Smith Jennifer R, Park Carissa A, Nigam Rajni, Laulederkind Stanley Jf, Hayman G Thomas, Wang Shur-Jen, Lowry Timothy F, Petri Victoria, Pons Jeff De, Tutaj Marek, Liu Weisong, Worthey Elizabeth A, Shimoyama Mary, Dwinell Melinda R
Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI, USA.
J Biomed Semantics. 2013 Oct 8;4(1):26. doi: 10.1186/2041-1480-4-26.
The Clinical Measurement Ontology (CMO), Measurement Method Ontology (MMO), and Experimental Condition Ontology (XCO) were originally developed at the Rat Genome Database (RGD) to standardize quantitative rat phenotype data in order to integrate results from multiple studies into the PhenoMiner database and data mining tool. These ontologies provide the framework for presenting what was measured, how it was measured, and under what conditions it was measured.
There has been a continuing expansion of subdomains in each ontology with a parallel 2-3 fold increase in the total number of terms, substantially increasing the size and improving the scope of the ontologies. The proportion of terms with textual definitions has increased from ~60% to over 80% with greater synchronization of format and content throughout the three ontologies. Representation of definition source Uniform Resource Identifiers (URI) has been standardized, including the removal of all non-URI characters, and systematic versioning of all ontology files has been implemented. The continued expansion and success of these ontologies has facilitated the integration of more than 60,000 records into the RGD PhenoMiner database. In addition, new applications of these ontologies, such as annotation of Quantitative Trait Loci (QTL), have been added at the sites actively using them, including RGD and the Animal QTL Database.
The improvements to these three ontologies have been substantial, and development is ongoing. New terms and expansions to the ontologies continue to be added as a result of active curation efforts at RGD and the Animal QTL database. Use of these vocabularies to standardize data representation for quantitative phenotypes and quantitative trait loci across databases for multiple species has demonstrated their utility for integrating diverse data types from multiple sources. These ontologies are freely available for download and use from the NCBO BioPortal website at http://bioportal.bioontology.org/ontologies/1583 (CMO), http://bioportal.bioontology.org/ontologies/1584 (MMO), and http://bioportal.bioontology.org/ontologies/1585 (XCO), or from the RGD ftp site at ftp://rgd.mcw.edu/pub/ontology/.
临床测量本体（CMO）、测量方法本体（MMO）和实验条件本体（XCO）最初是在大鼠基因组数据库（RGD）开发的，用于标准化大鼠定量表型数据，以便将多项研究的结果整合到PhenoMiner数据库和数据挖掘工具中。这些本体为展示测量的内容、测量方式以及测量条件提供了框架。
每个本体的子领域持续扩展，术语总数相应增加了2至3倍，极大地扩大了本体的规模并拓展了其范围。带有文本定义的术语比例从约60%增加到了80%以上，并且在这三个本体中格式和内容的同步性更强。定义源统一资源标识符（URI）的表示方式已标准化，包括去除所有非URI字符，并且已对所有本体文件实施了系统版本控制。这些本体的持续扩展和成功推动了超过60,000条记录整合到RGD PhenoMiner数据库中。此外，在积极使用这些本体的网站（包括RGD和动物QTL数据库）上，增添了这些本体的新应用，如数量性状基因座（QTL）注释。
这三个本体已得到实质性改进，且开发工作仍在进行。由于RGD和动物QTL数据库的积极管理工作，新术语和本体扩展仍在不断添加。使用这些词汇表来标准化跨多个物种数据库的定量表型和数量性状基因座的数据表示，已证明它们在整合来自多个来源的不同数据类型方面很有用。这些本体可从NCBO生物门户网站（http://bioportal.bioontology.org/ontologies/1583（CMO）、http://bioportal.bioontology.org/ontologies/1584（MMO）和http://bioportal.bioontology.org/ontologies/1585（XCO））或RGD ftp站点（ftp://rgd.mcw.edu/pub/ontology/）免费下载和使用。
