1. A Comparative mapping resource http://www.gramene.org ONTOLOGY DEVELOPMENT AND INTEGRATION IN GRAMENE 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. 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. What is an Ontology ?

5. 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 a Plant Anatomy (e.g. panicle, flower, xylem, phloem) At a Growth 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) Ontology Types

6. Anatomy concept

7. 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 a type of fruit; a panicle is a type of inflorescence. Part of: Used to indicate the relationship between a child term that is a part of the parent term. For example: the ectocarp is a part of the pericarp, which in turn is part of the fruit. Develops from: Used to describe the relationship between a child term that develops from its parent term. For example: a seed coat (testa) develops from the integuments; a leaf develops from a leaf primordium. Each 'child term' has a unique relationship to its 'parent term'.

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

9. 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 ISSInferred from Sequence/Structural Similarity IDAInferred from Direct Assay IPIInferred from Physical Interaction TASTraceable Author Statement NASNon-traceable Author Statement IMPInferred from Mutant Phenotype IGIInferred from Genetic Interaction IEPInferred from Expression Pattern ICInferred by Curator IEAInferred from electronic annotation NDNo Data available

15. Ontology Annotation includes various experimental evidence codes ISSInferred from Sequence/Structural Similarity IDAInferred from Direct Assay IPIInferred from Physical Interaction TASTraceable Author Statement NASNon-traceable Author Statement IMPInferred from Mutant Phenotype IGIInferred from Genetic Interaction IEPInferred from Expression Pattern ICInferred by Curator NDNo Data available IEAInferred from electronic annotation

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

17. Stem is a PART OFvegetative Shoot and also a PART Ofsecondary axillary shoot # Number of mutants associated with this plant part Download/Display all the phenotypes associated with stem Features of a PO term

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

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

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

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

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 at gramene@gramene.org. We will be happy to help you guide through the annotation process.