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Rationalized development of a campus-wide cell line dataset for implementation in the biobank LIMS system at Bioresource center Ghent

Veronique T'Joen (UGent) , Lieven Vaneeckhaute (UGent) , Sara Priem (UGent) , Steven Van Woensel (UGent) , Sofie Bekaert (UGent) , Elke Berneel (UGent) and Catherine Van Der Straeten (UGent)
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Abstract
The Bioresource center Ghent is the central hospital-integrated biobank of Ghent University Hospital. Our mission is to facilitate translational biomedical research by collecting, storing and providing high quality biospecimens to researchers. Several of our biobank partners store large amounts of cell lines. As cell lines are highly important both in basic research and preclinical screening phases, good annotation, authentication, and quality of these cell lines is pivotal in translational biomedical science. A Biobank Information Management System (BIMS) was implemented as sample and data management system for human bodily material. The samples are annotated by the use of defined datasets, based on the BRISQ (Biospecimen Reporting for Improved Study Quality) and Minimum Information About Biobank data Sharing (MIABIS) guidelines completed with SPREC (Standard PREanalytical Coding) information. However, the defined dataset for human bodily material is not ideal to capture the specific cell line data. Therefore, we set out to develop a rationalized cell line dataset. Through comparison of different datasets of online cell banks (human, animal, and stem cell), we established an extended cell line dataset of 156 data fields that was further analyzed until a smaller dataset-the survey dataset of 54 data fields-was obtained. The survey dataset was spread throughout our campus to all cell line users to rationalize the fields of the dataset and their potential use. Analysis of the survey data revealed only small differences in preferences in data fields between human, animal, and stem cell lines. Hence, one essential dataset for human, animal and stem cell lines was compiled consisting of 33 data fields. The essential dataset was prepared for implementation in our BIMS system. Good Clinical Data Management Practices formed the basis of our decisions in the implementation phase. Known standards, reference lists and ontologies (such as ICD-10-CM, animal taxonomy, cell line ontology...) were considered. The semantics of the data fields were clearly defined, enhancing the data quality of the stored cell lines. Therefore, we created an essential cell line dataset with defined data fields, useable for multiple cell line users.
Keywords
biobank, cell line, data management system, dataset, quality, data quality, CULTURE, CONTAMINATION, INFORMATION

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Chicago
T’Joen, Veronique, Lieven Vaneeckhaute, Sara Priem, Steven Van Woensel, Sofie Bekaert, Elke Berneel, and Catherine Van Der Straeten. 2019. “Rationalized Development of a Campus-wide Cell Line Dataset for Implementation in the Biobank LIMS System at Bioresource Center Ghent.” Frontiers in Medicine 6.
APA
T’Joen, V., Vaneeckhaute, L., Priem, S., Van Woensel, S., Bekaert, S., Berneel, E., & Van Der Straeten, C. (2019). Rationalized development of a campus-wide cell line dataset for implementation in the biobank LIMS system at Bioresource center Ghent. FRONTIERS IN MEDICINE, 6.
Vancouver
1.
T’Joen V, Vaneeckhaute L, Priem S, Van Woensel S, Bekaert S, Berneel E, et al. Rationalized development of a campus-wide cell line dataset for implementation in the biobank LIMS system at Bioresource center Ghent. FRONTIERS IN MEDICINE. 2019;6.
MLA
T’Joen, Veronique et al. “Rationalized Development of a Campus-wide Cell Line Dataset for Implementation in the Biobank LIMS System at Bioresource Center Ghent.” FRONTIERS IN MEDICINE 6 (2019): n. pag. Print.
@article{8620544,
  abstract     = {The Bioresource center Ghent is the central hospital-integrated biobank of Ghent University Hospital. Our mission is to facilitate translational biomedical research by collecting, storing and providing high quality biospecimens to researchers. Several of our biobank partners store large amounts of cell lines. As cell lines are highly important both in basic research and preclinical screening phases, good annotation, authentication, and quality of these cell lines is pivotal in translational biomedical science. A Biobank Information Management System (BIMS) was implemented as sample and data management system for human bodily material. The samples are annotated by the use of defined datasets, based on the BRISQ (Biospecimen Reporting for Improved Study Quality) and Minimum Information About Biobank data Sharing (MIABIS) guidelines completed with SPREC (Standard PREanalytical Coding) information. However, the defined dataset for human bodily material is not ideal to capture the specific cell line data. Therefore, we set out to develop a rationalized cell line dataset. Through comparison of different datasets of online cell banks (human, animal, and stem cell), we established an extended cell line dataset of 156 data fields that was further analyzed until a smaller dataset-the survey dataset of 54 data fields-was obtained. The survey dataset was spread throughout our campus to all cell line users to rationalize the fields of the dataset and their potential use. Analysis of the survey data revealed only small differences in preferences in data fields between human, animal, and stem cell lines. Hence, one essential dataset for human, animal and stem cell lines was compiled consisting of 33 data fields. The essential dataset was prepared for implementation in our BIMS system. Good Clinical Data Management Practices formed the basis of our decisions in the implementation phase. Known standards, reference lists and ontologies (such as ICD-10-CM, animal taxonomy, cell line ontology...) were considered. The semantics of the data fields were clearly defined, enhancing the data quality of the stored cell lines. Therefore, we created an essential cell line dataset with defined data fields, useable for multiple cell line users.},
  articleno    = {137},
  author       = {T'Joen, Veronique and Vaneeckhaute, Lieven and Priem, Sara and Van Woensel, Steven and Bekaert, Sofie and Berneel, Elke and Van Der Straeten, Catherine},
  issn         = {2296-858X},
  journal      = {FRONTIERS IN MEDICINE},
  keywords     = {biobank,cell line,data management system,dataset,quality,data quality,CULTURE,CONTAMINATION,INFORMATION},
  language     = {eng},
  pages        = {21},
  title        = {Rationalized development of a campus-wide cell line dataset for implementation in the biobank LIMS system at Bioresource center Ghent},
  url          = {http://dx.doi.org/10.3389/fmed.2019.00137},
  volume       = {6},
  year         = {2019},
}

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