International Coordination Meeting of Ontology-Based Efforts for Plant Biology PRO-PO-GO Meeting

1. International Coordination Meeting of Ontology-Based Efforts for Plant BiologyPRO-PO-GO Meeting Buffalo NY May 15-16, 2013 Sponsored by

2. The genomics and genetics data • More than 30 Reference Plant genomes sequenced from important and diverse plant species including several crops by various international consortiums. • Millions of data points representing: • Genetic diversity of crop plants from wild and cultivated collections. • Arabidopsis 1001 genomes, 3000 rice, 5000 maize lines. • Phenotypes/agronomic traits. • Discovery of novel gene functions. • Climate modeling and impacts on various traits. • Crop improvement programs by plant breeding . • Data hosted in various international projects and data archives. • Users: • Researchers, Students, • Farmers, Agriculture extension programs • Policy makers and governments

3. RELATION TO TIME GRANULARITY Ontologies for Plants-1 Gene Ontologies to the Rescue

4. Ontologies allowed computational reasoning of questions like: • What is the function of my favorite gene (product)? • What role does it play in a biological process? • What is the cellular component location of this gene product? All provided by the excellent use of Gene Ontology. However we needed to add more contextual information to this annotation?

5. Differences in vocabularies & problems in data interpretations Rice Corn Banana Soybean Crop products Bunch Fruit Pod Grain Kernel Berry Tuber Root Tomato Traits Color Size Shape Yield Texture Weight Nutrition Composition Anatomy Stress Diseases Phenotypes Yellow Red Green Elongated Rough Juicy Hard Resistant Tolerant Sorghum Cassava Potato

6. Ontologies allowed computational reasoning of questions like: • What is the function of my favorite gene (product)? • What role does it play in a biological process? • What is the cellular component location of this gene product? • In what plant part the gene product is expressed or display phenotype? • At what growth stage of a plant do we see the gene expression or displayed phenotype? • What anatomical plant structures and growth/developmental stages inherit the function and biological process associated with the above gene product? • What is the phenotype of this gene? All provided by the excellent use of Gene Ontology, Plant Ontology and Phenotype and Attribute Ontology (PATO). However we needed more contextual information for annotation and refine the ontologies as well to cover all plant species?

7. Details: Term-Term Relationships (anatomy example) is_a andpart_ofare the backbone of all ontologies develops_from describes shared developmental pathways across all taxons has_part allows the PO to handle structural variation between taxons

8. How Relationships Help In Comparative Genomics? ZM:zfl1 OS:RFL AT:LFY Bomblies K et al. Development 2003;130:2385-2395 Source: Gramene

9. RELATION TO TIME GRANULARITY Ontologies for Plants-2 Plant Ontology to the rescue

10. More Context is Required Crop Varieties, Germplasm and Genetic resources Environment Geographic location Climate Treatments Pests Pathogens Genomes Genetics Genes Genomics Phenotypes Characters Gene Functions Physiology Biochemistry

11. Biological Questions • List all the genes expressed differentially in the leaves of Rice plant varieties IRBB5 and IR24 at the 5-leaf visible growth stage, when the plants were infected with Xanthomonasoryzaepv. oryzaewere grown in a growth camber. IRBB5 is resistant and IR24 is susceptible to rice bacterial blight disease. • Filter the differentially expressed gene set for those with • LRR-domains • Transmembrane domains (e.g. in excess of 1) • Receptor like kinase function • Plasmamembrane cellular location • OR those having Tryptophan decarboxylase function • Tryptophan metabolism • Have known alleles and homologs with disease resistance phenotype

12. Environment Ontology (ENVO) Plant Environmental Conditions (EO)

13. Biological Questions PATO PO Tax OBJ PO • List all the genes expressed differentially in the leaves of Rice plant varieties IRBB5 and IR24 at the 5-leaf visible growth stage, when the plants were infected/treated with Xanthomonasoryzaepv. oryzaewere grown in a growth chamber with 60% humidity. IRBB5 is resistant and IR24 is susceptible to rice bacterial blight disease. • List all the genes expressed differentially in response to pathogen Xanthomonasoryzaepv. in the leaves of rice IRBB5 and IR29. • Filter the differentially gene set for those with • LRR-domains • Transmembrane domains (in excess of 5) • Receptor like kinase function • Plasmamembrane cellular location • OR those having Tryptophan decarboxylase function • Tryptophan metabolism • Have known alleles and homologs with disease resistance phenotype Tax/EO EO PATO PATO EO Disease GO PRO GO TO

14. Annotation: Ontology Requirements * PRO = Protein Ontology

15. Project Partners OBO Crop Trait Ontology Workshop. Oregon State University12-15 September 2012

16. Project focus areas for crops • Build bridges between diverse set of vocabularies by using reference ontologies. • Core traits for target are: Yield, Quality, Drought and Disease resistance. • Develop new and enrich existing field books and guides by integrating ontologies for use in data collection, training and education. • Develop International partners and collaborations on data collection, annotation and analysis. • Develop tools for comparative analysis using open data. • Develop APPs for agriculture extension, genetics and biology researchers.

