OHDSI Home | Forums | Wiki | Github

OHDSI F2F: Phenotyping Instructions

General
#1

Hello Phenotypers,

Here’s how to test our fancy new phenotypes:

  1. If you have R and connectivity to CDMs, please grab the PhenotypeCharacterization package from
    https://github.com/alondhe/PhenotypeCharacterization. You can use the codeToRun.R script to execute the 3 functions.

  2. If you don’t have R, but have SQL access to CDMs, you can grab templated Sql from here:
    https://github.com/alondhe/PhenotypeCharacterization/tree/master/inst/sql/sql_server. You can then translate and render parameters using this web tool courtesy of @lee_evans: http://sqlrenderweb.ohdsi.org:2121/

Regardless of which approach above you choose, run all 3 functions in the codeToRun.R script in the R package / all 3 SQL scripts to generate CSVs about your cohort. You can find cohorts in the OHDSI version of Atlas at www.ohdsi.org/web/atlas, most are tagged with “F2F” in some fashion.

Once finished, if you are comfortable posting the CSVs to the Phenotype Git Repo: https://github.com/OHDSI/PhenotypeLibrary.

**Please note: some strata may be very small, so be mindful of this if you have concerns about identifiability of data. Also, please be certain your dataset license / usage agreements allow for dissemination of aggregated data. **

Thanks,
Ajit

1 Like
#2

the link http://sqlrenderweb.ohdsi.org:2121 is not working. tagging @lee_evans

#3

Hi @Vojtech_Huser

I checked and http://sqlrenderweb.ohdsi.org:2121 is working.

Perhaps port 2121 is blocked by your organization’s firewall?

#4

As a side note, is Sqlrender updated to its latest version here? In the past I have gotten some outdated translations of MSSQL code into PostgreSQL when using this site.

#5

@Juan_Banda I’ve now updated sqlrenderweb to use the latest Sqlrender version.

2 Likes
#6

@Juan_Banda and @bailey what version of Postgres are you using? Just wanted to try to replicate the issue you faced during the F2F with selecting string literals in Postgres.

#7

@Ajit_Londhe We’re on 9.5.

#8

We are on version 9.3.16

#9

Thanks!

t