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Exploring the portability of informatics capabilities from a clinical application to a bioscience application
Mark A Shifman1, Ranjana Srivastava, Cynthia A Brandt
1Center for Medical Informatics, Yale University School of Medicine, PO Box 208009, New Haven, CT 06520-8009. mark.shifman@yale.edu.
Summary
This study shows how clinical informatics tools, like XDesc (eXperiment Description), can be adapted for bioscience research, specifically for microarray data. This cross-domain application enhances both clinical and biological data management.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Clinical research databases often develop advanced informatics capabilities.
- Bioscience research, particularly microarray experiments, requires robust data description methods.
- Existing clinical informatics tools may have potential applications in biological research.
Purpose of the Study:
- To explore the portability of a clinical informatics system (XDesc) for biosciences.
- To adapt the Entity-Attribute-Value (EAV) database model from TrialDB for microarray sample description in the Yale Microarray Database (YMD).
- To identify and implement new capabilities beneficial for bioscience data within the XDesc framework.
Main Methods:
- Utilized the Entity-Attribute-Value (EAV) database implementation from the TrialDB clinical database.
- Applied XDesc to describe samples in three Drosophila microarray research projects.
- Integrated XDesc with both TrialDB and the Yale Microarray Database (YMD).
Main Results:
- Successfully linked XDesc with TrialDB and YMD.
- Demonstrated the utility of XDesc for describing microarray experimental data.
- Identified and implemented new informatics capabilities valuable for biosciences.
Conclusions:
- Informatics capabilities developed for clinical applications can be effectively ported to the biosciences.
- Cross-domain synergy between clinical and bioscience informatics is feasible and beneficial.
- Enhancements made to XDesc for biosciences were successfully integrated back into the clinical TrialDB system.