The Cell Line Ontology integration and analysis of the knowledge of LINCS cell lines

Edison Ong, Jiangan Xie, Zhaohui Ni, Qingping Liu, Yu Lin, Vasileios Stathias, Caty Chung, Stephan C Schuerer, Yongqun He

Research output: Contribution to journalArticle

Abstract

Cell lines are crucial to study molecular signatures and pathways, and are widely used in the NIH Common Fund LINCS project. The Cell Line Ontology (CLO) is a community-based ontology representing and classifying cell lines from different resources. To better serve the LINCS research community, from the LINCS Data Portal and ChEMBL, we identified 1,097 LINCS cell lines, among which 717 cell lines were associated with 121 cancer types, and 352 cell line terms did not exist in CLO. To harmonize LINCS cell line representation and CLO, CLO design patterns were slightly updated to add new information of the LINCS cell lines including different database cross-reference IDs. A new shortcut relation was generated to directly link a cell line to the disease of the patient from whom the cell line was originated. After new LINCS cell lines and related information were added to CLO, a CLO subset/view (LINCS-CLOview) of LINCS cell lines was generated and analyzed to identify scientific insights into these LINCS cell lines. This study provides a first time use case on how CLO can be updated and applied to support cell line research from a specific research community or project initiative.

Original languageEnglish (US)
JournalCEUR Workshop Proceedings
Volume1747
StatePublished - 2016

Keywords

  • Cell
  • Cell line
  • ChEMBL
  • CLO
  • LINCS
  • Ontology

ASJC Scopus subject areas

  • Computer Science(all)

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  • Cite this

    Ong, E., Xie, J., Ni, Z., Liu, Q., Lin, Y., Stathias, V., Chung, C., Schuerer, S. C., & He, Y. (2016). The Cell Line Ontology integration and analysis of the knowledge of LINCS cell lines. CEUR Workshop Proceedings, 1747.