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Comparison, alignment, and synchronization of cell line information between CLO and EFO
- Source :
- BMC Bioinformatics, BMC Bioinformatics, Vol 18, Iss S17, Pp 25-33 (2017)
- Publication Year :
- 2017
- Publisher :
- Springer Science and Business Media LLC, 2017.
-
Abstract
- Background 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. 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. Results In 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. Conclusion Our 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. Electronic supplementary material The online version of this article (10.1186/s12859-017-1979-z) contains supplementary material, which is available to authorized users.
- Subjects :
- 0301 basic medicine
Databases, Factual
Experimental factor ontology
Computer science
Ontology (information science)
lcsh:Computer applications to medicine. Medical informatics
computer.software_genre
Biochemistry
Cell Line
Cell Physiological Phenomena
03 medical and health sciences
0302 clinical medicine
Text mining
Structural Biology
Data Mining
Humans
lcsh:QH301-705.5
Molecular Biology
Cell line ontology
business.industry
Gene Expression Profiling
Research
Applied Mathematics
Design pattern
Computational Biology
Biological Ontologies
Semantics
Computer Science Applications
Data mapping
030104 developmental biology
lcsh:Biology (General)
Cellosaurus
030220 oncology & carcinogenesis
Software design pattern
Ontology
lcsh:R858-859.7
Data integration
Data mining
business
computer
Algorithms
Subjects
Details
- ISSN :
- 14712105
- Volume :
- 18
- Database :
- OpenAIRE
- Journal :
- BMC Bioinformatics
- Accession number :
- edsair.doi.dedup.....21d7c8de7d58e7efe561d10a2ae90f15