17. cROP Project Partners J. Hutton Luke Ramsay Dave Marshall Cyril Pommier –INRA,BAP; Ephesis Jacques Legouis –INRAGEDEC, Breedwheat Francois Tardieu-INRAPhenome, DROPS BBSRC Ruth Bastow-GARnet Chris Rawling-Rothamsted Res. UNITED KINGDOM FRANCE EBI Paul Kersey • ERA-CAPS • Coordinators • John Doonan, Aber Univ. • GeorgiosGkutos, Aber Un. Fabio Florani - Julich Bjorn Usadel – Aacehn UliSchurr – Julich DROPS • Focus = Semantic integration framework • Develop Trait ontology for wheat, barley & brassicaceae • Environment ontology from Phenotyping platforms • Warehouse, mirroring on server –EBI • Community engagement • Generation Challenge Programme • Integrated Breeding Platform GERMANY Cornell, NYBG Gramene, SGN, MaizeGDB, UniProt, GO, SoyBase, etc. • CGIAR • Consortium • Elizabeth Arnaud iPlant Oregon State University KBase (DOE) USDA - ARS • Focus = Crop Ontology, Integrated Breeding Platform services- Breeding for development • Provision of traits and annotations of Wheat, Rice , Maize and other crops : Cassava, Sorghum, Potato, Yam. • Contribution to the semantic framework • Community engagement NCBO & OBO-Foundry RCN Phenotype • Focus = Expansion & Maintenance of the Reference Ontology for Plants and US Outreach • Coordinate the overall project and lead Ontology Development • Use case for the semantic integration framework • Develop data warehouse, visualization and analysis tools • Manage online resource at iPlant OBO-foundry Barry Smith

18. http://crop.cgrb.oregonstate.edu Or http://tinyurl.com/crop-plants

19. Genotype Polymorphism Candidate gene Gene models Transcripts Peptides Function Expression Pathway Orthologs Genetic markers & phenotypes (genes and QTL) Map-1 Map-2 Physical and/or Sequence map Phenotype Comparative and Translational Genomics Forward Reverse

20. Phenotype Data Analysis Genotype Trait Germplasm Marker Environment Map Genome Pathway Genes Ortholog Are entities connected ?

21. Host Pathogen InteractionOrganism And Molecular Interactions Plant HOST CELL PM Extra cellular space Pathogen

22. Plant (Disease) Stress Ontology disease: rice bacterial leaf blight disease (IDO) | host species: Oryza sativa (rice) (taxon) | caused by: Xanthomonasoryzae (Taxon)| has symptom: leaf color pale yellow (TO+PATO) | plant structure: vascular leaf | reported in: Northern Territory (GAZ) |

23. Ontologies Spectrum of Controlled Vocabularies http://www.mkbergman.com/?m=20070516

24. Key: Purple stars: New Ontologies to be developed Cyan stars: work with the existing collaborator ontologies for desired plant enrichment Yellow stars: ongoing in-house efforts Environment Ontology (ENVO) Plant Environmental Conditions (EO)

25. GO: response to pathogen Disease Ontology Example Building genotype-phenotype associations Allele-B GO: Receptor like Kinase Gene:XA21 maps_to Allele-A has_function inheres_in belongs_to Oryza genotype

26. cROP Goals • A distributed international effort on development of ontologies for plant specific knowledge domains . • Collaborate with existing ontology development efforts for enrichment of Plant specific terms. • Develop standards for annotation of various plant biology data sets. • Encourage adoption and integration of cROP ontologies. • Invite collaborations on distributed annotation of plant biology data sets. • Develop search and analysis tools. Includes integration of on/off-site datasets and maintain a common information portal for ontology based annotations. • Provide ontologies and annotations via webservices. • Collaborate with publishers and NLP projects on integration of cROP markups, active learning and annotation.

27. Open Biomedical and Biological Ontologies Environment Ontology (ENVO) Plant Environmental Conditions (EO)

28. Website: http://tinyurl.com/Trait-Ontology Plant Trait Ontology Workshop Alumni Center Oregon State University Corvallis, OR September 13-15, 2012 Funded by Several Other Agencies Supporting Travel For Participants