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LeGOO: An Expertized Knowledge Database for the Model Legume Medicago truncatula.
Plant & Cell Physiology ( IF 3.9 ) Pub Date : 2020-01-01 , DOI: 10.1093/pcp/pcz177
Sï Bastien Carrï Re 1 , Marion Verdenaud 2 , Clare Gough 1 , Jï Rï Me Gouzy 1 , Pascal Gamas 1
Affiliation  

Medicago truncatula was proposed, about three decades ago, as a model legume to study the Rhizobium-legume symbiosis. It has now been adopted to study a wide range of biological questions, including various developmental processes (in particular root, symbiotic nodule and seed development), symbiotic (nitrogen-fixing and arbuscular mycorrhizal endosymbioses) and pathogenic interactions, as well as responses to abiotic stress. With a number of tools and resources set up in M. truncatula for omics, genetics and reverse genetics approaches, massive amounts of data have been produced, as well as four genome sequence releases. Many of these data were generated with heterogeneous tools, notably for transcriptomics studies, and are consequently difficult to integrate. This issue is addressed by the LeGOO (for Legume Graph-Oriented Organizer) knowledge base (https://www.legoo.org), which finds the correspondence between the multiple identifiers of the same gene. Furthermore, an important goal of LeGOO is to collect and represent biological information from peer-reviewed publications, whatever the technical approaches used to obtain this information. The information is modeled in a graph-oriented database, which enables flexible representation, with currently over 200,000 relations retrieved from 298 publications. LeGOO also provides the user with mining tools, including links to the Mt5.0 genome browser and associated information (on gene functional annotation, expression, methylome, natural diversity and available insertion mutants), as well as tools to navigate through different model species. LeGOO is, therefore, an innovative database that will be useful to the Medicago and legume community to better exploit the wealth of data produced on this model species.

中文翻译:

LeGOO:豆科植物紫花苜蓿模型的专业知识数据库。

大约三十年前,有人提出将紫花苜蓿作为研究豆科植物根瘤菌共生的模型豆科植物。现在已被采用来研究广泛的生物学问题,包括各种发育过程(特别是根,共生结节和种子发育),共生(固氮和丛枝菌根内生共生酶)和致病性相互作用以及对非生物反应压力。在truncatula中建立了许多用于组学,遗传学和反向遗传学方法的工具和资源,已产生了大量数据,并发布了四个基因组序列。其中许多数据是使用异构工具生成的,尤其是用于转录组学研究的数据,因此难以整合。LeGOO(面向豆类图的组织者)知识库(https://www.legoo.org)解决了此问题,该知识库可找到同一基因的多个标识符之间的对应关系。此外,LeGOO的一个重要目标是从经过同行评审的出版物中收集和代表生物学信息,而无论采用何种技术方法来获取这些信息。该信息在面向图形的数据库中建模,该数据库可实现灵活的表示形式,目前从298种出版物中检索了20万种以上的关系。LeGOO还为用户提供了挖掘工具,包括指向Mt5.0基因组浏览器的链接和相关信息(有关基因功能注释,表达,甲基化组,自然多样性和可用的插入突变体),以及用于浏览不同模型物种的工具。乐高是
更新日期:2020-01-24
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