Comparison, alignment, and synchronization of cell line information between CLO and EFO

Edison Ong,Yongqun He,Sirarat Sarntivijai,Simon Jupp,Helen Parkinson

doi:10.1186/s12859-017-1979-z

Edison Ong, Yongqun He + Show 3 more

Open Access

https://doi.org/10.1186/s12859-017-1979-z

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Abstract

BackgroundThe Experimental Factor Ontology (EFO) is an application ontology driven by experimental variables including cell lines to organize and describe the diverse experimental variables and data resided in the EMBL-EBI resources. The Cell Line Ontology (CLO) is an OBO community-based ontology that contains information of immortalized cell lines and relevant experimental components. EFO integrates and extends ontologies from the bio-ontology community to drive a number of practical applications. It is desirable that the community shares design patterns and therefore that EFO reuses the cell line representation from the Cell Line Ontology (CLO). There are, however, challenges to be addressed when developing a common ontology design pattern for representing cell lines in both EFO and CLO.ResultsIn this study, we developed a strategy to compare and map cell line terms between EFO and CLO. We examined Cellosaurus resources for EFO-CLO cross-references. Text labels of cell lines from both ontologies were verified by biological information axiomatized in each source. The study resulted in the identification 873 EFO-CLO aligned and 344 EFO unique immortalized permanent cell lines. All of these cell lines were updated to CLO and the cell line related information was merged. A design pattern that integrates EFO and CLO was also developed.ConclusionOur study compared, aligned, and synchronized the cell line information between CLO and EFO. The final updated CLO will be examined as the candidate ontology to import and replace eligible EFO cell line classes thereby supporting the interoperability in the bio-ontology domain. Our mapping pipeline illustrates the use of ontology in aiding biological data standardization and integration through the biological and semantics content of cell lines.

Highlights

The Experimental Factor Ontology (EFO) is an application ontology driven by experimental variables including cell lines to organize and describe the diverse experimental variables and data resided in the European Molecular Biology Laboratory (EMBL)-European Bioinformatics Institute (EBI) resources
The Experimental Factor Ontology (EFO) is a datadriven biomedical application ontology developed by the European Bioinformatics Institute (EMBL-EBI) to organize the diverse experimental variables needed to describe data resided in the EMBL-EBI resources, including cell line data [1]
There were 874 EFO-Cell Line Ontology (CLO) mapped cell lines aligned and cell line related information would be merged into CLO and 344 EFO unique immortalized permanent cell lines added to CLO (Additional file 2: Table S2)

Summary

Introduction

The Experimental Factor Ontology (EFO) is an application ontology driven by experimental variables including cell lines to organize and describe the diverse experimental variables and data resided in the EMBL-EBI resources. It is desirable that the community shares design patterns and that EFO reuses the cell line representation from the Cell Line Ontology (CLO). There are, challenges to be addressed when developing a common ontology design pattern for representing cell lines in both EFO and CLO. The Experimental Factor Ontology (EFO) is a datadriven biomedical application ontology developed by the European Bioinformatics Institute (EMBL-EBI) to organize the diverse experimental variables needed to describe data resided in the EMBL-EBI resources, including cell line data [1]. Cellosaurus is a manually curated knowledgebase of cell line resources for biomedical research, and it provides high quality cross references to other resources including EFO and CLO, which can be used to facilitate cross-linking between the two resources

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