Information systems for scientific laboratories: a narrative review

Authors

DOI:

https://doi.org/10.33448/rsd-v11i4.27163

Keywords:

Information Systems; Laboratory Information Systems; Health Information Management; Database Management Systems; Computer applications software.

Abstract

Data originated from scientific laboratories require appropriate management. In this sense, there are information systems tailored for this type of working environment, ranging from physical notebooks to personalized electronic platforms. Over time, physical annotation instruments have become no longer sufficient to meet the existing demand in more dynamic research environments. In this context, the objective of this work was to present a narrative review on the key elements surrounding the development of efficient information systems applied to scientific laboratories. In this paper, it is emphasized how essential it is to build customized systems that can specifically meet the needs of the user. This paper also exemplifies the contribution of digital information systems towards research in the areas of life and health sciences. For this, the main concepts and principles involved in the development of scientific research information systems are described, which may be used in the planning stage of new platforms.

References

Abbott Informatics. (2022). Sistema de gestão de informações laboratoriais (LIMS) | STARLIMS. Retrieved January 2022, from https://www.informatics.abbott/int/pt/home

Amorim, R. C., Castro, J. A., Rocha da Silva, J., & Ribeiro, C. (2017). A comparison of research data management platforms: Architecture, flexible metadata and interoperability. Universal Access in the Information Society, 16(4), 851–862. https://doi.org/10.1007/s10209-016-0475-y

Anderson, N. R., Lee, E. S., Brockenbrough, J. S., Minie, M. E., Fuller, S., Brinkley, J., & Tarczy-Hornoch, P. (2007). Issues in Biomedical Research Data Management and Analysis: Needs and Barriers. Journal of the American Medical Informatics Association, 14(4), 478–488. https://doi.org/10.1197/jamia.M2114

Barillari, C., Ottoz, D. S. M., Fuentes-Serna, J. M., Ramakrishnan, C., Rinn, B., & Rudolf, F. (2016). openBIS ELN-LIMS: An open-source database for academic laboratories. Bioinformatics, 32(4), 638–640. https://doi.org/10.1093/bioinformatics/btv606

Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Research, 28(1), 235–242. https://doi.org/10.1093/nar/28.1.235

Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977). The protein data bank: A computer-based archival file for macromolecular structures. Journal of Molecular Biology, 112(3), 535–542. https://doi.org/10.1016/S0022-2836(77)80200-3

Cooray, M. (2012). Molecular biological databases: Evolutionary history, data modeling, implementation and ethical background. Sri Lanka Journal of Bio-Medical Informatics, 3(1), 2–11. https://doi.org/10.4038/sljbmi.v3i1.2489

Craig, T., Holland, R., D’Amore, R., Johnson, J. R., McCue, H. V., West, A., Zulkower, V., Tekotte, H., Cai, Y., Swan, D., Davey, R. P., Hertz-Fowler, C., Hall, A., & Caddick, M. (2017). Leaf LIMS: A Flexible Laboratory Information Management System with a Synthetic Biology Focus. ACS Synthetic Biology, 6(12), 2273–2280. https://doi.org/10.1021/acssynbio.7b00212

Date, C. J. (2004). Introdução a Sistemas de Bancos de Dados (1a edição). GEN LTC.

Dirnagl, U., & Przesdzing, I. (2016). A pocket guide to electronic laboratory notebooks in the academic life sciences. F1000Research, 5, 2. https://doi.org/10.12688/f1000research.7628.1

Elmasri, R., & Navathe, S. B. (2010). Sistemas de Banco de Dados (6a edição). Pearson Universidades.

Ferreira, A. L. da C. (2019). Application of the LabTablet app in a laboratory environment: Case study I3S [Integrated Master in Bioengineering]. Universidade do Porto.

