On the Ontology Based Representation of Cell Lines
On the Ontology Based Representation of Cell Lines
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DOI：
10.1371/journal.pone.0048584
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发表时间：
2012-11-07
期刊：
影响因子：
3.7
通讯作者：
Knaup, Petra
中科院分区：
文献类型：
--
作者：
Ganzinger, Matthias;He, Shan;Knaup, Petra
细胞系经常用作生物医学分析和测定的高度标准化和可重复的体外模型。细胞系由操作描述其产物的数据库的细胞库分发。然而，不同细胞库的细胞系特性描述并不标准化。现有的细胞系相关本体主要集中在对细胞系名称的描述上，而没有涉及细胞系的来源和最佳生长条件等方面。这项工作的目标是开发一个本体，允许更全面的描述细胞系及其元数据，其中应涵盖细胞库提供的数据元素。这将为生物医学研究中细胞系和相应测定的标准化注释提供基础。此外，本体论将在未来的自动化评估，这样的测定和他们各自的协议的基础。为了实现这一点，广泛的细胞库数据库以及现有的本体进行了全面的分析。我们确定了现有的本体能够涵盖不同方面的细胞系域。然而，并非所有来自细胞库数据库的数据字段都可以映射到现有的本体。因此，我们创建了一个新的本体称为细胞培养本体（CCONT）整合现有的本体在可能的情况下。CCONT提供了细胞系鉴定、来源、细胞系特性、繁殖和检测等领域的课程。
Cell lines are frequently used as highly standardized and reproducible in vitro models for biomedical analyses and assays. Cell lines are distributed by cell banks that operate databases describing their products. However, the description of the cell lines' properties are not standardized across different cell banks. Existing cell line-related ontologies mostly focus on the description of the cell lines' names, but do not cover aspects like the origin or optimal growth conditions. The objective of this work is to develop an ontology that allows for a more comprehensive description of cell lines and their metadata, which should cover the data elements provided by cell banks. This will provide the basis for the standardized annotation of cell lines and corresponding assays in biomedical research. In addition, the ontology will be the foundation for automated evaluation of such assays and their respective protocols in the future. To accomplish this, a broad range of cell bank databases as well as existing ontologies were analyzed in a comprehensive manner. We identified existing ontologies capable of covering different aspects of the cell line domain. However, not all data fields derived from the cell banks' databases could be mapped to existing ontologies. As a result, we created a new ontology called cell culture ontology (CCONT) integrating existing ontologies where possible. CCONT provides classes from the areas of cell line identification, origin, cell line properties, propagation and tests performed.