Explorations into the provenance of high throughput biomedical experiments

Abstract

The field of translational biomedical informatics seeks to integrate knowledge from basic science, directed research into diseases, and clinical insights into a form that can be used to discover effective treatments of diseases. We demonstrate methods and tools to generate RDF representations of a commonly used experimental description format, MAGE-TAB, mappings of MAGE documents to two general-purpose provenance representations, OPM (Open Provenance Model) and PML (Proof Markup Language). We show through a use case simulation that the data represented in MAGE documents can be completely represented in OPM and PML through use of round trip analysis of certain examples. The success in mapping MAGE documents into general-purpose provenance models shows that promise in the implementation of the translational research provenance vision. © 2010 Springer-Verlag Berlin Heidelberg.