Overview of the Plant Ontology: development and general structure

1. Overview of the Plant Ontology: development and general structure Katica Ilic TAIR, Carnegie Institution of Washington, Stanford, CA

2. What is an ontology? • A specification of a conceptualization (T. Gruber, 1993). • Formal representation of knowledge domains (Bard & Rhee, 2004). • A formal ontology is a controlled vocabulary expressed in an ontologyrepresentation language. • Bio-ontology • A complex hierarchical structure in which biological concepts are described by their meaning (definitions) and by their relationships to each other. The most well-known example of a biological ontology is the Gene Ontology (GO), which describes three biological domains: sub-cellular localization, molecular function and biological process.

3. Plant ontologies Plant model organism databases have created their own ontologies.

4. Why do we need a controlled vocabulary? Need: The ability to make cross database/species queries such as "What mutations affect inflorescences in tomato, rice, maize and Arabidopsis?“ Problem: Terminology between databases and taxa is heterogeneous (e.g., an inflorescence can be called an ear, tassel, raceme, cyme, etc.). For instance, a type of query: search for all the genes expressed in fruit of Arabidopsis, rice and maize. Fruit? No such term! Instead, silique, caryopsis, kernel are used. Solution: Create a set of controlled vocabularies that are used by databases to describe biological data from different organisms.

5. The Plant Ontology Consortium (POC) Plant Ontology Consortium (POC) was formed in response to the need for a set of uniform terms to describe plant structures and developmental stages. The POC is a collaboration among plant genome databases and plant systematists to create, maintain and use controlled vocabularies to describe phenotypes and expression patterns of plant genes.

6. What are the goals of the Plant Ontology Consortium? Develop and maintain a set of controlled vocabularies (ontologies) to describe anatomy/morphology and developmental stages for Arabidopsis, rice, maize and other angiosperms. To use this common language to describe gene expression and phenotypes in experimentally and agronomically important plants. To create a semantic framework for comparative plant genomics. To actively involve researchers, breeders and systematists in the development and application of the plant ontologies.

7. The relationship of PO to other ontologies Plant Ontology does not overlap with other Bio-ontologies GO: biological process GO: molecular function GO: cellular component gene PO: developmental stages PO: plant structure

8. Using ontologies to describe gene products One or more ontologies can be used to describe different aspects of the gene product. gene Phenotype PO: plant structure PO: developmental stage GO: biological process Function/Role GO: molecular function GO: biological process Expression/Protein localization PO: developmental stage PO: plant structure GO: cellular component

9. Aspects of Plant Ontology Plant Ontology has two biological domains: Plant structure Terms that describe morphological/anatomical structures of whole plants, including organs, tissues and cell types (does not include subcellular structures). Examples are stamen, gynoecium, petal, parenchyma, guard cell,etc. • Plant growth and developmental stages • Terms that describe stages in the growth and development of an entire organism, including development of individual organs and tissue systems. • Examples are embryo development, seedling stages, flowering stages, etc.

10. Plant Structure Ontology (release date: 23 July, 04) • Integration of controlled vocabularies for Arabidopsis, maize and rice • Currently, PO has 635 terms with definitions describing plant • anatomy and morphology • Next step, integrations of terms for legumes (soybean and Medicago), tomato and wheat

11. What the Plant Ontology is NOT It is NOT a vocabulary for taxonomy It exists to facilitate the description/annotation of genes and phenotypes, not for taxonomic description. It is NOT an exhaustive glossary of terms The goal is to provide a vocabulary for relating genes from different organisms. The vocabulary will only be as complex required to make detailed annotations.

12. What are the organizing principles? Keep it simple: strive for a robust extensible structure, rather than comprehensiveness. Where possible, rely on synonymy (equivalence of terms) rather than creating a new term. The criterion for creating an anatomy term include: location, morphology, derivation and spatial/positional organization. Include species specific terminology to accommodate annotation and biological accuracy (i.e., maintain the true path rule). All terms must be defined.

13. How are terms defined? The precise definition of terms is critical to the integrity of the ontologies. Definitions are obtained primarily from standard references such as textbooks and glossaries. Definitions may be taken verbatum from references or modified for clarity or to reflect common usage. Most definitions come from Plant Anatomy(K.Esau) and the Angiosperm Phylogeny website (Missouri Botanical Garden).

14. Directed acyclic graph (DAG) and the true path rule • Structured as Directed Acyclic Graphs (DAG) • The true path rule states that the path from any node (term) all the way to the top node of the tree must be biologically correct.

15. Plant Structure Ontology (top nodes)

16. Elements and attributes of terms

17. Species-specificity: the problem In cases where more specific instances of terms are created the children terms cannot be generic because this violates the true path rule. An Arabidopsis gene annotated to a generic anther term, should NOT be retrieved in a search for genes expressed in a tassel floret of maize. flower tassel floret (i) flower PO:0009046 (i) floret PO:0009082 (i) floret (sensu Poaceae) PO:0006318 (i) tassel floret PO:0006310 is a X anther part of part of

18. Species-specificity: the solution The solution is to create specific (sensu Zea) instances for the parts of the maize floret. The new sensu terms are also added as instances of the more generic term, so that a query for mutants affecting the anther will include genes from maize as well as other species. flower Tassel floret is a part of anther (sensu Zea) anther part of is a

19. How are the ontologies maintained? • The most current versions of the ontologies can be downloaded from the POC CVS repository. • The updated ontology is used to upload the Plant Ontology browser (modified AmiGO) on a monthly basis.

20. www.plantontology.org

21. NSF Plant genome research award No. 0321666 Plant Ontology Consortium – people involved POC collaborators Paulien Adamse (Plant Research Int., PlaNet) Richard Bruskiewich (IRRI) Roger Wise (Iowa State University) Randy Shoemaker (Iowa State University) Rex Nelson (Iowa State University) Randy Scholl (ABRC) Cold Spring Harbor Laboratory Lincoln Stein Doreen Ware Shuly Avram Cornell University Susan McCouch Pankaj Jaiswal Anuradha Pujar Carnegie Inst. of Washington Sue Rhee Leonore Reiser Katica Ilic University of Missouri Elisabeth Kellogg UM-St Louis Peter Stevens UM-St Louis Felipe Zapata UM-St Louis Mary Polacco UM-Columbia Leszek Vincent UM-Columbia Maize Genetics Cooperation - Stock Center Marty Sachs Pioneer Hi-BredInternational Arthur Lane Dave Selinger Monsanto Vijay Paranjape Alice Clara Augustine