Hello everyone,
I am currently working on a master’s internship project with a French hospital group (GHICL - Lille (North of France)) with @AntoineLamer and Dr. Nicolas Baclet.
The objective of the project is to develop an ETL pipeline to standardize microbiology laboratory data into the OMOP Common Data Model. The data include:
- Microbiological culture results
- Identified microorganisms (bacteria, yeasts, etc.)
- Antimicrobial susceptibility testing (AST) / antibiograms
- Susceptibility interpretations based on EUCAST recommendations (S, I/SFE/SFP, R)
- Multidrug-resistant organisms (BMR)
- Hospitalization and specimen-related information
We are currently exploring how to best represent these data in OMOP, particularly regarding:
- Representation of antimicrobial susceptibility testing (AST) results in OMOP, including susceptibility interpretations (S, I/SFE, R) and quantitative measurements (MICs, inhibition zone diameters)
- Handling non-standard local laboratory terminology
- Mapping microorganisms whose taxonomy has changed over time (renamed, reclassified, or merged organisms)
- Managing organisms that do not have an obvious standard OMOP concept or direct mapping
- Handling local abbreviations and laboratory-specific codes for specimens, organisms, and resistance phenotypes
I would be very interested to know whether similar projects have already been conducted within the OHDSI community. If so, I would greatly appreciate any references to publications, presentations, ETL approaches, or lessons learned from previous implementations.
Thank you very much for your help and feedback.