Phenosite: a web database integrating the mouse phenotyping platform and the experimental procedures in mice.
Phenosite: a web database integrating the mouse phenotyping platform and the experimental procedures in mice.
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DOI：
10.1142/s0219720007003168
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发表时间：
2007-12-01
影响因子：
1
通讯作者：
Shiroishi, Toshihiko
中科院分区：
文献类型：
--
作者：
Masuya, Hiroshi;Yoshikawa, Sumi;Shiroishi, Toshihiko
最近，一些合作的大规模小鼠诱变计划已经启动。这些计划旨在更好地了解所有单个编码基因的作用以及这些基因参与的生物系统。在设施/研究所之间共享表型数据的国际努力中，期望可靠地整合从不同表型平台获得的信息。由于特定表型的定义通常取决于对概念的默契理解，而不同设施之间的概念往往会有所不同，因此有必要根据测定结果的明确证据来定义表型。我们开发了一个名为PhenoSITE（Phenome Semantics Information with Terminology of Experiments：http：//www.gsc.riken.jp/Mouse/）的网站，其中我们试图使用基于实验证据的方法整合表型相关信息。该网站的功能包括：（1）我们表型分析平台的基线数据库;（2）将国际表型定义与我们表型分析平台中使用的实验术语相关联的本体;（3）表型分析平台标准化操作程序的数据库;以及（4）使用RIKEN GSC大规模诱变程序产生的数据的小鼠突变体数据库。我们开发了两种类型的综合浏览器，以提高突变资源信息的可访问性。一个视图描绘了基于本体的分类和每个基因的染色体位置的矩阵视图;另一个视图描绘了实验方案、基线数据和突变信息的本体介导的整合。这些方法完全依赖于基于实验的证据，确保来自不同表型平台的综合数据的可靠性。
Recently, a number of collaborative large-scale mouse mutagenesis programs have been launched. These programs aim for a better understanding of the roles of all individual coding genes and the biological systems in which these genes participate. In international efforts to share phenotypic data among facilities/institutes, it is desirable to integrate information obtained from different phenotypic platforms reliably. Since the definitions of specific phenotypes often depend on a tacit understanding of concepts that tends to vary among different facilities, it is necessary to define phenotypes based on the explicit evidence of assay results. We have developed a website termed PhenoSITE (Phenome Semantics Information with Terminology of Experiments: http://www.gsc.riken.jp/Mouse/), in which we are trying to integrate phenotype-related information using an experimental-evidence-based approach. The site's features include (1) a baseline database for our phenotyping platform; (2) an ontology associating international phenotypic definitions with experimental terminologies used in our phenotyping platform; (3) a database for standardized operation procedures of the phenotyping platform; and (4) a database for mouse mutants using data produced from the large-scale mutagenesis program at RIKEN GSC. We have developed two types of integrated viewers to enhance the accessibility to mutant resource information. One viewer depicts a matrix view of the ontology-based classification and chromosomal location of each gene; the other depicts ontology-mediated integration of experimental protocols, baseline data, and mutant information. These approaches rely entirely upon experiment-based evidence, ensuring the reliability of the integrated data from different phenotyping platforms.