The cell line ontology-based representation, integration and analysis of cell lines used in China
Open accessAbstract
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.
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Six NV lines-BGC-803, BSG-823, GSE-1, HGC-7901, HGC-803 and MGC-823-were reported as obtained from the Chinese National Infrastructure of Cell Line Resource.
“Six NV cell lines (BGC-803, BSG-823, GSE-1, HGC-7901, HGC-803, MGC-823) were described as sourced from the Chinese National Infrastructure of Cell Line Resource (44)”
From Misspellings or “miscellings”—Non‐verifiable and unknown cell lines in cancer research publications (2024) · cites this paper as [44]
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Self-citation
- Authors
- Pan, H., Bian, X., Yang, S., He, Y., Yang, X., & Liu, Y.
- Affiliations
- Chinese Academy of Medical Sciences & Peking Union Medical College (CN)
- University of Michigan (US)
- Corresponding author
- Yang, Xiaolin
- Liu, Yuqin
- Venue
- BMC Bioinformatics
- Published
- 2019-04
- Volume
- 20
- Issue
- S5
- Pages
- 179-179
- ISSN
- 1471-2105 (ISSN-L)
- PMC
- PMC6509802
- OpenAlex
- W2941868238
- Cited by
- 20
- References
- 26
- Citations by year
- 2026: 1 · 2024: 1 · 2021: 7 · 2020: 8 · 2019: 3
- FWCI
- 1.48
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- BMC Bioinformatics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Deep Blue (University of Michigan) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- University of Pennsylvania
- University of Michigan
- Medical School, University of Michigan
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Physical Sciences › Computer Science › Artificial Intelligence › Semantic Web and Ontologies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- ontology mapping, ontology design patterns, disease models, model organisms, gene expression, protein expression, knowledge extraction
- MeSH terms
- Cell Line, China, Humans, User-Computer Interface, Databases, Factual, Biomedical Research, Biological Ontologies
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