Interoperability of Provenance Information in Clinical Research: a Case Study Combining HL7 FHIR and the Common Provenance Model - Supplementary materials
Creators
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1.
Center for Advanced Studies Research and Development in Sardinia
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2.
Masaryk University
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3.
Biobanking and Biomolecular Resources Research Infrastructure Consortium
Contributors
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1.
Masaryk University
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2.
Biobanking and Biomolecular Resources Research Infrastructure Consortium
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3.
Medical University of Graz
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4.
University of Würzburg
Description
This page contains the Supplementary Material for the paper Interoperability of Provenance Information in Clinical Research: a Case Study Combining HL7 FHIR and the Common Provenance Model, submitted for the 34th Medical Informatics Europe Conference (MIE2024).
This case study presents a simulated example of how the Common Provenance Model (CPM) can be applied in a simple research use case in the biomedical domain in combination with domain-specific provenance tracking methods, like the HL7 FHIR Provenance resource. Here we show how to express the provenance of a distributed process in which a large dataset related to colorectal cancer cohort cases (CRC-Cohort) is converted to HL7 FHIR resources and queried. In particular, the CRC-Cohort dataset is a collection of harmonised data related to over 10,000 cases of colorectal cancer samples collected by several European biobanks under the coordination of the national nodes of the Biobanking and Biomolecular Resources Research Infrastructure – European Research Infrastructure Consortium (BBMRI-ERIC) within the European Project ADOPT.
List of available resources:
| File name | Description |
| CRC_Cohort_ETL_and_query_provenance.ipynb | Python notebook used to generate and serialise the provenance of the use case. |
| prov_graphs.zip |
A folder containing the outputs of the script, which are:
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| HL7 FHIR resources.zip |
A folder containing a small set of synthetic HL7 FHIR Resources generated for this case study, in particular:
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Files
CRC_Cohort_ETL_and_query_provenance.ipynb
Additional details
Funding
Dates
- Submitted
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2024-04-03Date of submission of the paper to the MIE2024 conference editors for review.