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Establish criteria for validating transformed data against OMOP CDM expectations.
Dependent on the pipeline, and the OMOP Spark dataset, that needs to conform to the OMOP schema
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Here I want to:
- [ ] Explore the different tables from the extract to identify which ones contain the relevant data
- [ ] Match `concept` table to tables that contain the relevant microbiology d…
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1. `psql -h localhost -p 5432 -U postgres -W -d adrd1 -f /omop_ddl/OMOPCDM_postgresql_5.4_ddl.sql`
2.
```
ALTER TABLE person
ALTER COLUMN care_site_id TYPE float;
ALTER TABLE person
ALTER COLUMN prov…
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There are huge amounts of data being generated at hospitals every day. Up to 80% of this data is collected in an unstructured format and a large portion of it as free text. In order to extract value f…
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CCDA 1.1 and 2.1 are compatible, 2.0 isn't
We should check for 2.0, and log what we find.
We should also save the document Id and the filename, and find a way to tag OMOP rows with their source do…
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Now we have shown that LLettuce can work for drug concepts, we need to expand to non-drug concepts.
This could be as simple as removing references to "domain = 'Drug'" from queries. However, the OMOP…
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Atm lets do only the fct_LifeTrack.R file
We can do the other modules later
### function assertAnalysisSettings_LifeTrack
analysisSettings$cohortId cohort to extract data from
analysisSettings$n…
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## CDM or THEMIS convention?
THEMIS
## Table or Field level?
Table
## Is this a general convention?
Applies to multiple fields
## Summary of issues
Below is taken from a real EHR data (P…
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Check and summarize errors on last run in CCDA_OMOP_by_Pthon
- [ ] pull main and master branches from github and foundry, check they are synched. (We should be working in Foundry on the master b…
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PROBLEM STATEMENT:
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There can be problems with vocabularies that share a specific code, an example being:
ICD10: H05.1 - Chronic inflammatory disorders of orbit (https://ath…