mimic-omop
mimic-omop copied to clipboard
MIT-LCP
Mapping the MIMIC-III database to the OMOP schema
Fixes #75 Modifies hyperlinks so that they resolve to mimic iii documentation.
In the main repository README, hyperlinks to mimic III table descriptions result in a "404 Not Found" error under the sections for "OMOP TABLES LOADED" and "MIMIC TABLES EQUIVALENCE".
Hello! I may have found an issue with the MIMIC OMOP CDM mapping for the `note` table's `note_type_concept_id` column. The existing ETL script uses [a lookup table](https://github.com/MIT-LCP/mimic-omop/blob/master/extras/concept/note_category_to_concept.csv) to populate this...
The doc says: > The standard concepts from Athena have been downloaded and are available somewhere (including running the extra script to download CPT code definitions) what is meant by...
There seems to be an extra "AS" near line 67, that needs to be removed. SELECT org_name::TEXT, count(1) FROM ( SELECT DISTINCT ON (hadm_id, spec_type_desc, org_name, coalesce(charttime, chartdate)) **AS** org_name...
The query to build the populate the DEATH from MIMIC-III to OMOP looks for patients in two ways: 1) from the admission table, WHERE deathtime IS NOT NULL, joining then...
OHDSI researchers created a new mapping for mimic IV. Would you consider adding a link to it in readme? https://github.com/OHDSI/MIMIC
example unit test for HCUP https://github.com/OHDSI/JCdmBuilder/blob/master/tests/HCUPETLToV5/HcupTests.R Documentation: http://ohdsi.github.io/WhiteRabbit/riah_test_framework.html This framework does not test whole set of data but simply picks one row in source and specifies how it should appear...
Some checks are not comparing source and target but only looking at target. e.g., here https://github.com/MIT-LCP/mimic-omop/blob/master/etl/StandardizedClinicalDataTables/VISIT_DETAIL/check_etl.sql#L117 Such DQ checks may be added to OHDSI Tools. On the other hand, OHDSI...