Skip to main content
SpringerLink
Log in

LIMS and Clinical Data Management

  • Chapter
  • First Online:
Translational Biomedical Informatics

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 939))

Abstract

In order to achieve more accurate disease prevention, diagnosis, and treatment, clinical and genetic data need extensive and systematically associated study. As one way to achieve precision medicine, a laboratory information management system (LIMS) can effectively associate clinical data in a macrocosmic aspect and genomic data in a microcosmic aspect. This chapter summarizes the application of the LIMS in a clinical data management and implementation mode. It also discusses the principles of a LIMS in clinical data management, as well as the opportunities and challenges in the context of medical informatics.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Bakshi SR, Shukla SN, Shah PM. Customized laboratory information management system for a clinical and research leukemia cytogenetics laboratory. J Assoc Genetic Technol. 2009;35:7–8.

    Google Scholar 

  2. Barillari C, et al. openBIS ELN-LIMS: an open-source database for academic laboratories. Bioinformatics. 2016;32(4):638–40

    Google Scholar 

  3. Barry MJ, Edgman-Levitan S. Shared decision making-pinnacle of patient-centered care. N Engl J Med. 2012;366:780–1.

    Article  CAS  PubMed  Google Scholar 

  4. Bath TG, et al. LimsPortal and BonsaiLIMS: development of a lab information management system for translational medicine. Source Code Biol Med. 2011;6:9.

    Article  PubMed  PubMed Central  Google Scholar 

  5. Calabria A, et al. adLIMS: a customized open source software that allows bridging clinical and basic molecular research studies. BMC Bioinf. 2015;16 Suppl 9:S5.

    Article  Google Scholar 

  6. Cho SY, et al. An integrated proteome database for two-dimensional electrophoresis data analysis and laboratory information management system. Proteomics. 2002;2:1104–13.

    Article  CAS  PubMed  Google Scholar 

  7. Davidson DF. A survey of some pre-analytical errors identified from the Biochemistry Department of a Scottish hospital. Scott Med J. 2014;59:91–4.

    Article  PubMed  Google Scholar 

  8. Dhombres F, Bodenreider O. Interoperability between phenotypes in research and healthcare terminologies-Investigating partial mappings between HPO and SNOMED CT. J Biomed Semant. 2016;7:3.

    Article  Google Scholar 

  9. Eichhorst JC, et al. Drugs of abuse testing by tandem mass spectrometry: a rapid, simple method to replace immunoassays. Clin Biochem. 2009;42:1531–42.

    Article  CAS  PubMed  Google Scholar 

  10. Gavrielides M, et al. Onco-STS: a web-based laboratory information management system for sample and analysis tracking in oncogenomic experiments. Source Code Biol Med. 2014;9:0.

    Article  PubMed  Google Scholar 

  11. Grandjean G, Graham R, Bartholomeusz G. Essential attributes identified in the design of a Laboratory Information Management System for a high throughput siRNA screening laboratory. Comb Chem High Throughput Screen. 2011;14:766–71.

    Article  CAS  PubMed  Google Scholar 

  12. Grimes SM, Ji HP. MendeLIMS: a web-based laboratory information management system for clinical genome sequencing. BMC Bioinf. 2014;15:290.

    Article  Google Scholar 

  13. Hakkinen J, Levander F. Laboratory data and sample management for proteomics. Methods Mol Biol. 2011;696:79–92.

    Article  PubMed  Google Scholar 

  14. Harel A, et al. Omics data management and annotation. Methods Mol Biol. 2011;719:71–96.

    Article  CAS  PubMed  Google Scholar 

  15. Huang YW, Arkin AP, Chandonia JM. WIST: toolkit for rapid, customized LIMS development. Bioinformatics. 2011;27:437–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Isfahani SS, et al. The evaluation of hospital laboratory information management systems based on the standards of the American National Standard Institute. J Educ Health Promot. 2014;3:61.

    PubMed  PubMed Central  Google Scholar 

  17. Kuhn S, Schlorer NE. Facilitating quality control for spectra assignments of small organic molecules: nmrshiftdb2-a free in-house NMR database with integrated LIMS for academic service laboratories. Magn Reson Chem. 2015;53:582–9.

    Article  CAS  PubMed  Google Scholar 

  18. Lana-Peixoto MA, et al. NMO-DBr: the Brazilian Neuromyelitis Optica Database System. Arq Neuropsiquiatr. 2011;69:687–92.

