-
Notifications
You must be signed in to change notification settings - Fork 47
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Clarification on the "standard concepts from Athena" #45
Comments
Yeah not very well documented apologies. I am pretty sure the default concepts which are checked for download on the website were the only ones used. I successfully ran the ETL with the following files in my vocab folder:
If you can figure this out please do let us know it would save us a bit of effort in re-downloading and testing. |
Guys
easy to remember: when designing the etl we took all the available concepts
from athena that didn't need any proprietary licensing
2018-04-05 20:57 GMT+02:00 Alistair Johnson <[email protected]>:
… Yeah not very well documented apologies. I am pretty sure the default
concepts which are checked for download on the website were the only ones
used. I successfully ran the ETL with the following files in my vocab
folder:
-rw-rw-r-- 1 alistairewj alistairewj 475 Jun 15 2016 readme.txt
drwxrwxr-x 2 alistairewj alistairewj 4.0K Jun 15 2016 lib
-rw-rw-r-- 1 alistairewj alistairewj 32 Jun 15 2016 cpt.sh
-rw-rw-r-- 1 alistairewj alistairewj 31 Jun 15 2016 cpt.bat
-rw-rw-r-- 1 alistairewj alistairewj 7.2M Apr 7 2017 cpt4.jar
-rw-rw-r-- 1 alistairewj alistairewj 1.3G Sep 14 2017 vocab_download_v5_{9DBE59FA-D92B-0BB8-77A8-198AB3FE4736}.zip
-rw-r--r-- 1 alistairewj alistairewj 118M Sep 14 2017 DRUG_STRENGTH.csv
-rw-r--r-- 1 alistairewj alistairewj 896K Sep 14 2017 CONCEPT_CPT4.csv
-rw-r--r-- 1 alistairewj alistairewj 1.3G Sep 14 2017 CONCEPT_RELATIONSHIP.csv
-rw-r--r-- 1 alistairewj alistairewj 2.3G Sep 14 2017 CONCEPT_ANCESTOR.csv
-rw-r--r-- 1 alistairewj alistairewj 4.8K Sep 14 2017 VOCABULARY.csv
-rw-r--r-- 1 alistairewj alistairewj 30K Sep 14 2017 RELATIONSHIP.csv
-rw-r--r-- 1 alistairewj alistairewj 1.2K Sep 14 2017 DOMAIN.csv
-rw-r--r-- 1 alistairewj alistairewj 373M Sep 14 2017 CONCEPT_SYNONYM.csv
-rw-r--r-- 1 alistairewj alistairewj 13K Sep 14 2017 CONCEPT_CLASS.csv
-rw-r--r-- 1 alistairewj alistairewj 493M Feb 16 09:35 CONCEPT.csv
If you can figure this out please do let us know it would save us a bit of
effort in re-downloading and testing.
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
<#45 (comment)>,
or mute the thread
<https://github.com/notifications/unsubscribe-auth/AJF_doZuig91pCWqwxD7_kGM7ECb_GwNks5tlmkegaJpZM4TI4sm>
.
|
This is an OMOP stuff. The athena licensing for cpt4 codes used to have
a jar (this was years ago. no idea if this still apply)
|
Yeah, I figured it out the second after I added the comment! 🤣 In the Athena vocabulary distribution directory there's a JAR file and shell script that pull down CPT4 from UMLS. My confusion was due to the wording in I'd be happy to take a stab at clarifying that part of the instructions, if a PR would be welcome! |
The doc says:
what is meant by "standard"? the pre-selected ones on the webapp? or is there a list somewhere?
The text was updated successfully, but these errors were encountered: