The MGED Ontology: a resource for semantics-based description of microarray experiments
The MGED Ontology: a resource for semantics-based description of microarray experiments
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DOI：
10.1093/bioinformatics/btl005
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发表时间：
2006-04-01
期刊：
影响因子：
5.8
通讯作者：
Stoeckert, CJ
中科院分区：
文献类型：
--
作者：
Whetzel, PL;Parkinson, H;Stoeckert, CJ
动机：大量微阵列数据的产生以及共享这些数据的需求为数据管理和注释带来了挑战，并突出了对标准的需求。迈阿密指定描述微阵列实验和微阵列基因表达对象模型（MAGE-OM）所需的最低信息，并且由此产生的MAGE-ML提供了一种用于数据交换的数据表示的机制，但是需要进行数据交换的通用术语来支持数据交换这些标准：在这里我们描述了由微阵列基因表达数据（MGED）社会的本体论工作组开发的MGED本体论（MO）。 MO提供了从实验和阵列布局设计到生物样品的制备以及用于杂交RNA并分析数据的协议的术语，以注释微阵列实验的各个方面。 MO的开发是为了根据迈阿密指南提供注释实验的术语，即提供语义，以根据迈阿密的概念来描述微阵列实验。 MO不会尝试纳入现有本体论的术语，例如那些处理解剖零件或发育阶段术语但提供了一个在其他本体论中参考术语的框架，因此有助于在微阵列数据注释中使用本体。
Motivation: The generation of large amounts of microarray data and the need to share these data bring challenges for both data management and annotation and highlights the need for standards. MIAME specifies the minimum information needed to describe a microarray experiment and the Microarray Gene Expression Object Model (MAGE-OM) and resulting MAGE-ML provide a mechanism to standardize data representation for data exchange, however a common terminology for data annotation is needed to support these standards.Results: Here we describe the MGED Ontology (MO) developed by the Ontology Working Group of the Microarray Gene Expression Data (MGED) Society. The MO provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. The MO was developed to provide terms for annotating experiments in line with the MIAME guidelines, i.e. to provide the semantics to describe a microarray experiment according to the concepts specified in MIAME. The MO does not attempt to incorporate terms from existing ontologies, e.g. those that deal with anatomical parts or developmental stages terms, but provides a framework to reference terms in other ontologies and therefore facilitates the use of ontologies in microarray data annotation.