Logical development of the cell ontology.
Logical development of the cell ontology.
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DOI：
10.1186/1471-2105-12-6
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发表时间：
2011-01-05
影响因子：
3
通讯作者：
Diehl AD
中科院分区：
文献类型：
--
作者：
Meehan TF;Masci AM;Abdulla A;Cowell LG;Blake JA;Mungall CJ;Diehl AD
细胞本体（CL）是用于表示体内细胞类型的本体。随着生物本体（如CL）复杂性的增长，它们变得越来越难以使用和维护。通过使本体中的信息可计算，我们可以使用自动推理机来检测错误并协助分类。在这里，我们报告在CL中的造血细胞类型的可计算的定义的生成。超过340个CL类的可计算定义已经使用属差方法创建。这些根据多个分类轴定义细胞类型，例如在细胞类型表面上发现的蛋白质复合物，细胞类型参与的生物过程或与细胞类型相关的表型特征。我们采用自动推理机来验证本体，并揭示手动策展中的错误。该过程的实施暴露了本体中需要新的细胞类型类以适应细胞标记物的物种特异性表达的区域。我们使用的推理机也推断新的关系内的CL，CL和贡献的本体之间。这种重构的本体可用于通过流式细胞术识别免疫细胞，支持涉及细胞的复杂生物学查询，并有助于基于与其他细胞类型的相似性生成关于细胞功能的新假设。可计算定义的使用增强了CL的开发，并支持OBO本体的互操作性。
The Cell Ontology (CL) is an ontology for the representation of in vivo cell types. As biological ontologies such as the CL grow in complexity, they become increasingly difficult to use and maintain. By making the information in the ontology computable, we can use automated reasoners to detect errors and assist with classification. Here we report on the generation of computable definitions for the hematopoietic cell types in the CL. Computable definitions for over 340 CL classes have been created using a genus-differentia approach. These define cell types according to multiple axes of classification such as the protein complexes found on the surface of a cell type, the biological processes participated in by a cell type, or the phenotypic characteristics associated with a cell type. We employed automated reasoners to verify the ontology and to reveal mistakes in manual curation. The implementation of this process exposed areas in the ontology where new cell type classes were needed to accommodate species-specific expression of cellular markers. Our use of reasoners also inferred new relationships within the CL, and between the CL and the contributing ontologies. This restructured ontology can be used to identify immune cells by flow cytometry, supports sophisticated biological queries involving cells, and helps generate new hypotheses about cell function based on similarities to other cell types. Use of computable definitions enhances the development of the CL and supports the interoperability of OBO ontologies.
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影响因子：
30.5
作者：
Le Bourhis, Lionel;Martin, Emmanuel;Lantz, Olivier
通讯作者：
Lantz, Olivier
转录因子 PLZF 指导 NKT 细胞谱系的效应程序。
影响因子：
32.4
作者：
Savage, Adam K.;Constantinides, Michael G.;Han, Jin;Picard, Damien;Martin, Emmanuel;Li, Bofeng;Lantz, Olivier;Bendelac, Albert
通讯作者：
Bendelac, Albert
影响因子：
46.9
作者：
Smith, Barry;Ashburner, Michael;Lewis, Suzanna
通讯作者：
Lewis, Suzanna
影响因子：
9.8
作者：
Gold MC;Cerri S;Smyk-Pearson S;Cansler ME;Vogt TM;Delepine J;Winata E;Swarbrick GM;Chua WJ;Yu YY;Lantz O;Cook MS;Null MD;Jacoby DB;Harriff MJ;Lewinsohn DA;Hansen TH;Lewinsohn DM
通讯作者：
Lewinsohn DM
影响因子：
7
作者：
Hill, DP;Blake, JA;Ringwald, M
通讯作者：
Ringwald, M