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.
Since the boom of biomedical big data studies, various big data processing technologies have been developed rapidly. As an important form of knowledge representation, ontology has become an important means for the utilization and integration of biomedical big data. The emergence of new technologies for ontology development has resulted in the generation of many biomedical ontologies by many ontology development communities. The Open Biological and Biomedical Ontology Foundry, an academic organization for bio-ontology developers, has provided a set of principles to guide community-based open ontology construction. The Open Biological and Biomedical Ontology Foundry have also built many widely used ontologies, such as Gene Ontology, Human Phenotype Ontology, and Chemical Entities of Biological Interest. Other various ontology repositories have also been created and used to support ontology reuse. Many efficient tools for ontology applications, such as data annotation and terms mapping, have also been developed. High quality ontologies are also being used to develop new methods and tools for biomedical data analysis. The applications of Gene Ontology and Human Phenotype Ontology for data analysis and integration in recent years are reviewed here. To promote the development and applications of biomedical ontologies in China, a research community, OntoChina, was founded recently. OntoChina aims to support the development of reference ontologies, especially bilingual and Chinese translated ontologies. OntoChina also encourages ontology developers to follow the Open Biological and Biomedical Ontology Foundry principles.
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