1
|
Maier H, Schütt C, Steinkamp R, Hurt A, Schneltzer E, Gormanns P, Lengger C, Griffiths M, Melvin D, Agrawal N, Alcantara R, Evans A, Gannon D, Holroyd S, Kipp C, Raj NP, Richardson D, LeBlanc S, Vasseur L, Masuya H, Kobayashi K, Suzuki T, Tanaka N, Wakana S, Walling A, Clary D, Gallegos J, Fuchs H, de Angelis MH, Gailus-Durner V. Principles and application of LIMS in mouse clinics. Mamm Genome 2015. [PMID: 26208973 PMCID: PMC4602070 DOI: 10.1007/s00335-015-9586-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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 & 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.
Collapse
Affiliation(s)
- Holger Maier
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
| | - Christine Schütt
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Ralph Steinkamp
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Anja Hurt
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Elida Schneltzer
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Philipp Gormanns
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Christoph Lengger
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Mark Griffiths
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - David Melvin
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Neha Agrawal
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Rafael Alcantara
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Arthur Evans
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - David Gannon
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Simon Holroyd
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Christian Kipp
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Navis Pretheeba Raj
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - David Richardson
- Mouse Informatics Group, Wellcome Trust Sanger Institute, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Sophie LeBlanc
- Institut Clinique de la Souris - ICS, 1 rue Laurent Fries, BP 10142, 67404, Illkirch Cedex, France
| | - Laurent Vasseur
- Institut Clinique de la Souris - ICS, 1 rue Laurent Fries, BP 10142, 67404, Illkirch Cedex, France
| | - Hiroshi Masuya
- RIKEN BioResource Center, Kouyadai 3-1-1, Ibaraki, 306-0074, Japan
| | - Kimio Kobayashi
- RIKEN BioResource Center, Kouyadai 3-1-1, Ibaraki, 306-0074, Japan
| | - Tomohiro Suzuki
- RIKEN BioResource Center, Kouyadai 3-1-1, Ibaraki, 306-0074, Japan
| | - Nobuhiko Tanaka
- RIKEN BioResource Center, Kouyadai 3-1-1, Ibaraki, 306-0074, Japan
| | - Shigeharu Wakana
- RIKEN BioResource Center, Kouyadai 3-1-1, Ibaraki, 306-0074, Japan
| | - Alison Walling
- Mary Lyon Centre, Medical Research Council Harwell, Harwell Science and Innovation Campus, Harwell, Oxfordshire, OX11 0RD, UK
| | - David Clary
- Mouse Biology Program, University of California, Davis, 2795 2nd Street, Suite 400, Davis, CA, 95618, USA
| | - Juan Gallegos
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany. .,Chair for Experimental Genetics, Life and Food Science Center Weihenstephan, Technische Universität Munich, Freising-Weihenstephan, 85354, Munich, Germany. .,Member of German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany.
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| |
Collapse
|
3
|
Anderson JL, Macurak ML, Halpern ME, Farber SA. A versatile aquatics facility inventory system with real-time barcode scan entry. Zebrafish 2010; 7:281-7. [PMID: 20874493 DOI: 10.1089/zeb.2010.0661] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Research involving model organisms necessitates recording and archiving many types of animal maintenance and use data. We developed a comprehensive inventory system using FileMaker Pro® to incorporate, record, and archive data on zebrafish stocks, tank organization, husbandry, and fish usage. Our relational database is constructed of tables containing detailed information on fish identity, parents of origin, tank location, mutant phenotypes, caretakers, natural mating and in vitro fertilization experiments, and fish mortality. In addition to its basic annotation and reporting capabilities, the database allows barcode scan entry of several actions, for example, moving a tank of fish, mating or performing in vitro fertilization with specific fish, and recording dead fish. All data are input in real time using either barcode scanning or manual entry. The database provides several types of preformatted reports, as well as printed labels for tank location and stock identification. In summary, we have created a versatile, multipurpose inventory system that can be personalized and enhanced for any zebrafish facility and can be further adapted to organize data and archival information for other model systems or applications.
