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Exporting ICD9CM mapping from Athena

Hello guys, I guess I needed another thread for some newer attention.

I have a bunch of codes in ICD9CM concept code (e.g. 427.41) and I need it to OMOP.

There is a (next-to-)perfect map on Athena. However, it is very hard for me to convert my codes from one map to another and then back to OMOP. There are too much information loss over multiple mapping.

Is there a way to export the below webpage data into a big file of .csv?

The items in the red circles are exactly the data I need.


Hello @lychenus,

Could you please elaborate on what you’re trying to do? Are you finding ICD9 codes mapping manually using website and then mapping records one by one (“back to OMOP”)? What’s the reason behind “information loss” if “There is a (next-to-)perfect map on Athena”?

Your similar question in another thread has been answered. Have you tried following the steps?

Yes I followed the steps. I realize something is still missing. As my source_to_concept_map is still empty.

I saw the suggested map on Athena and I just wanted to take the suggested map as stated on there like

162.3 → 261236 Primary malignant neoplasm of upper lobe, bronchus or lung

And there was a thread like just now. I do not think it is a very idea to keep going on that as it gets convoluted.

I tried to download the ICD9CM vocabulary from Athena again. I looked at at CONCEPT_RELATIONSHIP.csv again,

something like

41881366 41881366 Maps to 20190221 20991231

There are some “Maps to”, but can never find where is the “Non-standard to Standard map (OMOP)” as on Athena

tried the SQL query, but has no idea how that would be helpful too.

On Athena the verbiage =

In the Concept relationship table the verbiage =

These are the same. Athena has a more friendly user interface term.

As Maxim suggested, you will find the EHDEN Academy on the OMOP CDM and on the OMOP vocabularies very helpful!

Ah I realize why something is missing. If I only download ICD9 or SNOMED seperately, the “maps to” relationship gets filtered out.

If I download the two vocab list selected together

44828793 201820 Maps to 20190228 20991231

shows up;.


Sorry for the mess and thanks for the help. Please have a nice weekend and so am i.