Poster presented at CGIAR Generation Challenge Programme, General Research Meeting. Hyderabad (India), 21-25 Sep 201

Arnaud, Elizabeth

Bakare, M.A.

Kulakow, P.A.

Shrestha, R.

English

Kulakow, Peter A.

CGSpace (CGIAR)

Expansion of the Crop Ontology by Adding Cassava Trait OntologyIntroductionThe Crop Ontology describes traits, methods and scales of several economically important plants (http://www.cropontology-curationtool.org). Cassava (Manihot esculenta Crantz)  ontology was added to Crop Ontology in 2010. Simultaneously, the cassava team is developing an ontology-driven cassava database called ICASS for researchers to record and annotate measurements linked to genotypes with defined pedigrees. The cassava crop ontology currently describes over 125 traits representing important trait groups (agronomic, biotic and abioticstress, morphological, physiological and quality traits). These traits describe phenotypic variability for characteristics needed for crop improvement. The cassava ontology will facilitate information sharing and collaboration among researchers from CIAT, IITA, national programs and other collaborators. New ontology-based online curation and annotation tools allow crop curators to provide standard protocols explaining scale, scale value, scoring guidelines and growth stages for scoring traits. AcknowledgementThis work was supported by GCP grant to IITA. We would like to acknowledge the contribution of trait information from Dr. Chidozie Egesi and Dr. Emmanuel Okogbenin of the National Root Crops Research Institute, Nigeria and Dr. Luis Augusto Becerra Lopez-Lavalle and Dr. Hernan Ceballos of the International Center for Tropical Agriculture.Shrestha R, Arnaud E, Mauleon R, et al. 2010. Multifunctional crop trait ontology for breeders’ data: field book, annotation, data discovery and semantic enrichment of the literature. AoB Plants. Plq008Dixon A.G.O., et al 2010.  Improved cassava variety handbook. IITA cassava project, Ibadan Nigeria. Document cassava trait ontology within the gramene trait ontology to develop a common internationally-shared crop trait ontology. Harmonize definition of cassava traits with  researchers including CIAT and National Agricultural Research Systems. Apply the ontology-based annotation tool to annotate cassava datasets. Facilitate ongoing communication among cassava researchers to continuously add new cassava traits to ontology. Define cassava traits using standard terminology shared among cassava researchers. Facilitate the sharing of information between research trials. Increase efficiency of information retrieval. Integrate information from various electronic sources. Enable annotation of research documents, reports, and databases with ontological terms. Allow researchers and end users to query keywords related to traitsOverview of definition of a trait term and its relationship within the ontology.Cassava trait ontology structureTrait group relationshipsquality traitagronomic traitfresh root yielddry yielddry matter contentfresh root weightDI II IDDIIDIs_a relationDerives_from relationstress traitquality traitphysiological traitagronomic trait morphological traitCGIAR cassava trait ontologyII I I I Ibiotic stress trait abiotic stress traitinsect damage viral diseasefungal diseasebacterial diseaseI II I I II Is_a relationOBO syntax Meaning ExampleID Unique Identifier CO_334:0000013Name Term Fresh root yieldDef Definition Fresh weight of harvested roots expressed in tons per hectares per plant. [ISBN:978-131-302-1Exact_synonym Synonym “FYLD”EXACT[]is_a Parentage CO_334:0000001 !Agronomic traitRelation Relationship type Derives_fromCO_334:0000012 ! Fresh root weightPeter Arthur Kulakow1*, Moshood Agba Bakare1, Elizabeth Arnaud2, Rosemary Shrestha3*1International Institute of Tropical Agriculture, IITA, PMB 5320, Ibadan NIGERIA; 2Bioversity International, Montpellier, France; 3Crop Research Informatics Laboratory - Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT), Mexico; *e-mail: p.kulakow@cgiar.orgObjectivesRoot Neck LengthCO_334:0000022Root ShapeCO_334:0000020Stem ColorCO_334:0000062Root NumberCO_334:0000011Outer Skin ColorCO_334:0000064www.iita.orgReferencesNext StepsOverview of ontological term having multiple inheritance from two classes of ontology traits.

Expansion of the crop ontology by adding cassava trait ontology

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Expansion of the crop ontology by adding cassava trait ontology

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