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EMR Data Exploration #61

Open gatechke opened 6 years ago

gatechke commented 6 years ago

Obtain access to Neptune
[x] Contact Patrick to help with getting login
[x] Install sqldeveloper to connect to Neptune
Understanding Neptune
[x] Ask Patrick to show you data summarization tool that he has built
[ ] Focus on diagnosis and medication tables in Neptune and understand the columns
[ ] Use SQL to conduct exploratory data analysis to understand type, amount and distribution of data on diagnosis and medication tables
[ ] Generate plot, summary and reports for EDA

shyamvis commented 6 years ago

Give Patrick (https://github.com/pohalloran) access here.

kayhan-batmanghelich commented 6 years ago

@gatechke what is the latest status on this?

gatechke commented 6 years ago

@kayhan-batmanghelich

I had a meeting with Patrick on last Thursday. He was still working with another person to get me the access to Neptune. I also asked Patrick to send existing data dictionary to me.

Currently, Diagnosis table, procedure table and a few reference tables are available on Neptune. Medication table hasn't been loaded yet.

Shyam and I will have one-o-one meeting on Monday morning.

gatechke commented 6 years ago

@shyamvis Table below: counts of distinct procedure code by procedure coding system. ~1.2 million records from 806 procedure codes have missing value in the filed of procedure coding system.

gatechke commented 6 years ago

@shyamvis Top 10 procedure codes that don't have procedure coding system populated

gatechke commented 6 years ago

@shyamvis Good news is that no missing value has been found in procedure code filed.

select count(*) from SAM_ETL.PROCEDURES where PROC_CODE is null;

shyamvis commented 6 years ago

Ke, Create a document that gives a brief description of the columns in the Diagnosis table fro future reference. You can include the counts table in it. Do the same for Procedures table. Upload them to dropbox.

shyamvis commented 6 years ago

Ke, Talk to Patrick and Brian McLay (who Patrick can introduce) to get a description of each of the 11 procedure coding systems.

gatechke commented 5 years ago

@shyamvis I contacted Brian McLay to find out the description of the 11 procedure coding systems. Based on his reply

CPT(R) is the same as CPT4 which is the Level I of HCPCS
HCPCS, ICD10PC, ICD9CM, CPT(R), CPT4 are standard code types
The other small procedure code types are custom values in the source systems. So we don’t know their exact mapping to standard code types.