cROP: Common Reference Ontologies and Applications for Plant Biology

首席研究员：Dennis W. Stevenson（纽约植物园），Sinisa Todorovic和Eugene Zhang（俄勒冈州立大学），Elizabeth Arnaud（国际生物多样性/CGIAR，法国），Christopher Mungall（劳伦斯伯克利国家实验室）高级人员：Barry Smith（布法罗大学），Georgios V. Gkoutos和John Doonan（英国阿伯里斯特威斯大学）。植物研究人员必须能够从广泛的在线数据库中快速搜索遗传信息。不幸的是，最初提供数据的研究人员和分析数据的研究人员经常使用不一致的术语，这使得关键字搜索的效率降低。为了解决这个问题，该项目将制定通用的基因注释标准和植物生物学和疾病的通用词汇。它还将为创建和管理这些术语制定标准和工作流程。此外，它将开发一个门户网站和数据仓库来承载这些共享词汇表和相关注释信息，以使更广泛的植物社区能够访问。该项目将创建一个集中的平台，在这个平台上，植物的参考本体将被用来访问尖端的数据资源，以分析植物的性状、表型、疾病、基因组、遗传多样性和基因表达数据，涵盖广泛的植物物种。它将使研究人员能够建立假设，发现、查询和分析植物基因组学数据，以解决否则无法处理的复杂问题。最终，植物育种者可以利用这些信息培育出产量更高、营养更丰富、能承受压力和抗病的作物。作为一个教育组成部分，项目团队将接触到K-12和本科生以及植物研究界。通过这个项目，科学界将能够通过一个协作网站向基因库提供基因注释数据，该网站还将提供多种方法来分析和下载数据和其他资源。

PI: Pankaj Jaiswal (Oregon State University)CoPIs: Dennis W. Stevenson (New York Botanical Garden), Sinisa Todorovic and Eugene Zhang (Oregon State University), Elizabeth Arnaud (Bioversity International/CGIAR, France), Christopher Mungall (Lawrence Berkeley National Laboratory) Senior Personnel: Barry Smith (University at Buffalo), Georgios V. Gkoutos and John Doonan (University of Aberystwyth, UK).Plant researchers must be able to quickly search for genetic information from a wide range of online databases. Unfortunately, the researchers who originally provided the data and those who are analyzing it often use inconsistent terminology, making keyword searches less effective. To remedy this problem, the project will develop common gene annotation standards and a universal vocabulary of plant biology and diseases. It will also draw up standards and workflows for the creation and curation of such terminology. Additionally, it will develop a web portal and data warehouse to host this shared vocabulary and related annotation information to enable access by the broader plant community.This project will create a centralized platform where reference ontologies for plants will be used to access cutting-edge data resources for analyzing plant traits, phenotypes, diseases, genomes, genetic diversity and gene expression data across a wide range of plant species. It will empower researchers to build hypotheses and discover, query, and analyze plant genomics data to address complex questions that would not otherwise be tractable. Ultimately, plant breeders can use this information to develop higher-yielding, more nutritious crops that tolerate stress and resist disease. As an educational component, the project team will reach out to K-12 and undergraduate students and the plant research community. Through this project, the scientific community will be able to contribute genetic annotation data to the warehouse via a collaborative web site that will also provide multiple ways to analyze and download data and other resources.