SDOP-DB;A database for international sharing of mouse phenotyping protocols

Available mouse phenotyping protocols

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Downloads
SDOP data are available in the PPML format

Links
Japan Mouse Clinic (JMC)
European Mouse Disease Clinic (EUMODIC)
SOPDB in JMC
EMPReSS in EUMODIC

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Technology and Development Unit for Knowledge Base of Mouse Phenotype, RIKEN BRC, Japan

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COUNTER from July 1, 2009

News

March 7, 2011 : Add a filtering feature in each of protocol databases for mouse phenotypic analyses.

June 7, 2010 : PPML files have become downloadable [Link].

March 1, 2010 : An article on the SDOP-DB is published in Bioinformatics [Link].

October 27, 2009 : SDOPs of five kinds of mouse phenotyping tests (Tail suspension test, Hot plate test, Tail flick test, Prepulse inhibition test, and Oral glucose tolerance test) have been published.

July 1, 2009 : SDOPs of three kinds of mouse phenotyping tests (Hematological test, Clinical biochemical test, Body fat percentage and bone mineral density-DEXA-) have been published.

June 1, 2009 : SDOP-DB has been published on the web. SDOPs of five kinds of mouse phenotyping tests (Open-field test, Rota-rod test, SHIRPA test, ABR, and Blood pressure) have been published. Further, SDOPs of “Husbandry” and “Reproductive technologies” in the item of “Others” have been published.

Introduction

Results of a specific experimental analysis come under the considerable influence of its own protocol differences. Therefore, standardised data formats to describe detailed laboratory workflows are essential for the integration and sharing of experimental results with high reliability. For that purpose, we have developed a new data format termed Standardised Description of Operating Procedures (SDOP), which provides an assay-specific descriptive framework and enables direct and detailed comparison of procedural parameters. Using this data format, here we present a comparative standardised-protocol database, SDOP-DB, as a practical application to share, compare, and evaluate the contents of protocols to enable data comparisons and analyses in the field of mouse phenotype assessments.

About SDOP and SDOP-DB

1) SDOP is a new data format to provide an assay-specific descriptive framework (ref. Outline of parameter items defined in the SDOP format），enabling users to easily and directly compare detailed protocol differences among institutes/laboratories.

2) Using the SDOP format，we have developed a comparative standardised-protocol database， SDOP-DB， for the integration and sharing of mouse phenotyping protocols.

3) Because assay-specific SDOPs for mouse phenotypic analyses were developed in complete compliance with international standard data models，a draft version of Minimal Information to describe Mouse Phenotyping Procedures (MIMPP) and Phenotyping Procedures Markup Language (PPML)， they are in accordance with international standards for data exchange.

4) The SDOP-DB is helpful for identifying procedural parameter(s) that can result in differences in data between different protocols， because users can easily access phenotype data through hyperlinks to mouse phenotype databases.