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首页> 外文期刊>Journal of Biomedical Semantics >Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD
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Rat Strain Ontology: structured controlled vocabulary designed to facilitate access to strain data at RGD

机译：大鼠应变本体：结构化受控词汇表，旨在促进在RGD中访问应变数据

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Background The Rat Genome Database (RGD) ( http://rgd.mcw.edu/ webcite) is the premier site for comprehensive data on the different strains of the laboratory rat (Rattus norvegicus). The strain data are collected from various publications, direct submissions from individual researchers, and rat providers worldwide. Rat strain, substrain designation and nomenclature follow the Guidelines for Nomenclature of Mouse and Rat Strains, instituted by the International Committee on Standardized Genetic Nomenclature for Mice. While symbols and names aid in identifying strains correctly, the flat nature of this information prohibits easy search and retrieval, as well as other data mining functions. In order to improve these functionalities, particularly in ontology-based tools, the Rat Strain Ontology (RS) was developed. Results The Rat Strain Ontology (RS) reflects the breeding history, parental background, and genetic manipulation of rat strains. This controlled vocabulary organizes strains by type: inbred, outbred, chromosome altered, congenic, mutant and so on. In addition, under the chromosome altered category, strains are organized by chromosome, and further by type of manipulations, such as mutant or congenic. This allows users to easily retrieve strains of interest with modifications in specific genomic regions. The ontology was developed using the Open Biological and Biomedical Ontology (OBO) file format, and is organized on the Directed Acyclic Graph (DAG) structure. Rat Strain Ontology IDs are included as part of the strain report (RS: ######). Conclusions As rat researchers are often unaware of the number of substrains or altered strains within a breeding line, this vocabulary now provides an easy way to retrieve all substrains and accompanying information. Its usefulness is particularly evident in tools such as the PhenoMiner at RGD, where users can now easily retrieve phenotype measurement data for related strains, strains with similar backgrounds or those with similar introgressed regions. This controlled vocabulary also allows better retrieval and filtering for QTLs and in genomic tools such as the GViewer. The Rat Strain Ontology has been incorporated into the RGD Ontology Browser ( http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=RS:0000457#s webcite) and is available through the National Center for Biomedical Ontology ( http://bioportal.bioontology.org/ontologies/1150 webcite) or the RGD ftp site ( ftp://rgd.mcw.edu/pub/ontology/rat_strain/ webcite).
机译：背景技术大鼠基因组数据库（RGD）（http://rgd.mcw.edu/ webcite）是有关实验室大鼠（Rattus norvegicus）不同品系的全面数据的首要站点。品系数据收集自各种出版物，个人研究人员和全球老鼠提供者的直接投稿。大鼠品系，亚菌株名称和命名遵循小鼠标准化遗传命名国际委员会制定的《小鼠和大鼠品系命名准则》。虽然符号和名称有助于正确识别应变，但是此信息的扁平性质禁止轻松搜索和检索以及其他数据挖掘功能。为了改善这些功能，特别是在基于本体的工具中，开发了大鼠应变本体论（RS）。结果大鼠品系本体（RS）反映了大鼠品系的繁殖历史，亲本背景和遗传操作。这种受控的词汇按类型组织品系：近交，近交，染色体改变，同基因，突变等。另外，在染色体改变的类别下，菌株按染色体组织，进一步按操纵类型组织，例如突变体或同基因。这使用户可以轻松检索特定基因组区域中经过修饰的目标菌株。本体是使用开放生物学和生物医学本体（OBO）文件格式开发的，并以有向无环图（DAG）结构进行组织。大鼠应变本体ID包含在应变报告中（RS：######）。结论由于大鼠研究人员通常不知道繁殖系中亚菌株或突变菌株的数量，因此该词汇表现在提供了一种检索所有亚菌株和随附信息的简便方法。它的用途在RGD的PhenoMiner等工具中尤为明显，用户现在可以轻松检索相关菌株，背景相似或渗入区域相似的菌株的表型测量数据。这种受控词汇还可以更好地对QTL和基因组工具（如GViewer）进行检索和过滤。大鼠应变本体已整合到RGD本体浏览器（http://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=RS:0000457#s网站上），可通过国家生物医学本体中心获得（http://bioportal.bioontology.org/ontologies/1150网站）或RGD ftp网站（ftp://rgd.mcw.edu/pub/ontology/rat_strain/ webcite）。

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