A Comparative mapping resource

1. A Comparative mapping resource ONTOLOGY DEVELOPMENT AND INTEGRATION IN GRAMENE http://www.gramene.org Pankaj Jaiswal Cornell University

3. Acknowledgements Leonore Reiser Sue Rhee Tanya Berardini Leszek Vincent Mary Polacco Toby Kellogg Peter Stevens Yukiko Yamazaki Nori Kurata Michael Ashburner Midori Harris Dom Paolillo Jr. Richard Bruskiewich Graham McLaren

4. What is an Ontology ? An Ontology is a glossary of keywords arranged in a structured order or a network, and the organization is based on biological concepts. This structure is a type of hierarchy that reflects biological concepts and relationships. The nodes at the top (“root”) of the tree are more general cases, and the more specific terms are at the bottom (“leaves”) of the structure.

5. Ontology Types • In Gramene we have ontologies that are organized around three different types of biological concepts. • Gene Ontology (GO) describes a protein/gene's biochemical properties • Molecular Function (e.g. transporter, enzyme) • Role in a Biological Process (e.g. photosynthesis, defense response) • Localization in a Cellular Component (e.g. plastid, cell wall) • Plant Ontology (PO)describes where and when a protein, gene or phenotype is expressed • In aPlant Anatomy(e.g. panicle, flower, xylem, phloem) • At aGrowth Stage(e.g. germination, embryo development) • Trait Ontology (TO)describes the observable features that are assayed to determine the phenotype. • Plant traits (e.g. leaf color, plant height, disease resistance)

6. Anatomy concept

7. Each 'child term' has a unique relationship to its 'parent term'. Instance of (is a type of): Used to describe the relationship between a child term and a more general parent term. For example: a caryopsis is atype offruit; a panicleis a type ofinflorescence. Part of: Used to indicate the relationship between a child term that is a part of the parent term. For example: theectocarpis apart ofthepericarp, which in turn ispart ofthefruit. Develops from: Used to describe the relationship between a child term that develops from its parent term. For example: aseed coat (testa)develops fromthe integuments; aleafdevelops fromaleaf primordium.

8. Plant structure Part of Instance of shoot organ inflorescence tissue flower floral organ sepal petal stamen anther tapetum pollen Ontology concept term genes Fl1 dl1 stl1 cps Du8 dl1 stl1 cps Du8 Cps stl1 Du8 Du8

9. How to build associations?

10. How to build associations?

11. Ontology Uses • The vocabularies/keywords (ontology) are used to annotate: • Molecular characteristics of a protein and/or gene. • Tissue specific expression profile of a gene or phenotype • Observable feature (trait) assayed to determine a phenotype • These annotations (associations) are recorded in databases such as Gramene. • These keywords help in searching your favorite gene/protein/phenotype • Can help find your favorite gene/phenotype and also discover other functional or phenotypic homologs

12. How to find your favorite gene product (protein) ? Click “Ontology” on the Gramene navigation bar Select “Gene Ontology” Type your query e.g. search for function alpha-amylase in Gene Ontology Click here for more help on Ontology

13. Suggests the type of experiments carried out to ascertain its function. IEP: Inferred from Expression Pattern ISS: Inferred from sequence or structural similarity

14. Ontology Annotation includes various experimental evidence codes ISS Inferred from Sequence/Structural Similarity IDA Inferred from Direct Assay IPI Inferred from Physical Interaction TAS Traceable Author Statement NAS Non-traceable Author Statement IMP Inferred from Mutant Phenotype IGI Inferred from Genetic Interaction IEP Inferred from Expression Pattern IC Inferred by Curator IEA Inferred from electronic annotation ND No Data available

15. Ontology Annotation includes various experimental evidence codes ISS Inferred from Sequence/Structural Similarity IDA Inferred from Direct Assay IPI Inferred from Physical Interaction TAS Traceable Author Statement NAS Non-traceable Author Statement IMP Inferred from Mutant Phenotype IGI Inferred from Genetic Interaction IEP Inferred from Expression Pattern IC Inferred by Curator ND No Data available IEA Inferred from electronic annotation

16. How to find your favorite phenotype ? Type your query e.g. search for plant part stem in Plant Ontology Select “Plant Ontology”

17. Features of a PO term Stem is a PART OF “vegetative Shoot” and also a PART Of “secondary axillaryshoot” # Number of mutants associated with this plant part Download/Display all the phenotypes associated with “stem”

18. PO Associations Mutant gene symbol (allows alphabetical sorting) Suggests the type of experiments carried out to ascertain its function. TAS: Traceable Author Statement IAGP: Inferred from association between genotype and phenotype Children terms in the tree following the Primary vocabulary term for which the protein function was annotated Mutant gene name. Links to the Gramene mutant entry page

19. How to find your favorite phenotype expressed at a given growth stage ? Type your query e.g. search for plant growth stage germination in Plant Ontology Select “Plant Ontology” Follow the search results by selecting the term e.g.“germination” in rice(GRO:0007051). Display / download all associations to view associated phenotypes.

21. How to find your favorite phenotype by trait association ? C. Hit Search button B. Select “Trait Ontology” A. Type your query e.g. search for plant trait plant height

23. Where was it assayed ? When was it assayed ? The assayed trait

24. What else can YOU do? • Send us your review of the terms, definitions and relationships to ensure accuracy. • Suggest new terms, definitions, or improvements to the structures. • Use the terms in describing data in publications and databases. • If your project on cereal plants is generating data sets that may require these kinds of annotations and associations, please feel free to reach us atgramene@gramene.org.We will be happy to help you guide through the annotation process.