Collapse
Affiliation(s)
- Jennifer L Anderson
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA.
| | | | | | | |
Collapse
|
5
|
Maier H, Lengger C, Simic B, Fuchs H, Gailus-Durner V, Hrabé de Angelis M. MausDB: an open source application for phenotype data and mouse colony management in large-scale mouse phenotyping projects. BMC Bioinformatics 2008; 9:169. [PMID: 18366799 PMCID: PMC2292142 DOI: 10.1186/1471-2105-9-169] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2007] [Accepted: 03/26/2008] [Indexed: 12/11/2022] Open
Abstract
Background Large-scale, comprehensive and standardized high-throughput mouse phenotyping has been established as a tool of functional genome research by the German Mouse Clinic and others. In all these projects, vast amounts of data are continuously generated and need to be stored, prepared for data-mining procedures and eventually be made publicly available. Thus, central storage and integrated management of mouse phenotype data, genotype data, metadata and linked external data are highly important. Requirements most probably depend on the individual mouse housing unit or project and the demand for either very specific individual database solutions or very flexible solutions that can be easily adapted to local demands. Not every group has the resources and/or the know-how to develop software for this purpose. A database application has been developed for the German Mouse Clinic in order to meet all requirements mentioned above. Results We present MausDB, the German Mouse Clinic web-based database application that integrates standard mouse colony management, phenotyping workflow scheduling features and mouse phenotyping result data management. It links mouse phenotype data with genotype data, metadata and external data such as public web databases, which is a prerequisite for comprehensive data analysis and mining. We describe how this can be achieved with a lean and user-friendly system built on open standards. Conclusion MausDB is suited for large-scale, high-throughput phenotyping facilities but can also be used exclusively for mouse colony management within smaller units or projects. The system is successfully used as the primary mouse and data management tool of the German Mouse Clinic and other mouse facilities. We offer MausDB to the scientific community as open source software to provide a system for storage of data from functional genomics projects in a well-structured, easily accessible form.
Collapse
Affiliation(s)
- Holger Maier
- Helmholtz Zentrum München - German Research Center for Environmental Health, Institute of Experimental Genetics (IEG), Ingolstädter Landstr, 1, D-85764 Neuherberg, Germany.
| | | | | | | | | | | |
Collapse
|
6
|
Calder RB, Beems RB, van Steeg H, Mian IS, Lohman PHM, Vijg J. MPHASYS: a mouse phenotype analysis system. BMC Bioinformatics 2007; 8:183. [PMID: 17553167 PMCID: PMC1899519 DOI: 10.1186/1471-2105-8-183] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2006] [Accepted: 06/06/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Systematic, high-throughput studies of mouse phenotypes have been hampered by the inability to analyze individual animal data from a multitude of sources in an integrated manner. Studies generally make comparisons at the level of genotype or treatment thereby excluding associations that may be subtle or involve compound phenotypes. Additionally, the lack of integrated, standardized ontologies and methodologies for data exchange has inhibited scientific collaboration and discovery. RESULTS Here we introduce a Mouse Phenotype Analysis System (MPHASYS), a platform for integrating data generated by studies of mouse models of human biology and disease such as aging and cancer. This computational platform is designed to provide a standardized methodology for working with animal data; a framework for data entry, analysis and sharing; and ontologies and methodologies for ensuring accurate data capture. We describe the tools that currently comprise MPHASYS, primarily ones related to mouse pathology, and outline its use in a study of individual animal-specific patterns of multiple pathology in mice harboring a specific germline mutation in the DNA repair and transcription-specific gene Xpd. CONCLUSION MPHASYS is a system for analyzing multiple data types from individual animals. It provides a framework for developing data analysis applications, and tools for collecting and distributing high-quality data. The software is platform independent and freely available under an open-source license 1.
Collapse
Affiliation(s)
- R Brent Calder
- Buck Institute for Age Research, Novato, California, USA
| | - Rudolf B Beems
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Harry van Steeg
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - I Saira Mian
- Buck Institute for Age Research, Novato, California, USA
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Paul HM Lohman
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Jan Vijg
- Buck Institute for Age Research, Novato, California, USA
| |
Collapse
|