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OHDSI / Aegis

Application for Epidemiological Geographic Information System (AEGIS): a system for semi-automatic GIS visualization based on the OMOP Common Data Model.
Apache License 2.0
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Adding Aegis to the OHDSI Shiny server #1

Open schuemie opened 6 years ago

schuemie commented 6 years ago

Hi @JaehyeongCho , @chandryou !

As briefly discussed at the symposium, I think it would be great if AEGIS was also running on the OHDSI Shiny server.

How do you envision this would work? Currently, when I try to run AEGIS locally it asks me for the IP, user name, and password of a database server. But I also see rds files in the repo, so the Korean data you demonstrated at the symposium is already available?

JaehyeongCho commented 6 years ago

Hi @schuemie !

First, I updated the rds file to use raster package so that no special repo is needed.

We will create and upload a synthetic cohort based on Korean data. Also, what do you think about making a synthetic cohort in the United States so that it can be demonstrated?

I wonder if it is automatically linked with the shiny server when I put AEGIS on this URL (https://github.com/OHDSI/ShinyDeploy).

It will take about a month to update AEGIS and run on the OHDSI shiny server.

schuemie commented 6 years ago

Hi!

You can't push to the ShinyDeploy repo directly. We'd like to set up a process where changes to the AEGIS repo automatically trigger a push to the ShinyDeploy repo. In other words: put the fully functioning version of AEGIS including data somewhere in a folder in the AEGIS repo and we'll make sure it gets deployed.

Just curious: are there strong reasons for using only synthetic data? I agree it would be nice to have US data as well. If possible real data.

chandryou commented 6 years ago

If there is any real world data with location, we’ll be so happy to apply AEGIS on it, of course!!

schuemie commented 6 years ago

What about the dialysis data you demonstrated earlier? Would it be possible to use the real data in the public Shiny app?

We might be able to use the HCUP database to generate dialysis numbers at a per-county level. But I'd need to check the license to see if we're allowed to do so. And I'd need to think about what to use as the denominator.

chandryou commented 6 years ago

AEGIS has two options. It can show only target cohort on map, or outcome cohort among target cohort on map.

We'd like to show both of them by AEGS (eg target cohort: ESRD / outcome cohort: on hemodialysis ->only target: ESRD / outcome among target: HD population among ESRD target cohort: lung cancer (observed two year)/ outcome cohort : mortality ->only target: lung cancer prevalence / outcome among target : 2-year mortality of lung cancer )

Thank you for your advice! That kind of DB is what we're looking for!!

gowthamrao commented 6 years ago

Hi @chandryou @schuemie is the Aegis app available for a public demo using the HCUP database for example?

JaehyeongCho commented 6 years ago

@gowthamrao Thanks for your comments!

In fact, I will be demonstrating AEGIS at this OHDSI symposium, which will be demonstrated using Synthea data from the US.

Because the Synthea data only contains data from Massachusetts, I could only make a figure for Massachusetts: image

What do you think about this figure?

gowthamrao commented 6 years ago

Thank you @JaehyeongCho

This is fantastic! Thank you so much for your contribution to the community. Looking forward to the demo at the symposium.