. 6. Two main branches of the PO • plant anatomical entity (PO:0025131): An anatomical entity that is or was part of a plant. – CARO:0000000 (anatomical entity) is defined as: Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. • plant structure development stage (PO:0009012): A stage in the life of a plant structure (PO:0009011) during which the plant structure undergoes developmental processes. – Refers to GO:0032502 (developmental process), including growth, differentiation, and senescence.
  7. 7. Upper level plant structure development stages mirror plant anatomical entity terms
  8. 8. Whole plant development stages Gametophyte development stage also has subclasses for vegetative, reproductive, dormant, and senescent stages.
  9. 9. Development stage boundaries based on processes
  10. 10. Under development: adding temporal relations to order stages = preceded_by
  11. 11. Making the PO work across all green plants: General terms for any species, plus specific subclasses where needed

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