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Development of the Generation Challenge Program Ontology for Crops Elizabeth Arnaud (Bioversity International) and Rosemary Shrestha (CRIL-CIMMYT), Richard Bruskiewich (IRRI) TDWG 2008 Annual Conference, 20-25 October 2008 Fremantle, Western Australia The Generation Challenge Programme Science for better crops in the tropics For the majority of crop farmers in the developing world, the ravages of drought, low soil fertility, crop pests and diseases are aggravated by their limited access to improved crops. TDWG annual conference, 20-25 October 2008, Fremantle, Western Australia The Generation Challenge Programme Science for better crops in the tropics By using advances in molecular biology and harnessing the rich global stocks of crop genetic resources, the Generation CP creates and provides a new generation of plants that meet farmer needs. http://www.generationcp.org/ Consultative Group on International Agricultural Research (CGIAR) TDWG annual conference, 20-25 October 2008, Fremantle, Western Australia GCP subprograms SP1- Genetic Diversity of Global Genetic Resources SP2 - Genomics towards gene discovery SP3 - Trait Capture for Crop Improvement SP4 - Bioinformatics and Crop Information Systems Building an 'integrated platform' of molecular biology and bioinformatics tools = Molecular breeding platform SP5 - Capacity Building and Enabling Delivery TDWG annual conference, 20-25 October 2008, Fremantle, Western Australia The Generation Challenge Programme Target areas Drought-prone environments Mandate crops All the CGIAR mandate crops = 22 crops Commissioned and competitive projects 275 projects in 5 years TDWG annual conference, 20-25 October 2008, Fremantle, Western Australia GCP New Challenge initiatives Cereals 1. Rice/drought/Africa 2. Wheat/drought/Asia 3. Sorghum/drought/Africa 4. Rice-Sorghum-Maize/soil problem/Asia & Africa Legumes 5. Cowpeas/drought/Africa 6. Chickpeas/drought/Africa and Asia Root and tubers 7. Cassava/virus/Africa Integration across diverse crop datasets Volume and complexity of biological data is increasing Historical data are scattered in numerous crop specific databases Each database uses slightly different terminologies for terms related to phenotypes TDWG annual conference, 20-25 October 2008, Fremantle, Western Australia Integration across Diverse GCP Crop Data • Inventory • Identification (passport) • Genealogy SP1 Genotype has has • Genetic Maps • Physical Maps • DNA Sequence • Functional Annotation • Molecular Variation (Natural or Induced) e SP2 Expressio n • Transcripteome • Proteome • Metabolome • Physiology affects Environment SP3 • Anatomical • Developmental • Field Performance • Stress Response Molecular • Location (GIS) • Climate • Day Length • Ecosystem • Agronomy • Stresses Phenotyp Germplasm SP3 TDWG annual conference, 20-25 October 2008, Fremantle, Western Australia An integrated platform for molecular breeding To support and encourage researchers to share and reuse information among agricultural databases To form the basis for the generation of data templates, web services and software. TDWG annual conference, 20-25 October 2008, Fremantle, Western Australia GCP Scientific Domain Model Germplasm identification (“passport") and pedigree data Phenotypic characterization and evaluation data Geographic location and environmental descriptions Genotype and molecular data Genomic map data for markers and loci Functional genomics data TDWG annual conference, 20-25 October 2008, Fremantle, Western Australia The exchange of new findings and joint work on projects presuppose that all those involved have the same understanding of the terms they use. This calls the need for an extensively standardized description of plant development stages with phenological characteristics and coding. Prof. Dr. F. Klingauf President of the Federal Biological Research Centre for Agriculture and Forestry, Berlin and Braunschweig TDWG annual conference, 20-25 October 2008, Fremantle, Western Australia Importance of crop ontology Similar plant structures are described by their speciesspecific