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A unified framework for managing provenance information in translational research

DOI: 10.1186/1471-2105-12-461

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Abstract:

We identify a common set of challenges in managing provenance information across the pre-publication and post-publication phases of data in the translational research lifecycle. We define the semantic provenance framework (SPF), underpinned by the Provenir upper-level provenance ontology, to address these challenges in the four stages of provenance metadata:(a) Provenance collection - during data generation(b) Provenance representation - to support interoperability, reasoning, and incorporate domain semantics(c) Provenance storage and propagation - to allow efficient storage and seamless propagation of provenance as the data is transferred across applications(d) Provenance query - to support queries with increasing complexity over large data size and also support knowledge discovery applicationsWe apply the SPF to two exemplar translational research projects, namely the Semantic Problem Solving Environment for Trypanosoma cruzi (T.cruzi SPSE) and the Biomedical Knowledge Repository (BKR) project, to demonstrate its effectiveness.The SPF provides a unified framework to effectively manage provenance of translational research data during pre and post-publication phases. This framework is underpinned by an upper-level provenance ontology called Provenir that is extended to create domain-specific provenance ontologies to facilitate provenance interoperability, seamless propagation of provenance, automated querying, and analysis.The key notion of translational research is the flow of information resources (experiment data, publications/literature, clinical trial data, or patient records) across organizations, domains, and projects that impacts both patient care and (through a feedback process) basic research. This necessitates keeping track of the provenance metadata of resources from the point of their creation to intermediate processing, and finally their end use. Provenance, derived from the French term provenir meaning "to come from", has traditionally played an impor

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