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BMC Bioinformatics. 2019 Apr 25;20(Suppl 5):179. doi: 10.1186/s12859-019-2724-6.

The cell line ontology-based representation, integration and analysis of cell lines used in China.

Author information

1
Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China.
2
University of Michigan Medical School, Ann Arbor, MI 48109, USA.
3
Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China. yangxl@pumc.edu.cn.
4
Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing, China. liuyuqin@pumc.edu.cn.

Abstract

BACKGROUND:

The Chinese National Infrastructure of Cell Line stores and distributes cell lines for biomedical research in China. This study aims to represent and integrate the information of NICR cell lines into the community-based Cell Line Ontology (CLO).

RESULTS:

We have aligned, represented, and added all identified 2704 cell line cells in NICR to CLO. We also proposed new ontology design patterns to represent the usage of cell line cells as disease models by inducing tumor formation in model organisms, and the relations between cell line cells and their expressed or overexpressed genes or proteins. The resulting CLO-NICR ontology also includes the Chinese representation of the NICR cell line information. CLO-NICR was merged into the general CLO. To serve the cell research community in China, the Chinese version of CLO-NICR was also generated and deposited in the OntoChina ontology repository. The usage of CLO-NICR was demonstrated by DL query and knowledge extraction.

CONCLUSIONS:

In summary, all identified cell lines from NICR are represented by the semantics framework of CLO and incorporated into CLO as a most recent update. We also generated a CLO-NICR and its Chinese view (CLO-NICR-Cv). The development of CLO-NICR and CLO-NIC-Cv allows the integration of the cell lines from NICR into the community-based CLO ontology and provides an integrative platform to support different applications of CLO in China.

KEYWORDS:

Cell line cell; Cell line ontology; Data integration; Ontology

PMID:
31272367
PMCID:
PMC6509802
DOI:
10.1186/s12859-019-2724-6
[Indexed for MEDLINE]
Free PMC Article

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