Comparison, alignment, and synchronization of cell line information between CLO and EFO
Edison Ong1,2, Sirarat Sarntivijai2, Simon Jupp2
1Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
BMC Bioinformatics
|January 12, 2018
Summary
The Experimental Factor Ontology (EFO) and Cell Line Ontology (CLO) were aligned to improve biological data standardization. This study mapped cell line terms, identified common and unique cell lines, and developed an integrated design pattern for enhanced interoperability.
Area of Science:
- Bioinformatics
- Ontology Engineering
- Genomics
Background:
- The Experimental Factor Ontology (EFO) organizes experimental variables, including cell lines, for EMBL-EBI resources.
- The Cell Line Ontology (CLO) provides information on immortalized cell lines and experimental components.
- Integrating EFO and CLO requires addressing challenges in representing cell lines consistently.
Purpose of the Study:
- To develop a strategy for comparing and mapping cell line terms between EFO and CLO.
- To create a common ontology design pattern for cell line representation.
- To enhance interoperability within the bio-ontology domain.
Main Methods:
- Compared and mapped cell line terms between EFO and CLO.
- Utilized Cellosaurus resources for cross-referencing.
- Verified cell line labels using biological information from each source.
Main Results:
- Identified 873 EFO-CLO aligned and 344 EFO unique immortalized cell lines.
- Updated CLO with aligned cell line information and merged related data.
- Developed an integrated design pattern for EFO and CLO.
Conclusions:
- Successfully compared, aligned, and synchronized cell line information between CLO and EFO.
- The updated CLO is a candidate for replacing EFO cell line classes to support interoperability.
- The mapping pipeline demonstrates ontology's role in biological data standardization and integration.
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