Journal:Principles and application of LIMS in mouse clinics

Full article title	Principles and application of LIMS in mouse clinics
Journal	Mammalian Genome
Author(s)	Maier, Holger; Schütt, Christine; Steinkamp, Ralph et al.
Author affiliation(s)	Helmholtz Zentrum München - German Research Center for Environmental Health, Wellcome Trust Sanger Institute, Institut Clinique de la Souris - ICS, RIKEN BioResource Center, Medical Research Council Harwell, University of California, Baylor College of Medicine
Primary contact	Email: hrabe at helmholtz-muenchen dot de
Year published	2015
Volume and issue	26 (9)
Page(s)	467–481
DOI	10.1007/s00335-015-9586-7
ISSN	1432-1777
Distribution license	Creative Commons Attribution 4.0 International
Website	http://link.springer.com/article/10.1007%2Fs00335-015-9586-7
Download	http://link.springer.com/content/pdf/10.1007%2Fs00335-015-9586-7.pdf (PDF)

Abstract

Large-scale systemic mouse phenotyping, as performed by mouse clinics for more than a decade, requires thousands of mice from a multitude of different mutant lines to be bred, individually tracked and subjected to phenotyping procedures according to a standardised schedule. All these efforts are typically organised in overlapping projects, running in parallel. In terms of logistics, data capture, data analysis, result visualisation and reporting, new challenges have emerged from such projects. These challenges could hardly be met with traditional methods such as pen and paper colony management, spreadsheet-based data management and manual data analysis. Hence, different laboratory information management systems (LIMS) have been developed in mouse clinics to facilitate or even enable mouse and data management in the described order of magnitude. This review shows that general principles of LIMS can be empirically deduced from LIMS used by different mouse clinics, although these have evolved differently. Supported by LIMS descriptions and lessons learned from seven mouse clinics, this review also shows that the unique LIMS environment in a particular facility strongly influences strategic LIMS decisions and LIMS development. As a major conclusion, this review states that there is no universal LIMS for the mouse research domain that fits all requirements. Still, empirically deduced general LIMS principles can serve as a master decision support template, which is provided as a hands-on tool for mouse research facilities looking for a LIMS.

Introduction

Most generally, laboratory information management systems (LIMS) may be defined as software tools with implemented features that support processes conducted in modern laboratories. Usually, this involves functions like sample tracking, data capture and data management, and some sort of workflow management. Additional specialised functionality like electronic laboratory notebook (ELN), scientific data management system (SDMS) and enterprise resource planning (ERP) tools may be included in LIMS, possibly as optional modules. Many commercial vendors offer LIMS solutions for industry and test laboratories that operate in a highly regulated environment. Typically, these systems are highly customisable and adaptable to user-defined processes and offer standard instrument interfacing protocols, e.g. ASTM E1394. However, such LIMS are not subject to this review, as it is not meant to be a case study or a questionnaire-based feature comparison of available LIMS. It rather follows an empiric approach by trying to derive general principles from a limited selection of LIMS descriptions, provided by seven large-scale mouse phenotyping facilities (mouse clinics).

Such mouse clinics are predominantly running in an academic environment. In this field, mice or mouse-derived samples (blood, urine, tissue) serve as specimens that are subjected to a series of phenotyping procedures. Individual mouse-specific demographic attributes, e.g. sex, genotype, lineage and allelic composition, are required to be linked to captured data throughout the whole process in order to allow subsequent data analysis. Hence, in this field, LIMS have to offer livestock and breeding functionality in addition to standard LIMS features.

In the academic domain, some custom mouse husbandry systems have been developed and published in the past, e.g. LAMS, MouseNet, MICE, MouseBank, MUSDB, MouseTRACS, MausDB, LAMA and JCMS, ranging from pure mouse management systems to integrated mouse LIMS. Certainly, commercial mouse LIMS or colony management products are also available. However, these are not discussed here, as the review does not intend to provide a mere product comparison but rather aims to enable readers to evaluate LIMS solutions by themselves, by providing empirically supported mouse LIMS principles and decision criteria.

Acknowledgements

Martin Hrabě de Angelis and Valerie Gailus-Durner have contributed equally to this work.

We thank Manuela Östereicher and Susan Marschall for critical reading of the manuscript. This work was funded by the German Federal Ministry of Education and Research (Infrafrontier grant 01KX1012).

Supplementary material

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Supplementary material 1 (XLSX 43 kb)

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Supplementary material 2 (DOCX 11 kb)

Notes

This presentation is faithful to the original, with only a few minor changes to presentation. In most of the article's references DOIs and PubMed IDs were not given; they've been added to make the references more useful. In some cases important information was missing from the references, and that information was added.