Authors: Alice Clara Augustine, Vijayalakshmi K, Shobha Char, Naveen Sylvester, Mittur N Jagadish; Mike Edgerton Organizations: Monsanto Research Centre, Monsanto Company

1. Ontology development and use for efficient information input and retrieval 1 Alice Clara Augustine, Vijayalakshmi K, Shobha Char, Naveen Sylvester, Mittur N Jagadish; 2 Mike Edgerton 1 Monsanto Research Centre. Divn. of Monsanto Holdings Pvt. Ltd. #44/2A, “Vasants Business Park”. Bellary Road, NH-7, Hebbal. Bangalore 560 092, India 2 Monsanto Company. 800 North Lindbergh Blvd. Creve Coeur, Missouri 63167 United States Seventh Agricultural Ontology Services Workshop NOVEMEBER 9-10, 2006: BANGALORE (INDIA)

4. Why do we need an ontology? There is tremendous variation in the way in which phenotypes, traits, gene expression and protein localization are described. In addition, the nomenclature used to describe anatomy and development varies across taxa. For example: 1. A plant that flowers late can be described in many ways (late flowering, delayed flowering, flowers at 36 days after sowing). 2. Panicle, ear, tassel are all words used to describe an inflorescence. To make meaningful comparisons within and across different databases, we need a shared descriptive language that is uniformly applied to the data. Slide is a courtesy of Plant Ontology Consortium (POC)

5. Precision (The degree of mutual agreement / strict conformity to a rule or a standard e.g Gene Ontology terms) Systematic (characterized by order and planning e.g. Hierarchy ) Explicitness unambiguous (indicating a single clearly defined meaning: e.g: ‘Flower’ ) Flexibility (the quality of being adaptable or variable e.g. Thesaurus ) Ontology Desiderata

9. Instance of (is a, type of): Used to describe the relationship between a child term that represents a specific type of a more general parent term. For example: a silique is a type of fruit; a panicle is an 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'

10. 4 wheelers Safari Tyre Two wheelers TATA truck Leyland SUV A graphical view of some terms and their relationships Car Bus Truck SUMO Sierra Indica V2 Indigo Indiva Carburetor Clutch plate Shock absorber The terms can be children of other parents too Part of Instance of term

11. anatomy Whole plant inflorescence flower tissue organ tapetum stamen anther filament shoot floral organ Part of Instance of A graphical view of some terms and their relationships term Yfg1 gene petal Petal primordium Develops from Plant Ontology (PO)

12. What genes are expressed in the same tissues or organs as my gene of interest? When and where are homologous genes expressed in different organisms? What genes are expressed in both monocot and dicot flowers? What genes are expressed in maize leaves but NOT in Arabidopsis or rice? Examples of queries that will be possible using annotations with POC terms.

13. Terms are then used to annotate genes Trait ontology Stress related WUE Yield related Pod length Pod shatter Pod weight abiotic term gene ALC abiotic NUE Cold Root mass Root volume Root weight The terms can be children of other parents too Root related Shoot related Fruit related Plant anatomy related Pod related What are the genes that are associated with conferring a pod shatter related trait? What are the genes that are associated with WUE AND increased root mass phenotype? P5CS AGL8

14. Using linguistics for Database interoperability Cross database - querying and reporting

17. Acknowledgements Jagadish Mittur Shobha Char Vijay Paranjape BSIB team@MRC, Bangalore The organizers of this conference – in particular Dr. Gauri Salokhe (Information Management Officer) Dr. V. C. Patil (The Organizing Secretary)