University of California Davis
University of Cincinnati Medical Center
University of Massachusetts Medical School
University of Michigan Medical School
Vanderbilt University School of Medicine
Protocols & Methods
Reagents & Resources
Tissues & Samples
Conditions of Use
Data Usage Policy
Energy Expenditure Analysis
CalR: Indirect Calorimetry Analysis
Guidelines & Policies
Coordinating and Bioinformatics unit
The MMPC web portal was developed using an n-tier architecture design (illustrated above). The user interface is an ASP.NET application written in C# using the .NET framework. The middle object layer is a .NET dynamic link library. This layer has a number of biological domains and provides object oriented access to the data. The data layer is a relational database (SQL Server 2000) used to store all the data generated by the consortium. These systems have been developed to minimize maintenance, but provide a robust scalable model for future growth and interactions at the national level with other organism databases.
The requirements analysis for the MMPC consortium was accomplished over several months through conversations with the investigators, reading the documentation produced by the validation committees and face to face meetings during the biannual steering committee meetings. Use-case diagrams were produced for those interactions described in the analysis and a careful assessment of the data model requirements was conducted. Because this portal is membership driven, there are two broad categories of data that we have to persist and use. The system stores both the administrative data dealing with the details of the consortium membership as well as the animal model data generated by the MMPC membership. In addition to the data requirements, we also developed the requirements for the object model (API) necessary to support the data model in a production environment. The object model was developed to not only support the local programming environment, but also to be deployable as a SOAP or Web Service for machine to machine interactions. This is important in order for outside institutions (eg. NCBI, NCI,etc) to download load the animal model data from the MMPC in an automated fashion.
We use controlled vocabularies extensively throughout the website. All the drop down boxes used during data entry or data query use either existing controlled vocabularies or ones developed by the consortium. We have populated our ontology “terms” table with
terms (Stanford) and anatomy terms from the
Computational Biology and Informatics Laboratory
(University of Pennsylvania). For mice, we have used the Standard Anatomical Nomenclature Database (University of Edinburgh/The Jackson Laboratory) to relate these terms to developmental (Theiler) stages. In addition, we have imported mouse gene information from the
for those genes currently associated with GO terms. This enables searches using the gene name, symbol, or GO concept. We are currently completing programs for automatic, scheduled retrieval and import of externally maintained data (such as GO). Note that we do not reproduce these databases; rather, we import enough information to permit structured data entry and searches. Should users require further details about a term or gene, we will provide hyperlinks to the appropriate web resource. The ontologies required for microarray data exchange were imported from Chris Stoeckert’s work in the
MGED Ontology Workgroup
. The MMPC CBU has been very careful to align our vocabulary with existing groups whenever possible. This will be very important for automated data exchange between the MMPC and other biological databases.
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Please acknowledge all posters, manuscripts or scientific materials that were generated in part or whole using funds from the MMPC using the following text:
Financial support for this work was provided by the NIDDK Mouse Metabolic Phenotyping Centers (National MMPC, RRID:SCR_008997,
) under the MICROMouse Program, grants DK076169.
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Warranty disclaimer and copyright notice
THE NATIONAL MMPC MAKES NO REPRESENTATION ABOUT THE SUITABILITY OR ACCURACY OF THE SOFTWARE OR DATA FOR ANY PURPOSE, AND MAKES NO WARRANTIES, EITHER EXPRESS OR IMPLIED, INCLUDING MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE OR THAT THE USE OF THE SOFTWARE OR DATA WILL NOT INFRINGE ANY THIRD PARTY PATENTS, COPYRIGHTS, TRADEMARKS, OR OTHER RIGHTS. THE SOFTWARE AND DATA ARE PROVIDED "AS IS".
The Mouse Metabolic Phenotyping Centers (MMPC) is an NIDDK funded consortium and adheres to the
NIH Data Sharing Policy
MMPC clients make their data freely available whereby MMPC users may freely build upon, enhance and reuse those data for any purpose without restriction. Scholarly citation norms must be followed for content reuse. Please acknowledge the MMPC using the following text: 'The MMPC data used in this manuscript was supported by the NIDDK National Mouse Metabolic Phenotyping Centers (National MMPC, RRID:SCR_008997,
)'. To cite specific MMPC centers, please use the appropriate RRID available from the MMPC website (
Please note that the acknowledgment text includes a Research Resource Identifier (RRID) for the MMPC CU and Centers. Reproducibility is one of the corner stones of effective, open and transparent biomedical published research. However, too often, resources (e.g. model organisms, antibodies, and tools) are not reported with adequate detail to ensure others can replicate or expand upon the published results. The Research Resource Identification Initiative (#RII) seeks to change these limitations in reporting by the use of unique Research Resource Identifiers (RRIDs). This initiative is designed to encourage authors to provide identification of the types of resources used in their research by adding a globally unique accession number to the resources described in the their manuscripts. These identifiers, called RRIDs, will allow authors to cite the resources that they use in their manuscripts. RRIDs allow for easy tracking of all papers that have used the same resource making it easy to access how the same resources works in other scenarios.
It is expected that MMPC users follow scholarly citation norms, giving credit to fellow scholars when accessing/using protocols and data, including data derived by MMPC (such as summary data) and any plots, tables or screenshots depicting those data.
It is possible for invalid or incomplete results to be presented on the MMPC web site due to software bugs, data problems, or artifacts of human error. Data sets are not necessarily static; we reserve the right to post corrections and updates as needed.
Data contributors and data users may not use MMPC in any unlawful manner, or in any manner that could impair MMPC services, security or functionality. Automated usage (webcrawlers and similar) must observe each page's "meta robots" html tags and space requests by ≥ 2 seconds. We reserve the right to block any IP associated with what we consider to be excessive or abusive usage patterns, and/or to take any action we deem necessary.
The MMPC is a National Institutes of Health-sponsored resource that provides experimental testing services to scientists studying diabetes, obesity, diabetic complications, and other metabolic diseases in mice.
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