title: CLO: The cell line ontology.
abstract: BACKGROUND
  Cell 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.
  Collaboration 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.
  
  
  CONCLUSIONS
  The 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.
authors: US Food and Drug Administration, Silver Spring, MD, USA ; University of Michigan, Ann Arbor, MI, USA.
authors: Sirarat
authors: S
authors: Sarntivijai
authors: University of Michigan, Ann Arbor, MI, USA.
authors: Yu
authors: Y
authors: Lin
authors: University of Michigan, Ann Arbor, MI, USA.
authors: Zuoshuang
authors: Z
authors: Xiang
authors: European Molecular Biology Laboratory, (EMBL-EBI), Hinxton, UK.
authors: Terrence F
authors: TF
authors: Meehan
authors: University at Buffalo, Buffalo, NY, USA.
authors: Alexander D
authors: AD
authors: Diehl
authors: University of Miami, Miami, FL, USA.
authors: Uma D
authors: UD
authors: Vempati
authors: University of Miami, Miami, FL, USA.
authors: Stephan C
authors: SC
authors: Schürer
authors: University Medical Center Groningen, Groningen, Netherlands.
authors: Chao
authors: C
authors: Pang
authors: European Molecular Biology Laboratory, (EMBL-EBI), Hinxton, UK.
authors: James
authors: J
authors: Malone
authors: European Molecular Biology Laboratory, (EMBL-EBI), Hinxton, UK.
authors: Helen
authors: H
authors: Parkinson
authors: University of Michigan, Ann Arbor, MI, USA.
authors: Yue
authors: Y
authors: Liu
authors: RIKEN BioResource Center, Tsukuba, Japan.
authors: Terue
authors: T
authors: Takatsuki
authors: RIKEN BioResource Center, Tsukuba, Japan.
authors: Kaoru
authors: K
authors: Saijo
authors: RIKEN BioResource Center, Tsukuba, Japan.
authors: Hiroshi
authors: H
authors: Masuya
authors: RIKEN BioResource Center, Tsukuba, Japan.
authors: Yukio
authors: Y
authors: Nakamura
authors: Oregon Health & Science University, Portland, USA.
authors: Matthew H
authors: MH
authors: Brush
authors: Oregon Health & Science University, Portland, USA.
authors: Melissa A
authors: MA
authors: Haendel
authors: University of Pennsylvania, Philadelphia, USA.
authors: Jie
authors: J
authors: Zheng
authors: University of Pennsylvania, Philadelphia, USA.
authors: Christian J
authors: CJ
authors: Stoeckert
authors: La Jolla Institute for Allergy & Immunology, La Jolla, CA, USA.
authors: Bjoern
authors: B
authors: Peters
authors: Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
authors: Christopher J
authors: CJ
authors: Mungall
authors: University of Michigan, Ann Arbor, MI, USA.
authors: Thomas E
authors: TE
authors: Carey
authors: OncProTech LLC, Ann Arbor, MI, USA.
authors: David J
authors: DJ
authors: States
authors: University of Michigan, Ann Arbor, MI, USA.
authors: Brian D
authors: BD
authors: Athey
authors: University of Michigan, Ann Arbor, MI, USA.
authors: Yongqun
authors: Y
authors: He
keywords: Anatomy; Cell line; Cell line cell; Cell line cell culturing; Immortal cell line cell; Mortal cell line cell