Cell line ontology: Redesigning the cell line knowledgebase to aid integrative translational informatics

Sirarat Sarntivijai, Zuoshuang Xiang, Terrence F. Meehan, Alexander D. Diehl, Uma Vempati, Stephan Schurer, Chao Pang, James Malone, Helen Parkinson, Brian D. Athey, Yongqun He

Research output: Contribution to journalConference article

11 Scopus citations

Abstract

The Cell Line Ontology (CLO) is a community-based ontology in the domain of biological cell lines with a focus on permanent cell lines from culture collections. Upper ontology structures that frame the skeleton of CLO include the Basic Formal Ontology and Relation Ontology. Cell lines contained in CLO are associated with terms from other ontologies such as Cell Type Ontology, NCBI Taxonomy, and Ontology for Biomedical Investigation. A common design pattern for the cell line is used to model cell lines and their attributes, with the Jurkat cell line as an example. Currently CLO contains over 36.000 cell line entries obtained from ATCC, HyperCLDB, Coriell, and by manual curation. The cell lines are derived from 194 cell types, 656 anatomical entries, and 217 organisms. The OWL-based CLO is machine-readable and can be used in various applications.

Original languageEnglish (US)
Pages (from-to)25-32
Number of pages8
JournalCEUR Workshop Proceedings
Volume833
StatePublished - Dec 1 2011
Event2nd International Conference on Biomedical Ontology, ICBO 2011 - Buffalo, NY, United States
Duration: Jul 26 2011Jul 30 2011

Keywords

  • Cell line
  • Cell line ontology
  • CLO

ASJC Scopus subject areas

  • Computer Science(all)

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    Sarntivijai, S., Xiang, Z., Meehan, T. F., Diehl, A. D., Vempati, U., Schurer, S., Pang, C., Malone, J., Parkinson, H., Athey, B. D., & He, Y. (2011). Cell line ontology: Redesigning the cell line knowledgebase to aid integrative translational informatics. CEUR Workshop Proceedings, 833, 25-32.