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

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.

Misspellings or “miscellings”-non-verifiable cell lines in cancer research publications

“…In papers where NV identifiers were referred to as independent cell lines, 4 NV cell lines (BGC-803, GSE-1, HGC-803, MGC-823) were described as sourced from the American Type Culture Collection (ATCC) (42). 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 (43), and 3 NV cell lines (BGC-803, GSE-1, MGC-823) were described as sourced from the China Center for Type Culture Collection (38–41). Searching the online catalogues of these 3 repositories did not identify the claimed NV identifiers or cell lines (Table S5).…”

Misspellings or “miscellings”—Non‐verifiable and unknown cell lines in cancer research publications

“…In papers where NV identifiers were referred to as independent cell lines, four NV cell lines (BGC‐803, GSE‐1, HGC‐803, and MGC‐823) were described as sourced from the American Type Culture Collection (ATCC) 43 . Six NV cell lines (BGC‐803, BSG‐823, GSE‐1, HGC‐7901, HGC‐803, and MGC‐823) were described as sourced from the Chinese National Infrastructure of Cell Line Resource, 44 and three NV cell lines (BGC‐803, GSE‐1, and MGC‐823) were described as sourced from the China Center for Type Culture Collection 38–41 . Searching the online catalogs of these three repositories did not identify the claimed NV identifiers or cell lines (Table S5).…”

TCDO: A Community-Based Ontology for Integrative Representation and Analysis of Traditional Chinese Drugs and Their Properties

“…Since TCDs are originally developed in China, we have also added Chinese to annotate the TCDs in TCDO. The method previously used for English-Chinese translation in the Cell Line Ontology (CLO) study [ 26 ] was also used for the differential representation. Specifically, the English term and Chinese term share the same ontology identifier but have their specific annotations.…”