Journal:Principles and application of LIMS in mouse clinics - Revision history

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	==Introduction==		==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 [[LIMS feature#Sample tracking\|sample tracking]], data capture and data management, and some sort of [[LIMS feature#Workflow management\|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 [[LIMS vendor\|commercial vendors]] offer LIMS solutions for industry and test [[Laboratory\|laboratories]] that operate in a highly regulated environment. Typically, these systems are highly customisable and adaptable to user-defined processes and offer standard [[LIMS feature#Instrument interfacing and management\|instrument interfacing]] protocols, e.g. ASTM E1394.<ref name="ASTME1394">{{cite web \|url=http://www.astm.org/Standards/E1394.htm \|title=ASTM E1394-97, standard specification for transferring information between clinical instruments and computer systems (withdrawn 2002) \|author=ASTM International \|publisher=ASTM International \|date=1997}}</ref> 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).		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 [[LIMS feature#Sample tracking\|sample tracking]], data capture and data management, and some sort of [[LIMS feature#Workflow management\|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 [[Vendor:LIMS vendor\|commercial vendors]] offer LIMS solutions for industry and test [[Laboratory\|laboratories]] that operate in a highly regulated environment. Typically, these systems are highly customisable and adaptable to user-defined processes and offer standard [[LIMS feature#Instrument interfacing and management\|instrument interfacing]] protocols, e.g. ASTM E1394.<ref name="ASTME1394">{{cite web \|url=http://www.astm.org/Standards/E1394.htm \|title=ASTM E1394-97, standard specification for transferring information between clinical instruments and computer systems (withdrawn 2002) \|author=ASTM International \|publisher=ASTM International \|date=1997}}</ref> 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.		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.

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	==Introduction==		==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 [[LIMS feature#Sample tracking\|sample tracking]], data capture and data management, and some sort of [[LIMS feature#Workflow management\|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 [[LIMS vendor\|commercial vendors]] offer LIMS solutions for industry and test [[Laboratory\|laboratories]] that operate in a highly regulated environment. Typically, these systems are highly customisable and adaptable to user-defined processes and offer standard [[LIMS feature#Instrument interfacing and management\|instrument interfacing]] protocols, e.g. ASTM E1394.<ref name="ASTME1394">{{cite web \|url=http://www.astm.org/Standards/E1394.htm \|author=ASTM International \|publisher=ASTM International \|date=1997}}</ref> 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).		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 [[LIMS feature#Sample tracking\|sample tracking]], data capture and data management, and some sort of [[LIMS feature#Workflow management\|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 [[LIMS vendor\|commercial vendors]] offer LIMS solutions for industry and test [[Laboratory\|laboratories]] that operate in a highly regulated environment. Typically, these systems are highly customisable and adaptable to user-defined processes and offer standard [[LIMS feature#Instrument interfacing and management\|instrument interfacing]] protocols, e.g. ASTM E1394.<ref name="ASTME1394">{{cite web \|url=http://www.astm.org/Standards/E1394.htm \|title=ASTM E1394-97, standard specification for transferring information between clinical instruments and computer systems (withdrawn 2002) \|author=ASTM International \|publisher=ASTM International \|date=1997}}</ref> 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.		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.

