Shrestha Rosemary, Matteis Luca, Skofic Milko, Portugal Arllet, McLaren Graham, Hyman Glenn, Arnaud Elizabeth
Genetic Resources Program, Centro Internacional de Mejoramiento de Maiz y Trigo Texcoco, Edo. de México, Mexico.
Front Physiol. 2012 Aug 25;3:326. doi: 10.3389/fphys.2012.00326. eCollection 2012.
The Crop Ontology (CO) of the Generation Challenge Program (GCP) (http://cropontology.org/) is developed for the Integrated Breeding Platform (IBP) (http://www.integratedbreeding.net/) by several centers of The Consultative Group on International Agricultural Research (CGIAR): bioversity, CIMMYT, CIP, ICRISAT, IITA, and IRRI. Integrated breeding necessitates that breeders access genotypic and phenotypic data related to a given trait. The CO provides validated trait names used by the crop communities of practice (CoP) for harmonizing the annotation of phenotypic and genotypic data and thus supporting data accessibility and discovery through web queries. The trait information is completed by the description of the measurement methods and scales, and images. The trait dictionaries used to produce the Integrated Breeding (IB) fieldbooks are synchronized with the CO terms for an automatic annotation of the phenotypic data measured in the field. The IB fieldbook provides breeders with direct access to the CO to get additional descriptive information on the traits. Ontologies and trait dictionaries are online for cassava, chickpea, common bean, groundnut, maize, Musa, potato, rice, sorghum, and wheat. Online curation and annotation tools facilitate (http://cropontology.org) direct maintenance of the trait information and production of trait dictionaries by the crop communities. An important feature is the cross referencing of CO terms with the Crop database trait ID and with their synonyms in Plant Ontology (PO) and Trait Ontology (TO). Web links between cross referenced terms in CO provide online access to data annotated with similar ontological terms, particularly the genetic data in Gramene (University of Cornell) or the evaluation and climatic data in the Global Repository of evaluation trials of the Climate Change, Agriculture and Food Security programme (CCAFS). Cross-referencing and annotation will be further applied in the IBP.
国际农业研究磋商组织（CGIAR）的多个中心：生物多样性国际、国际玉米小麦改良中心（CIMMYT）、国际马铃薯中心（CIP）、国际半干旱热带作物研究所（ICRISAT）、国际热带农业研究所（IITA）和国际水稻研究所（IRRI），为综合育种平台（IBP）（http://www.integratedbreeding.net/）开发了世代挑战计划（GCP）的作物本体（CO）（http://cropontology.org/）。综合育种要求育种者获取与特定性状相关的基因型和表型数据。CO提供了经作物实践社区（CoP）使用的经过验证的性状名称，以协调表型和基因型数据的注释，从而通过网络查询支持数据的可访问性和发现。性状信息通过测量方法和尺度的描述以及图像来完善。用于生成综合育种（IB）田间记录簿的性状词典与CO术语同步，以便对田间测量的表型数据进行自动注释。IB田间记录簿使育种者能够直接访问CO，以获取有关性状的更多描述性信息。木薯、鹰嘴豆、菜豆、花生、玉米、香蕉、马铃薯、水稻、高粱和小麦的本体和性状词典均在线提供。在线管理和注释工具便于作物社区直接维护性状信息并生成性状词典（http://cropontology.org）。一个重要特征是CO术语与作物数据库性状ID以及它们在植物本体（PO）和性状本体（TO）中的同义词进行交叉引用。CO中交叉引用术语之间的网络链接提供了对用类似本体术语注释的数据的在线访问，特别是康奈尔大学Gramene中的遗传数据或气候变化、农业和粮食安全计划（CCAFS）全球评估试验库中的评估和气候数据。交叉引用和注释将在IBP中进一步应用。
