Menda Naama, Ellerbrock Bryan J, Simoes Christiano C, Karaikal Srikanth Kumar, Nyaga Christine, Flores-Gonzalez Mirella, Tecle Isaak Y, Lyon David, Agbona Afolabi, Agre Paterne A, Peteti Prasad, Akech Violet, Asiimwe Amos, Fauvelle Eglantine, Meghar Karima, Tran Thierry, Dufour Dominique, Cooper Laurel, Laporte Marie-Angélique, Arnaud Elizabeth, Mueller Lukas A
Boyce Thompson Institute, 533 Tower Rd, Ithaca, NY 14853 , USA.
Plant and Environmental Sciences, Pee Dee Research and Education Center, Clemson University, 2200 Pocket Road, Florence, Clemson, SC 29506, USA.
Database (Oxford). 2025 Mar 21;2025. doi: 10.1093/database/baaf020.
Ontologies are widely used in databases to standardize data, improving data quality, integration, and ease of comparison. Within ontologies tailored to diverse use cases, post-composing user-defined terms reconciles the demands for standardization on the one hand and flexibility on the other. In many instances of Breedbase, a digital ecosystem for plant breeding designed for genomic selection, the goal is to capture phenotypic data using highly curated and rigorous crop ontologies, while adapting to the specific requirements of plant breeders to record data quickly and efficiently. For example, post-composing enables users to tailor ontology terms to suit specific and granular use cases such as repeated measurements on different plant parts and special sample preparation techniques. To achieve this, we have implemented a post-composing tool based on orthogonal ontologies providing users with the ability to introduce additional levels of phenotyping granularity tailored to unique experimental designs. Post-composed terms are designed to be reused by all breeding programs within a Breedbase instance but are not exported to the crop reference ontologies. Breedbase users can post-compose terms across various categories, such as plant anatomy, treatments, temporal events, and breeding cycles, and, as a result, generate highly specific terms for more accurate phenotyping.
本体广泛应用于数据库中，以实现数据标准化，提高数据质量、集成度和可比性。在针对不同用例定制的本体中，后组合用户定义术语一方面协调了标准化需求，另一方面兼顾了灵活性。在Breedbase（一个为基因组选择设计的植物育种数字生态系统）的许多实例中，目标是使用高度策划且严格的作物本体来捕获表型数据，同时适应植物育种者快速高效记录数据的特定要求。例如，后组合功能使用户能够调整本体术语，以适应特定且细致的用例，如对不同植物部位的重复测量和特殊样本制备技术。为实现这一目标，我们基于正交本体实现了一个后组合工具，为用户提供了引入额外表型粒度层次的能力，以适应独特的实验设计。后组合术语旨在供Breedbase实例中的所有育种计划重复使用，但不会导出到作物参考本体中。Breedbase用户可以跨各种类别（如植物解剖学、处理、时间事件和育种周期）进行术语后组合，从而生成高度特定的术语，以实现更准确的表型分析。