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{{Infobox journal article
|name =
|image =
|alt = 
|caption =
|title_full = Principles and application of LIMS in mouse clinics
|journal = ''Mammalian Genome''
|authors = Maier, Holger; Schütt, Christine; Steinkamp, Ralph ''et al.''
|affiliations = Helmholtz Zentrum München - German Research Center for Environmental Health, Wellcome Trust<br />Sanger Institute, Institut Clinique de la Souris - ICS, RIKEN BioResource Center, Medical Research<br />Council Harwell, University of California, Baylor College of Medicine
|contact = Email: hrabe at helmholtz-muenchen dot de
|editors =
|pub_year = 2015
|vol_iss = '''26''' (9)
|pages = 467–481
|doi = [http://dx.doi.org/10.1007/s00335-015-9586-7 10.1007/s00335-015-9586-7]
|issn = 1432-1777
|license = [http://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International]
|website = [http://link.springer.com/article/10.1007%2Fs00335-015-9586-7 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 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 system]]s (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 [[LIMS feature#Sample tracking|sample tracking]], data capture and data management, and some sort of [[LIMS feature#Workflow management|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 [[LIMS vendor|commercial vendors]] offer LIMS solutions for industry and test [[Laboratory|laboratories]] that operate in a highly regulated environment. Typically, these systems are highly customisable and adaptable to user-defined processes and offer standard [[LIMS feature#Instrument interfacing and management|instrument interfacing]] protocols, e.g. ASTM E1394.<ref name="ASTME1394">{{cite web |url=http://www.astm.org/Standards/E1394.htm |author=ASTM International |publisher=ASTM International |date=1997}}</ref> 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<ref name="FrankTheLab91">{{cite journal |title=The laboratory animal management system - An animal housing management data-processing system |journal=Journal of Experimental Animal Science |author=Frank, N.; Ridesel, H.; Lenz, R. |volume=34 |issue=4 |pages=140–6 |year=1991 |pmid=1793741}}</ref>, MouseNet<ref name="PargentMouse00">{{cite journal |title=MouseNet database: Digital management of a large-scale mutagenesis project |journal=Mammalian Genome |author=Pargent, W.; Heffner, S.; Schäble, K.F. et al. |volume=11 |issue=7 |pages=590–593 |year=2000 |doi=10.1007/s003350010112 |pmid=10886028}}</ref>, MICE<ref name="BoulukosMICE01">{{cite journal |title=MICE, a program to track and monitor animals in animal facilities |journal=BMC Genetics |author=Boulukos, K.E.; Pognonec, P. |volume=2 |pages=4 |year=2001 |doi=10.1186/1471-2156-2-4 |pmid=11252156 |pmc=PMC29084}}</ref>, MouseBank<ref name="HopleyMouse01">{{cite journal |title=MouseBank: A database application for managing transgenic mouse breeding programs |journal=BioTechniques |author=Hopley, R.; Zimmer, A. |volume=30 |issue=1 |pages=130–2 |year=2001 |pmid=11196303}}</ref>, MUSDB<ref name="MasuyaDev04">{{cite journal |title=Development and implementation of a database system to manage a large-scale mouse ENU-mutagenesis program |journal=Mammalian Genome |author=Masuya, H.; Nakai, Y.; Motegi, H. et al. |volume=15 |issue=5 |pages=404–411 |year=2004 |doi=10.1007/s00335-004-2265-8 |pmid=15170230 }}</ref>, MouseTRACS<ref name="ChingData06">{{cite journal |title=Data and animal management software for large-scale phenotype screening |journal=Mammalian Genome |author=Ching, K.A.; Cooke, M.P.; Tarantino, L.M.; Lapp, H. |volume=17 |issue=4 |pages=288–297 |year=2006 |doi=10.1007/s00335-005-0145-5 |pmid=16596450 |pmc=PMC1428800}}</ref>, MausDB<ref name="MaierMaus08">{{cite journal |title=MausDB: An open source application for phenotype data and mouse colony management in large-scale mouse phenotyping projects |journal=BMC Bioinformatics |author=Maier, H.; Lengger, C.; Simic, B. et al. |volume=9 |pages=169 |year=2008 |doi=10.1186/1471-2105-9-169 |pmid=18366799 |pmc=PMC2292142}}</ref>, [[LAMA]]<ref name="MilisavljevicLab10">{{cite journal |title=Laboratory Animal Management Assistant (LAMA): a LIMS for active research colonies |journal=Mammalian Genome |author=Milisavljevic, M.; Hearty, T.; Wong, T.Y.T. et al. |year=2010 |volume=21 |issue=5–6 |pages=224–230 |format=PDF |url=http://www.pleiades.org/pubs/Milisavljevic_2010.pdf |doi=10.1007/s00335-010-9258-6}}</ref> and JCMS<ref name="DonnellyJAX10">{{cite journal |title=JAX Colony Management System (JCMS): An extensible colony and phenotype data management system |journal=BMC Bioinformatics |author=Donnelly, C.J.; McFarland, M.; Ames, A. et al. |volume=21 |issue=3 |pages=205–15 |year=2010 |doi=10.1007/s00335-010-9250-1 |pmid=20140675 |pmc=PMC2844967}}</ref>, 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.

==Principles of LIMS==

==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==
;[https://static-content.springer.com/esm/art%3A10.1007%2Fs00335-015-9586-7/MediaObjects/335_2015_9586_MOESM1_ESM.xlsx 335_2015_9586_MOESM1_ESM.xlsx] (43 kb)
:Supplementary material 1 (XLSX 43 kb)

;[https://static-content.springer.com/esm/art%3A10.1007%2Fs00335-015-9586-7/MediaObjects/335_2015_9586_MOESM2_ESM.docx 335_2015_9586_MOESM2_ESM.docx] (12 kb)
:Supplementary material 2 (DOCX 11 kb)

==References==
{{Reflist|colwidth=30em}}

==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.


[[Category:LIMSwiki journal articles (added in 2016)‎]]
[[Category:LIMSwiki journal articles (all)‎]]
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