    Article  PubMed  Google Scholar 

  19. Lemmon VP, et al. Challenges in small screening laboratories: implementing an on-demand laboratory information management system. Comb Chem High Throughput Screen. 2011;14:742–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Levy BP. Implementation and user satisfaction with forensic laboratory information systems in death investigation offices. Am J Forensic Med Pathol. 2013;34:63–7.

    Article  PubMed  Google Scholar 

  21. Lopez MA, et al. The challenge of ciemat internal dosimetry service for accreditation according to Iso/Iec 17025 standard, for in vivo and in vitro monitoring and dose assessment of internal exposures. Radiat Protect Dosimetry. 2015.

    Google Scholar 

  22. Lopez-Campos G, Ofoghi B, Martin-Sanchez F. Enabling self-monitoring data exchange in participatory medicine. Stud Health Technol Inform. 2015;216:1102.

    PubMed  Google Scholar 

  23. Lu X. Development of an excel-based laboratory information management system for improving workflow efficiencies in early ADME screening. Bioanalysis. 2016;8:99–110.

    Article  CAS  PubMed  Google Scholar 

  24. Luo J, et al. Big data application in biomedical research and health care: a literature review. Biomed Inform Insights. 2016;8:1–10.

    Article  PubMed  PubMed Central  Google Scholar 

  25. Maier H, et al. Principles and application of LIMS in mouse clinics. Mamm Genome. 2015;26:467–81.

    Article  PubMed  PubMed Central  Google Scholar 

  26. Melo A, et al. SIGLa: an adaptable LIMS for multiple laboratories. BMC Genomics. 2010;11 Suppl 5:S8.

    Article  PubMed  PubMed Central  Google Scholar 

  27. Mirzazadeh M, et al Point-of-care testing of electrolytes and calcium using blood gas analysers: it is time we trusted the results. Emerg Med J. 2016;33(3):181–6

    Google Scholar 

  28. Mohammadzadeh N, Safdari R. The intelligent clinical laboratory as a tool to increase cancer care management productivity. Asian Pac J Cancer Prev. 2014;15:2935–7.

    Article  PubMed  Google Scholar 

  29. Monnier S, et al. T.I.M.S: TaqMan Information Management System, tools to organize data flow in a genotyping laboratory. BMC Bioinf. 2005;6:246.

    Article  Google Scholar 

  30. Morris C, et al. MOLE: a data management application based on a protein production data model. Proteins. 2005;58:285–9.

    Article  CAS  PubMed  Google Scholar 

  31. Nebrich G, et al. PROTEOMER: a workflow-optimized laboratory information management system for 2-D electrophoresis-centered proteomics. Proteomics. 2009;9:1795–808.

    Article  CAS  PubMed  Google Scholar 

  32. Nix DA, et al. Next generation tools for genomic data generation, distribution, and visualization. BMC Bioinf. 2010;11:455.

    Article  Google Scholar 

  33. Palla P, et al. QTREDS: a Ruby on Rails-based platform for omics laboratories. BMC Bioinf. 2014;15 Suppl 1:S13.

    Article  Google Scholar 

  34. Quo CF, Wu B, Wang MD. Development of a laboratory information system for cancer collaboration projects. Conference proceedings: annual international conference of the IEEE engineering in medicine and biology society. IEEE engineering in medicine and biology society. Annual Conference. 2005:3:2859–2862.

    Google Scholar 

  35. Romero AM, et al. Ciemat external dosimetry service: iso/iec 17025 accreditation and 3 y of operational experience as an accredited laboratory. Radiat Prot Dosimetry. 2015.

    Google Scholar 

  36. Russom D, et al. Implementation of a configurable laboratory information management system for use in cellular process development and manufacturing. Cytotherapy. 2012;14:114–21.

    Article  PubMed  Google Scholar 

  37. Shin Y, et al. First step to big data research in hospital. Stud Health Technol Inform. 2015;216:924.

    PubMed  Google Scholar 

  38. Singh KS, et al. SaDA: from sampling to data analysis-an extensible open source infrastructure for rapid, robust and automated management and analysis of modern ecological high-throughput microarray data. Int J Environ Res Public Health. 2015;12:6352–66.

