Usage of cell nomenclature in biomedical literature
License
http://creativecommons.org/licenses/by/4.0/Type
ArticleAuthors
Kafkas, SenaySarntivijai, Sirarat
Hoehndorf, Robert
KAUST Department
Bio-Ontology Research Group (BORG)Computational Bioscience Research Center (CBRC)
Computer Science Program
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Online Publication Date
2017-12-21Print Publication Date
2017-12Date
2017-12-21Abstract
Background Cell lines and cell types are extensively studied in biomedical research yielding to a significant amount of publications each year. Identifying cell lines and cell types precisely in publications is crucial for science reproducibility and knowledge integration. There are efforts for standardisation of the cell nomenclature based on ontology development to support FAIR principles of the cell knowledge. However, it is important to analyse the usage of cell nomenclature in publications at a large scale for understanding the level of uptake of cell nomenclature in literature by scientists. In this study, we analyse the usage of cell nomenclature, both in Vivo, and in Vitro in biomedical literature by using text mining methods and present our results. Results We identified 59% of the cell type classes in the Cell Ontology and 13% of the cell line classes in the Cell Line Ontology in the literature. Our analysis showed that cell line nomenclature is much more ambiguous compared to the cell type nomenclature. However, trends indicate that standardised nomenclature for cell lines and cell types are being increasingly used in publications by the scientists. Conclusions Our findings provide an insight to understand how experimental cells are described in publications and may allow for an improved standardisation of cell type and cell line nomenclature as well as can be utilised to develop efficient text mining applications on cell types and cell lines. All data generated in this study is available at https://github.com/shenay/CellNomenclatureStudy.Citation
Kafkas Åž, Sarntivijai S, Hoehndorf R (2017) Usage of cell nomenclature in biomedical literature. BMC Bioinformatics 18. Available: http://dx.doi.org/10.1186/s12859-017-1978-0.Acknowledgements
This work is supported by Wellcome Trust 108,437/Z/15/Z for Single Cell Expression Atlas, and the Chan Zuckerberg Initiative (CZI) for support of the Data Coordination Platform of the Human Cell Atlas. The funding body didn’t have any role in the design or conclusions of this study. Publication cost of this study was supported by funding from King Abdullah University of Science and Technology (KAUST).Publisher
Springer NatureJournal
BMC BioinformaticsDOI
10.1186/s12859-017-1978-0Additional Links
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1978-0Relations
Is Supplemented By:- [Software]
Title: shenay/CellNomenclatureStudy: This pipleine annotates open access full text articles (dictionary based approach). Publication Date: 2017-08-16. github: shenay/CellNomenclatureStudy Handle: 10754/666982