Gallagher, R. V., Falster, D. S., Maitner, B. S., Salguero-Gómez, R., Vandvik, V., Pearse, W. D., Schneider, F. D., Kattge, J., Poelen, J. H., Madin, J. S., Ankenbrand, M. J., Penone, C., Feng, X., Adams, V. M., Alroy, J., Andrew, S. C., Balk, M. A., Bland, L. M., Boyle, B. L., … Enquist, B. J. (2020). Open Science principles for accelerating trait-based science across the Tree of Life. Nature Ecology & Evolution, 4(3), 294–303. https://doi.org/10.1038/s41559-020-1109-6

Grand, A., Geda, E., Mignone, A., Bertotti, A., & Fiori, A. (2019). One tool to find them all: A case of data integration and querying in a distributed LIMS platform. Database: The Journal of Biological Databases and Curation, 2019, baz004. https://doi.org/10.1093/database/baz004

Haried, P., Claybaugh, C., & Dai, H. (2019). Evaluation of health information systems research in information systems research: A meta-analysis. Health Informatics Journal, 25(1), 186–202. https://doi.org/10.1177/1460458217704259

Heuser, C. A. (2008). Projeto de Banco de Dados: Volume 4 (6a edição). Bookman.

Kanare, H. M. (1985). Writing the Laboratory Notebook. American Chemical Society. https://eric.ed.gov/?id=ED344734

Kanehisa, M., Goto, S., Sato, Y., Kawashima, M., Furumichi, M., & Tanabe, M. (2014). Data, information, knowledge and principle: Back to metabolism in KEGG. Nucleic Acids Research, 42(D1), D199–D205. https://doi.org/10.1093/nar/gkt1076

Kanza, S., Willoughby, C., Gibbins, N., Whitby, R., Frey, J. G., Erjavec, J., Zupančič, K., Hren, M., & Kovač, K. (2017). Electronic lab notebooks: Can they replace paper? Journal of Cheminformatics, 9(1), 31. https://doi.org/10.1186/s13321-017-0221-3

Kumar, M. J. K. (2013). Electronic Lab Notebooks-Collaborative Tool for Managing Knowledge in Pharmaceutical Research and Development. Journal of Engineering Computers & Applied Sciences, 2(11), 14–19.

LabArchives. (2022). LabArchives Better Science. LabArchives. Retrieved January 2022, from https://www.labarchives.com/

Labfolder. (2022). Electronic Lab Notebook (ELN). Labfolder. Retrieved January 2022, from https://www.labfolder.com/

LabVantage. (2022). Lab Informatics Solution. LabVantage. Retrieved January 2022, from https://www.labvantage.com/

Lombard, V., Golaconda Ramulu, H., Drula, E., Coutinho, P. M., & Henrissat, B. (2014). The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Research, 42(D1), D490–D495. https://doi.org/10.1093/nar/gkt1178

Machina, H. K., & Wild, D. J. (2013a). Laboratory Informatics Tools Integration Strategies for Drug Discovery: Integration of LIMS, ELN, CDS, and SDMS. Journal of Laboratory Automation, 18(2), 126–136. https://doi.org/10.1177/2211068212454852

Machina, H. K., & Wild, D. J. (2013b). Electronic Laboratory Notebooks Progress and Challenges in Implementation. Journal of Laboratory Automation, 18(4), 264–268. https://doi.org/10.1177/2211068213484471

Mannino, M. V., Honorato, B., Prairo, D., Moura, L., Sonoe, S., Guardado, A. F. N., & Viana, S. da S. (2008). Projeto, Desenvolvimento de Aplicações e Administração de Banco de Dados (3a edição). AMGH.

Ministério da Saúde. (2009). A experiência brasileira em sistemas de informação em saúde (1st ed., Vol. 1). Editora MS.

