Map OMOP data to inpatient_microbiology table

[razekmh]

Extract data from the example OMOP data to fill the inpatient_microbiology table from the validate article. This is a split from #17

Please feel free to assign yourself to the issue. Please the respective branch for development.

[AngharadGreen]

• It has been difficult to map the simulated OMOP data I have been working with to the RAMSES inpatient_microbiology table.
• There isn't a clear way of storing lab microbiology results in the OMOP CDM.
• I have found this paper useful - https://pubmed.ncbi.nlm.nih.gov/35612079/
• When we receive OMOP extract data from UCLH it will be useful to see how lab microbiology results are stored within the CDM.
• I have been working on issue Map OMOP data to inpatient_episodes table  #28 instead

[zsenousy]

• It has been difficult to map the simulated OMOP data I have been working with to the RAMSES inpatient_microbiology table.
• There isn't a clear way of storing lab microbiology results in the OMOP CDM.
• I have found this paper useful - https://pubmed.ncbi.nlm.nih.gov/35612079/
• When we receive OMOP extract data from UCLH it will be useful to see how lab microbiology results are stored within the CDM.
• I have been working on issue Map OMOP data to inpatient_episodes table  #28 instead

@AngharadGreen, Would you like to discuss this further in a call?

[AngharadGreen]

• It has been difficult to map the simulated OMOP data I have been working with to the RAMSES inpatient_microbiology table.
• There isn't a clear way of storing lab microbiology results in the OMOP CDM.
• I have found this paper useful - https://pubmed.ncbi.nlm.nih.gov/35612079/
• When we receive OMOP extract data from UCLH it will be useful to see how lab microbiology results are stored within the CDM.
• I have been working on issue Map OMOP data to inpatient_episodes table  #28 instead

@AngharadGreen, Would you like to discuss this further in a call?

Hi @zsenousy I have found some useful resources to help me with this mapping, I am just working through those today. I can meet tomorrow if there is a time that works for you?

[AngharadGreen]

Following this paper https://pubmed.ncbi.nlm.nih.gov/35612079/ I will try to map the OMOP CDM to the inpatient_microbiology ramses table following this figure -