    Article  PubMed  PubMed Central  Google Scholar 

  39. Song Y, et al. A high efficiency, high quality and low cost internal regulated bioanalytical laboratory to support drug development needs. Bioanalysis. 2014;6:1295–309.

    Article  CAS  PubMed  Google Scholar 

  40. Stocker G, et al. iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis. BMC Bioinf. 2009;10:390.

    Article  Google Scholar 

  41. Swanson CM, et al. Update on inpatient glycemic control in hospitals in the United States. Endocr Pract. 2011;17:853–61.

    Article  PubMed  Google Scholar 

  42. Tai D, Chaguturu R, Fang J. K-Screen: a free application for high throughput screening data analysis, visualization, and laboratory information management. Comb Chem High Throughput Screen. 2011;14:757–65.

    Article  CAS  PubMed  Google Scholar 

  43. Townsend A, et al. eHealth, participatory medicine, and ethical care: a focus group study of patients’ and health care providers’ use of health-related internet information. J Med Internet Res. 2015;17, e155.

    Article  PubMed  PubMed Central  Google Scholar 

  44. Triplet T, Butler G. The EnzymeTracker: an open-source laboratory information management system for sample tracking. BMC Bioinf. 2012;13:15.

    Article  CAS  Google Scholar 

  45. Turner E, Bolton J. Required steps for the validation of a Laboratory Information Management System. Qual Assur. 2001;9:217–24.

    CAS  PubMed  Google Scholar 

  46. Ulma W, Schlabach DM. Technical considerations in remote LIMS access via the World Wide Web. J Autom Methods Manage Chem. 2005;2005:217–22.

    Article  Google Scholar 

  47. Venco F, et al. SMITH: a LIMS for handling next-generation sequencing workflows. BMC Bioinf. 2014;15 Suppl 14:S3.

    Article  Google Scholar 

  48. Viksna J, et al. PASSIM-an open source software system for managing information in biomedical studies. BMC Bioinf. 2007;8:52.

    Article  Google Scholar 

  49. Vreeman DJ, Hook J, Dixon BE. Learning from the crowd while mapping to LOINC. J Am Med Inform Assoc. 2015;22:1205–11.

    PubMed  PubMed Central  Google Scholar 

  50. Walzer M, et al. qcML: an exchange format for quality control metrics from mass spectrometry experiments. Mol Cell Proteomics. 2014;13:1905–13.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Wang N, et al. The Hawaiian Algal database: a laboratory LIMS and online resource for biodiversity data. BMC Plant Biol. 2009;9:117.

    Article  PubMed  PubMed Central  Google Scholar 

  52. Zhang Q, Gao S. [Design and realization of HL7 gateway], Sheng wu yi xue gong cheng xue za zhi. J Biomed Eng = Shengwu yixue gongchengxue zazhi. 2003;20:111–5.

    Google Scholar 

  53. Zhi YJ, et al. [Impact analysis of parenterally administered shuxuetong on abnormal changes of BUN index based on hospital information system data]. Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China J Chin materia medica. 2013;38:3048–52.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Center for Systems Biology, Soochow University, No. 1 Shizi Street, 206, 215006, Suzhou, Jiangsu, China

    Yalan Chen, Yuxin Lin, Xuye Yuan & Bairong Shen

  2. Department of Medical Informatics, School of Medicine, Nantong University, Nantong, Jiangsu, China

    Yalan Chen

Authors
  1. Yalan Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yuxin Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Xuye Yuan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Bairong Shen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Bairong Shen .

Editor information

Editors and Affiliations

  1. Center for Systems Biology, Soochow University, Jiangsu, China

    Bairong Shen

  2. School of Informatics and Computing, Indiana University, Bloomington, Indiana, USA

    Haixu Tang

  3. Department of Biomedical Informatics, University of California San Diego, La Jolla, California, USA

    Xiaoqian Jiang

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer Science+Business Media Singapore

About this chapter

Cite this chapter

Chen, Y., Lin, Y., Yuan, X., Shen, B. (2016). LIMS and Clinical Data Management. In: Shen, B., Tang, H., Jiang, X. (eds) Translational Biomedical Informatics. Advances in Experimental Medicine and Biology, vol 939. Springer, Singapore. https://doi.org/10.1007/978-981-10-1503-8_9

Download citation

Publish with us

Policies and ethics

Search

Navigation