Comments (5)
Opme:
Why do you want ICD9 to ICD10? We are mapping to the Standard Concepts, and they are in SNOMED for Conditions. Anything I am missing?
from etl-cms.
I am not an expert in this area but at least the CONDITION_SOURCE_VALUE (condition_occurrence) and PROCEDURE_SOURCE_VALUE (procedure_occurrence) codes are still in icd9 after the SynPuf ETL is run.
I think it will cause issues for application developers when there are mixed icd codes for a multi-year study? At least for the use case I am developing to calculate surgeon complication rates the code only works when the data is not using mixed codes. To make it easier to analyze this data, all codes would need to be converted to a common code.
Mike
from etl-cms.
Yes, the source_value contains these values, but they should be the one actually in the source. Not some mapped alternative.
The mapping happens in the condition_concept_id and procedure_concept_id. Conditions are mapped to SNOMED, whether they are ICD-9-CM or ICD-10-CM. What you are trying to do is part of the OMOP standard. Use those.
from etl-cms.
I see. That is good news. I will close this and test with some icd10 codes to make sure it is working.
from etl-cms.
The ETL code is designed to transform the Synpuf data as it is. That is- the source data uses specific vocabularies, including ICD9. Stuffing ICD10 codes into ICD9 data columns and expecting it to convert makes no sense. The Synpuf data is 2008-2010, before adoption of ICD10 in the US.
from etl-cms.
Related Issues (20)
- Column mismatch in create_CDMv5_tables.sql and load_CDMv5_vocabulary.sql HOT 1
- Error on Step 5 of Python ETL process HOT 2
- Person ID as integer, CMS's synthetic data has string IDs HOT 1
- CMS RIF to OMOP ETL? HOT 2
- CMS ACO CCLF --> OMOP V5 HOT 1
- md5 sums don't match files - https://github.com/OHDSI/ETL-CMS/blob/master/python_etl/README.md HOT 4
- Issue while running python code to get the claims data HOT 6
- Memory issue of steps 5 in ETL Script HOT 9
- drug_era, observation_period, cost column mismatch HOT 5
- Update ETL logic to support CDM 6.X HOT 5
- CDMv5.2 is not accessible HOT 2
- KeyError: 'Place of Service' HOT 3
- location_id is null for all care_site records HOT 3
- missing 'DE1_0_2010_Beneficiary_Summary_File_Sample_1.zip' HOT 5
- FTP server down? HOT 1
- Downloading final data HOT 1
- Incorrect URL to one source Synpuf file HOT 5
- Updating to newer CDM versions + upload R script available HOT 1
- key error '40213148'
- Convert CMS SynPUF to OMOP v5.4
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from etl-cms.