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Requirements Development for the OHDSI Gold Standard Phenotype Library

(Nataly Patino) #21

When I look at concept 443454 (Cerebral Infarction) in Athena, the following shows up in the mapping:

When I select OMOP Stroke 1 I find that it also defines hemorrhagic stroke as follows:

Not sure if this is under that cerebral infarction definition or not (Im still learning about the ATLAS mapping) but I would be concerned about using this definition since ischemic stroke differs from hemorrhagic. @SCYou Let me know if I’m understanding the mapping correctly. I am very interersted in learning as much as I can.

(Seng Chan You) #22

@Nataly_Patino Fortunately, cerebral hemorrhage (376713) or subarachnoid hemorrhage (432923) are not included in the descendant concept ids of cerebral infraction (443454).
I don’t know the exact meaning of ‘HOI contains SNOMED’. Could you help us @Christian_Reich @Dymshyts?

(Christian Reich) #23

OMG. Forget the HOIs. There are old concepts from the OMOP experiment. Old as dirt. Will remove them from the hierarchy.

(Patrick Ryan) #24

Hey @jon_duke, when is the next Phenotype meeting taking place?

@Nataly_Patino and I would like to attend.

(Jon Duke) #25

Thanks for the love @Patrick_Ryan. It would normally be 12/28 but we are closed next week. So the following meeting is scheduled for 1/16, same bat time, same bat WebEx. Link

(Seng Chan You) #26

I released the process and the result for validation of ischemic stroke phenotype to the Phenotype Library github.

The definition of cohort in json and in sql are available. I used
OhdsiRTools to insert cohort definition from ATLAS.

The condition concept identifiders, included concept ids, source code in ICD-9-CDM and ICD-10, and additional constraints (such as ‘first event only’ or ‘all event’, visit_concept_id, and condition_type_concept_id) are also summarized for each cohort at here.

I made very simple and primitive shiny app to visualize discharge note of each subject in the cohort and check the validity of them by manual chart review.

Positive predictive value for ischemic stroke (inpatient or ED) and primary condition was 0.69. Positive predictive value for ischemic stroke (inpatient or ED) and primary condition and first event was 0.81, which is summarized here. In conclusion, I suggest to use the last cohort definition for ischemic stroke (ischemic stroke (inpatient or ED) and primary condition and first event).

I hope this help a community.

I’ll validate the hemorrhagic stroke cohort, too.

Cohort Packaging & Registry as GitHub Repository?
(Christian Reich) #27


Happy New Year. Couple questions:

  1. Nice Shiny app, but hasn’t the Atlas built a validation module?
  2. Have you notice in your validation the situation where there are both ischemic and hemorrhagic strokes coded simultaneously at a frequency that is to high for what would be expected?

(Seng Chan You) #28

I didn’t know that ATLAS has a validation module. Still, the primary purpose of this shiny app is querying and visualizing the discharge note of the event.

As long as I remeber, 4 among 200 cases with code of ischemic stroke was actually hemorrhagic stroke. And about 5% of ischemic stroke had hemorrhagic transformation.
I focused on the etiology of the stroke, which usually of interest .But I didn’t see the situation you mentioned, the case with both ischemic and hemorrhagic stroke together. Ther first cohort I tried to validate is ‘ischemic stroke’. The second would be ‘hemorrhagic stroke’. And the third can be ‘ischemic or hemorrhagic stroke.’

Thank you for invaluable comment again and Happy New Year, @Christian_Reich :slight_smile:

(Jon Duke) #29

@Christian_Reich @SCYou Here are @TreySchneider’s designs for his Atlas-integrated annotation widget (WebAPI and Atlas) and the code ready for testing by community (Atlas branch).

We will be discussing on the call Weds January 16th (WG link)

(Seng Chan You) #30

Thank you for telling this to us, @jon_duke . It is a really awesome widget for ATLAS.

(Aaron Potvien) #31

Hello everyone,

Happy New Year! Throughout last year, we had great support for the OHDSI Gold Standard Phenotype Library, including this forum, a use case document, a mock-up on the wiki including a submission form template, and great ideas, among others. As a new year’s resolution, let’s make a goal to have a functional library to debut at the symposium this year (likely in September)!

Some common phenotype subthemes arose during our bi-weekly meetings:

  1. Design: Rule-Based (Heuristic) Phenotypes
  2. Design: Computable (Probabilistic) Phenotypes
  3. Evaluation: Manual Chart Review / Annotations
  4. Evaluation: Automated / Algorithmic
  5. Library Architecture and Implementation

Call for volunteers!
For each of the items listed above, we’re looking to have a community member act as a point person to help develop and formalize OHDSI best practices. The goal is to develop robust documentation that we can put to use, which may in some cases overlap with the documentation of accompanying packages (e.g. Aphrodite for #2). This work is particularly timely, since once they are sufficiently developed, it may make the most sense to house our best practices in the upcoming Book of OHDSI.

Folks, this is a call to arms! Are there any volunteers who would be willing to participate in and/or lead these subgroups?

(Seng Chan You) #32

Thank you @apotvien for leading this work group.

I’m working on developing best practice for manual chart evaluation as I posted earlier. I’m happy to continue this effort.

Happy New Year :wink:

(Sarah Seager) #33

I’d be keen to volunteer. I am however very new to the OHDSI world and so my learning curve is fairly vertical at present, but that being said I’d love to help where I can.

Tricky phenotyping in ATLAS
(Kristin Kostka, MPH) #34

@apotvien, perhaps @sseager and I could tag team. I’m always eager to help collaborators get off the ground and make an impact. :smiley:

Plus, I’d personally really like to get better plugged into this WG. The need for this resource is enormously important – I’ve seen multiple studies where this could have expedited some of our decision making and helped us get closer to generating and disseminating high quality evidence. Count me in! Let’s chat on the 16th… (and maybe @MauraBeaton can add this to the 2019 OHDSI WG google doc. :wink:)

(Matt Spotnitz) #35

I have been designing phenotypes and cohorts at Columbia, and am happy to help with this effort. Thanks!

(Juan M. Banda) #36

Hello Aaron, I would like to volunteer for #2 I am definitely doing some work on documenting and should overlap nicely.

(Aaron Potvien) #37

Thank you all very much for volunteering and for your enthusiasm! We’re off to a great start!

I’ve just updated the wiki and have included all of you as members, with @Juan_Banda in charge of the computable phenotype design and @SCYou in charge of the manual chart evaluation.

We’ll certainly chat more about this on the 16th. The meeting time has been added to the wiki as well, but we may change the time for 2019 to best accomodate as many people as possible. I’d also like to point out that the Gold Standard Phenotype Library will be a subject of the community call on the 15th (12-1 ET), in case anyone wants to tune in then as well to hear more about this initiative.

Thanks again!

(Joel N. Swerdel) #38

Hi Aaron,
I’d like to be a part of the #4. It would be a good test for PheValuator.

(Aaron Potvien) #39

That’s great to hear, @jswerdel! I’ve put you down as the lead for Task #4 on the Wiki. Thanks for joining in!

(Andrew Williams) #40

Way to go @apotvien!
I’ll happily be Juan and/or Joel’s minion.