terms. Grain or caryopsis in Rice Kernel in Maize Fruit Pod in Beans Grain in Wheat TDWG annual conference, 20-25 October 2008, Fremantle, Western Australia The GCP Ontology "Thesaurus" of biological concepts that can be shared and used across species to which genetic and phenotypic data can be associated integrative data mining on GCP annotated data using the platform and web services Developed with crop experts, for plant structure, developmental stages, traits and expression of the traits for selected priority GCP crops: Wheat, Maize, Sorghum, Chickpea, Banana & Plantain TDWG annual conference, 20-25 October 2008, Fremantle, Western Australia GCP Sources for mapping the terms International Crop Information Systems ICIS model (http://www.icis.cgiar.org ) IMIS (maize) IRIS (rice) IWIS (wheat) Musa germplasm information system (http://www.musa-diversity.org ) ICRISAT information system (Sorghum, chickpea) CIP information system (potato) Crop descriptors for traits (Bioversity International) GCP data templates GCP datasets TDWG annual conference, 20-25 October 2008, Fremantle, Western Australia http://www.generationcp.org GCP Ontology TDWG annual conference, 20-25 October 2008, Fremantle, Western Australia Developing the GCP ontology 1 Crop DB 2 GCP crop ontology GCP concept ID 3 mapping DBXref PO concept ID & TO concept ID GCP data Templates 4 Plant Structure ontology www.plantontology.org/ Trait Ontology www.gramene.org/plant_ontology/ Data annotation with GCP ontology TDWG annual conference, 20-25 October 2008, Fremantle, Western Australia GCP ontology term has: Term: ID: Namespace: Definition: plant height GCP_322*.0000021 maize_trait Synonyms: Dbxrefs: is_a: PHT, PTHT, Planth. Shoot height PO:10202TO:0000207, IMIS_TRAITID:1008 GCP_322.0000108 Measurement of plant height from soil surface to the highest point in plant. TDWG annual conference, 20-25 October 2008, Fremantle, Western Australia Building ontology with OBO.Edit http://oboedit.org/ Terms are linked by the relationships such as is-a part-of has-a disjoint from derived from, etc. It is structured as a hierarchical directed acyclic graph (DAG) Terms can have more than one parent and zero, one or more children Draft releases of the OBO formatted ontology files for rice, wheat and maize trait are available at http://cropforge.org/projects/gcpontology/ TDWG annual conference, 20-25 October 2008, Fremantle, Western Australia Complex trait's names created by breeders in the crop databases %HSATIVUM_TILLER1_FLAG_1 Complex trait name Description: The trait is scored for severity of the disease caused by Helminthosporium sativum (leaf spot) at tiller 1 and flag 1 stage in percentage. to be decomposed into simple terms that are readable for both human and computer and mapped against Ontology TDWG annual conference, 20-25 October 2008, Fremantle, Western Australia Ontology for Crops Phenoptype Genotype Factor (G) Plant structure Plant Ontology Markers/alleles/sequence ontology Development stages “values” have Qualities & “units” Units Ontology (units implicitly indicates attribute) EFFECTS External environmental data (E) Treatment, Location, Climatic variables /water, Growth conditions, Stress Management/agronomy Temporal factor (T) phenotypic qualities PATO Qualifier Assessment Methods Ontology (e.g. ICIS) Time Ontology Experiment factor (ED) Experimental design GCP Ontology – present and future prospects: GCP data templates ICIS dataset Data Source CGIAR General Science Ontology GCP Domain Module Ontology General Germplasm Ontology Taxonomic Ontology GCP Ontology Plant Anatomy & Development Ontology Location & Environment Ontology Structural & Functional Genomic Ontology Phenotype & Trait Ontology Web Interface (Chado/koios) Query Linkage to external ontologies TDWG annual conference, 20-25 October 2008, Fremantle, Western Australia http://pantheon.generationcp.org http://pantheon.generationcp.org TDWG annual conference, 20-25 October 2008, Fremantle, Western Australia Thank you ! Crops' Harvest Celebration San Isidoro Feria Lucban, Philippines TDWG annual conference, 20-25 October 2008, Fremantle, Western Australia