1. 1 Building Communities Around Ontology Development Pankaj Jaiswal Dept. of Plant Breeding and Genetics Cornell University Ithaca, NY pj37@cornell.edu FAO, Rome, Italy September 22, 2007

2. 2 Gene Ontology Collaborators Core funding by the National Institute of Health. Several other individual institutional grants from NSF, USDA, MRC, etc. Many More Organizations and Numerous Users

3. 3 Plant Ontology Collaborators Funded by the National Science Foundation Many More Organizations and Numerous Users

4. 4 LOC_Os06g04200.1 LOC_Os06g06560.1 LOC_Os06g12450.1 LOC_Os06g14510.1 LOC_Os06g51084.1 AQBN003 Amylose content AQGA015 - Amylose content, AQBP002 -Wx AQCV027 -Chalky endosperm, AQFU016-Amylose content AQBN002 -Amylose content, AQCF021 - Grain yield AQCV039 Chalky endosperm Chr – 6, Genomic region Gene QTL Mutant phenotype wx du11 du9sbe1 Starch biosynthesis pathway

5. 5 Polymorphism Candidate gene Gene models Transcripts Peptides Function Expression Pathway Orthologs/homologs Inter and Intra Specific Comparative and Translational Genomics and Genetics Phenotypes/traits/ genes identified/ mapped genetically Physical or Sequence map Genetic map-2 Genetic map-1

6. 6 Nucleotide variation at the Waxy gene GroupSample size (n) Nucleotide diversity (π) a a Haplotype diversity Tajima's D O. sativa730.00560.845+0.4991 cv indica210.00590.952+0.3726 cv trop japonica180.00020.739−1.5037 cv temp japonica220.001090.476−2.6149 cv aus60.00280.733+2.0874 cv aromatic60.00370.800−1.5374 O. rufipogon90.02130.972+1.1864 Olsen et al, 2006 – GR_Ref_ID -7050 Germplasm information Starch Biosynthesis From pathway to diversity/germplasm

7. 7 “Infected” Group the relevant genes for Function, location in a cell, role in a process or by phenotypes using Ontologies

8. 8 plant structure tissue sporophyte root trichoblast root hair root epidermis epidermis cell organ is_a (subtype) part_of develops_from Building the ontology and term-to-term relationships

9. 9 Some of the ontologies describing the biology. Gene Ontology (GO) to describe a protein/gene's biochemical property 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) to describe a protein/gene/phenotype expression In a Plant Anatomy (e.g. panicle, flower, xylem, phloem) At a Growth Stage (e.g. germination, embryo development) Trait Ontology (TO) to describe the observable feature assayed to determine the phenotype. Plant traits (e.g. leaf color, plant height, disease resistance) Environment Ontology (EO) to describe the supplemental treatments and the ecological habitats where a plant sample is subjected to phenotype evaluation (UV light, drought, pests and pathogens) How does it work?

10. 10 Ontology collections and registry

11. 11 Ontologies for use in different formats

12. 12 Ontology request monitoring via bug tracking tools

13. 13 Ontology request monitoring via bug tracking tools and open mailing lists

14. 14 Ontology Management and Standards

15. 15 Editing and Managing the Ontology LiteratureOBO-EditorCommit to cvsDatabaseAnnotation

16. 16

17. 17 Ontology mappings to various other database vocabularies

18. 18 Ontology Annotations driving the ontology development and uses

19. 19 Participation in ontology development

20. 20 Google analytics score for Plant Ontology website traffic tracking

21. 21

22. 22 Helpful things www.geneontology.org www.plantontology.org www.gramene.org www.obofoundry.org OBOrelations: paper by Chris Mungall and Barry Smith oboL: paper by Chris Mungall OBOEdit (ontology editor) download from Sourceforge