NCBI Resource Coordinators. (2018). Database resources of the National Center for Biotechnology Information. Nucleic Acids Research, 46(D1), D8–D13. https://doi.org/10.1093/nar/gkx1095

Nussbeck, S. Y., Weil, P., Menzel, J., Marzec, B., Lorberg, K., & Schwappach, B. (2014). The laboratory notebook in the 21st century: The electronic laboratory notebook would enhance good scientific practice and increase research productivity. EMBO Reports, 15(6), 631–634. https://doi.org/10.15252/embr.201338358

Office of The Director, NIH. (2020). Final NIH Policy for Data Management and Sharing. National Institutes of Health. https://grants.nih.gov/grants/guide/notice-files/NOT-OD-21-013.html

Park, S. L., Pantanowitz, L., Sharma, G., & Parwani, A. V. (2012). Anatomic Pathology Laboratory Information Systems: A Review. Advances in Anatomic Pathology, 19(2), 81–96. https://doi.org/10.1097/PAP.0b013e318248b787

Paskal, W., Paskal, A. M., Dębski, T., Gryziak, M., & Jaworowski, J. (2018). Aspects of Modern Biobank Activity – Comprehensive Review. Pathology Oncology Research, 24(4), 771–785. https://doi.org/10.1007/s12253-018-0418-4

Pressman, R. S., Maxim, B. R., Arakaki, R., Arakaki, J., & Andrade, R. M. de. (2016). Engenharia de Software: Uma Abordagem Profissional (8a edição). AMGH.

Punta, M., Coggill, P. C., Eberhardt, R. Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J., Heger, A., Holm, L., Sonnhammer, E. L. L., Eddy, S. R., Bateman, A., & Finn, R. D. (2012). The Pfam protein families database. Nucleic Acids Research, 40(D1), D290–D301. https://doi.org/10.1093/nar/gkr1065

Ramakrishnan, R., Gehrke, J., Taniwake, C., Tortello, J. E. N., & Sousa, E. P. M. de. (2007). Sistemas de Gerenciamento de Bancos de Dados (3a edição). AMGH.

Riley, E. M., Hattaway, H. Z., & Felse, P. A. (2017). Implementation and use of cloud-based electronic lab notebook in a bioprocess engineering teaching laboratory. Journal of Biological Engineering, 11(1), 40. https://doi.org/10.1186/s13036-017-0083-2

Sapio Sciences. (2022). Laboratory Information Management System Software (LIMS). Sapio Sciences. Retrieved January 2022, from https://www.sapiosciences.com/

Sayers, E. W., Cavanaugh, M., Clark, K., Pruitt, K. D., Schoch, C. L., Sherry, S. T., & Karsch-Mizrachi, I. (2021). GenBank. Nucleic Acids Research, 49(D1), D92–D96. https://doi.org/10.1093/nar/gkaa1023

Setzer, V. W., & Silva, F. S. C. da. (2005). Bancos de Dados: Aprenda o que São, Melhore seu Conhecimento, Construa os Seus (1a edição). Blucher.

Sigrist, C. J. A., de Castro, E., Cerutti, L., Cuche, B. A., Hulo, N., Bridge, A., Bougueleret, L., & Xenarios, I. (2013). New and continuing developments at PROSITE. Nucleic Acids Research, 41(D1), D344–D347. https://doi.org/10.1093/nar/gks1067

Stair, R., & Reynolds, G. (2020). Principles of Information Systems. Cengage Learning.

Surkis, A., & Read, K. (2015). Research data management. Journal of the Medical Library Association : JMLA, 103(3), 154–156. https://doi.org/10.3163/1536-5050.103.3.011

The UniProt Consortium. (2015). UniProt: A hub for protein information. Nucleic Acids Research, 43(D1), D204–D212. https://doi.org/10.1093/nar/gku989

Published

11/03/2022

How to Cite

BONETTI, G. D. .; ABREU, F. P. de .; CASA, P. L. .; SILVA, S. de A. e .; SALVADOR, M. Information systems for scientific laboratories: a narrative review. Research, Society and Development, [S. l.], v. 11, n. 4, p. e6811427163, 2022. DOI: 10.33448/rsd-v11i4.27163. Disponível em: https://rsdjournal.org/index.php/rsd/article/view/27163. Acesso em: 16 nov. 2024.

Issue

Section

Health Sciences