CLO: The cell line ontology

Sirarat Sarntivijai,Bjoern Peters,Yue Liu,Terue Takatsuki,Kaoru Saijo,Jie Zheng,Helen Parkinson,Yongqun He,James Malone,Hiroshi Masuya,Yukio Nakamura,Zuoshuang Xiang,Matthew Brush ,Yuling Lin ,Pang Chen ,Thomas E Carey ,David J States ,Alexander D Diehl ,Uma D Vempati ,Brian D Athey ,Melissa Haendel ,Stephan C Schürer ,Terrence F Meehan ,Christian J Stoeckert ,Christopher J Mungall

doi:10.1186/2041-1480-5-37

Abstract

BackgroundCell lines have been widely used in biomedical research. The community-based Cell Line Ontology (CLO) is a member of the OBO Foundry library that covers the domain of cell lines. Since its publication two years ago, significant updates have been made, including new groups joining the CLO consortium, new cell line cells, upper level alignment with the Cell Ontology (CL) and the Ontology for Biomedical Investigation, and logical extensions.Construction and contentCollaboration among the CLO, CL, and OBI has established consensus definitions of cell line-specific terms such as ‘cell line’, ‘cell line cell’, ‘cell line culturing’, and ‘mortal’ vs. ‘immortal cell line cell’. A cell line is a genetically stable cultured cell population that contains individual cell line cells. The hierarchical structure of the CLO is built based on the hierarchy of the in vivo cell types defined in CL and tissue types (from which cell line cells are derived) defined in the UBERON cross-species anatomy ontology. The new hierarchical structure makes it easier to browse, query, and perform automated classification. We have recently added classes representing more than 2,000 cell line cells from the RIKEN BRC Cell Bank to CLO. Overall, the CLO now contains ~38,000 classes of specific cell line cells derived from over 200 in vivo cell types from various organisms.Utility and discussionThe CLO has been applied to different biomedical research studies. Example case studies include annotation and analysis of EBI ArrayExpress data, bioassays, and host-vaccine/pathogen interaction. CLO’s utility goes beyond a catalogue of cell line types. The alignment of the CLO with related ontologies combined with the use of ontological reasoners will support sophisticated inferencing to advance translational informatics development.

Highlights

Cell lines have been widely used in biomedical research
Based on the demands of Bioassay Ontology (BAO) bioassay modelling, extended parameters are being added to the Cell Line Ontology (CLO), including different sources of cell lines, cell modification methods, culture conditions, morphology, growth properties, short tandem repeat (STR) profiling and other properties that are relevant for cellular screening [19]
This paper introduces many use cases utilizing CLO ontological features

Summary

Background

Cell culturing dates back to as early as 1911 when Alexis Carrel attempted to grow living cells outside an organism. A cell line is supplied, maintained, or catalogued by a specific organization such as American Type Cell Culture (ATCC) that ‘has cell line repository role’ Since relation terms such as ‘supply, ‘own’, or ‘manage’ have not been fully developed in any ontology, we have created a CLO-specific relation reflecting this activity with the label ‘is in cell line repository’. This object property designates the representation of a particular cell line’s information in such repository. To solve these issues, the updated CLO includes a new multi-layer hierarchical structure based on welldefined design patterns, making it easier to browse, query, and perform automated classification. Other information such as cell line originators and registers are included in the CLO annotations for these new RIKEN cell lines

Utility and discussion

Discussion and perspectives

Conclusions