Abstract
BackgroundSystematic, standardized and in-depth phenotyping and data analyses of rodent behaviour empowers gene-function studies, drug testing and therapy design. However, no data repositories are currently available for standardized quality control, data analysis and mining at the resolution of individual mice.DescriptionHere, we present AHCODA-DB, a public data repository with standardized quality control and exclusion criteria aimed to enhance robustness of data, enabled with web-based mining tools for the analysis of individually and group-wise collected mouse phenotypic data. AHCODA-DB allows monitoring in vivo effects of compounds collected from conventional behavioural tests and from automated home-cage experiments assessing spontaneous behaviour, anxiety and cognition without human interference. AHCODA-DB includes such data from mutant mice (transgenics, knock-out, knock-in), (recombinant) inbred strains, and compound effects in wildtype mice and disease models. AHCODA-DB provides real time statistical analyses with single mouse resolution and versatile suite of data presentation tools. On March 9th, 2017 AHCODA-DB contained 650 k data points on 2419 parameters from 1563 mice.ConclusionAHCODA-DB provides users with tools to systematically explore mouse behavioural data, both with positive and negative outcome, published and unpublished, across time and experiments with single mouse resolution. The standardized (automated) experimental settings and the large current dataset (1563 mice) in AHCODA-DB provide a unique framework for the interpretation of behavioural data and drug effects. The use of common ontologies allows data export to other databases such as the Mouse Phenome Database. Unbiased presentation of positive and negative data obtained under the highly standardized screening conditions increase cost efficiency of publicly funded mouse screening projects and help to reach consensus conclusions on drug responses and mouse behavioural phenotypes. The website is publicly accessible through https://public.sylics.com and can be viewed in every recent version of all commonly used browsers.
Highlights
Systematic, standardized and in-depth phenotyping and data analyses of rodent behaviour empowers gene-function studies, drug testing and therapy design
The standardized experimental settings and the large current dataset (1563 mice) in AHCODA-DB provide a unique framework for the interpretation of behavioural data and drug effects
Several repositories are available to archive and mine qualitative data on mouse mutants (e.g. Mouse Genome Informatics (MGI) website [6]) and precomputed group averages of inbred mouse lines (e.g. WebQTL [7], the Mouse Phenome Database [8], the International Mouse Phenotyping Consortium [9]), no repository is currently available for quantitative high-content mouse phenomics data other than the supplementary data of scientific publications
Summary
The ongoing production of high-content datasets and integration in AHCODA-DB allows –omics scale comparison of behavioural tests, mouse phenotypes and pharmacological responses. By the unbiased publishing of both positive and negative results, AHCODA-DB facilitates scientists in reducing animal usage by avoiding unnecessary repetition of experiments. The integration of data obtained from different phenotyping platforms, in both common inbred strains as well as mutant lines, with and without drug treatments, increases the scientific value of this open-access repository. Through its accessible web interface and various data analysis and mining opportunities, this repository will increase cost efficiency of publicly funded mouse screening projects and help to reach consensus conclusions on drug responses and mouse phenotypes. Availability and requirements The website is publicly accessible through https://public.sylics.com and can be viewed in every recent version of all commonly used browsers
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