RodImAnD: a MySQL-Database for analysing functional MRI Data from rodents in drug research
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1
Technische Universität Berlin, Neural Information Processing Group, Germany
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2
I. f. Pharmacology, Germany
Purpose Neuroscience has been revolutionized by two superior technologies: Functional brain imaging by MRI (fMRI), allowing repetitive, non-invasive observation of CNS functions, and mouse genomics, providing mice with defined deviations giving insight into molecular processes of brain function. The combination of these cutting-edge technologies opens a new avenue in brain research: Defining the role of gene products for delineating brain regions involved in information processing, in our case pain research in hypo- and hyperalgesic transgenic mice. The investigation of gene-drug-interactions incorporates the exploration of a high-dimensional space spun by variables like mouse strain, stimuli (i.e. different painfulness), analgesic drugs and differential response of brain regions of the pain matrix. Here even the pure administration of the huge amount of generated data is a complex task. Therefore, we aimed at developing a database allowing for (1) structured organization of the fMRI-data and (2) dynamic and interactive access to the data for performing statistical evaluation. Moreover, the integration of various other data sources like ABA, INCF WHS (see contributions on this meeting) becomes easily possible. This integrated database for brain function in transgenic mice strongly supports data sharing and collaboration with other working groups. Method We developed a database using the relational MySQL database management system, which works on many different system platforms and allows access from every SQL-aware application. The free integrated environment MySQL Workbench is used for database engineering. The database scheme reflects the workflow of the experiments (Fig. 1). The tables contain information about MRI measurement, experimental animals (including physiological monitoring), stimuli and pharmacological substances used during acquisition. Moreover, the database keeps track of the analysis tools used, their parameterisation and versions. Our major image analysis tool (MagnAn) is based on IDL (® ITTVIS), a high-level development environment for data analysis and visualization. Data is passed from the database and vice versa via a Java-based bridge component, which could easily be ported to other Java-capable environments like e.g. MATLAB. After acquisition the data are stored in the database alongside a first analysis grouping activated voxels into so-called blobs. The user can then select a group of experiments, e.g. different transgenic mice for same stimulation conditions, including already present analysis results and perform higher order analysis like average map generation on these data. The results are passed back to the database and linked to the original measurement. Results We obtained a data management system that allows for more efficient data handling, reading and processing. Compared to earlier storage in file folders, which implies a data organisation hierarchy complicating searches beyond the folder structure, lookups based on complex filter criteria are now easily possible. The laborious and error-prone manual assembly of interrelated data is eliminated. Search results include old matching experiments which might have been overlooked without a central database, effectively enlarging the base of statistical analysis and possibly reducing the need for new experiments. Furthermore, compared to file system based storage, interrelated datasets cannot be displaced, renamed or cleared accidentally. Conclusion The presented database allows for an effective storage and retrieval of the huge amount of f MRI data and their subsequent analysis. It is more robust than pure file system based storage and simplifies and encourages the reuse of formerly acquired results. The possibility of reusing results will largely increase as other groups start to incorporate their data into the database. This will hopefully further decreasing the need for new animal experiments and thereby supports animal welfare (3R concept).
Conference:
Neuroinformatics 2010 , Kobe, Japan, 30 Aug - 1 Sep, 2010.
Presentation Type:
Poster Presentation
Topic:
Neuroimaging
Citation:
Gaudnek
MA,
Hess
A and
Konerth
L
(2010). RodImAnD: a MySQL-Database for analysing functional MRI Data from rodents in drug research.
Front. Neurosci.
Conference Abstract:
Neuroinformatics 2010 .
doi: 10.3389/conf.fnins.2010.13.00144
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Received:
21 Jun 2010;
Published Online:
21 Jun 2010.
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Correspondence:
Andreas Hess, I. f. Pharmacology, Erlangen, Germany, andreas.hess@pharmakologie.uni-erlangen.de