Week 1: Peer review only
- P1 Acute Pancreatitis - Evan Minty MD @Evan_Minty (Peer reviewer )
- P2 Anaphylaxis - Andrea Noel MD @Andrea_Noel (Peer reviewer )
- P3 Appendicitis - Azza Shoaibi PhD BPharm @Azza_Shoaibi (Peer reviewer )
- P4 Neutropenia - Anna Ostropolets MD PhD @aostropolets (Peer reviewer )
Week 2: Evaluation and Peer review
- P5 Systemic Lupus Erythematous - (Evaluator) @jswerdel , (Peer reviewer ) @Daniel_Prieto
- P6 Acute Hepatic Failure - unassigned
- P7 - unassigned
Week 3:
- Parkinsons Disease - Allan Wu (need peer reviewer)
- Acute Myocardial Infarction - unassigned
Week 4:
- Hypoxic Ischemic Encephalopathy - Khyzer Aziz MD
We are looking for volunteers to take on P6, P7 and P9.
Week 1: Peer review only
- P1 Acute Pancreatitis - Evan Minty MD @Evan_Minty (Peer reviewer )
- P2 Anaphylaxis - Andrea Noel MD @Andrea_Noel (Peer reviewer )
- P3 Appendicitis - Azza Shoaibi PhD BPharm @Azza_Shoaibi (Peer reviewer )
- P4 Neutropenia - Anna Ostropolets MD PhD @aostropolets (Peer reviewer )
Week 2: Evaluation and Peer review
- P5 Systemic Lupus Erythematous - (Evaluator) @jswerdel , (Peer reviewer ) @Daniel_Prieto
- P6 Acute Hepatic Failure - (Evaluator) @Christian_Reich , (Peer reviewer) @Patrick_Ryan
- P7 Idiopathic Inflammatory Myopathies (Evaluator) @Christopher_Mecoli (Peer reviewer) pending
Week 3:
- P8 Parkinsons Disease - Need to run network study, (Evaluator) @allanwu, (peer reviewer) pending
- P9 Myocardial Infarction (Evaluator) @mirza_khan, (Peer reviewer) pending
Week 4:
- Hypoxic Ischemic Encephalopathy - @Khyzer_Aziz
Week 1: Peer review only
- P1 Acute Pancreatitis - Evan Minty MD @Evan_Minty (Peer reviewer )
- P2 Anaphylaxis - Andrea Noel MD @Andrea_Noel (Peer reviewer )
- P3 Appendicitis - Azza Shoaibi PhD BPharm @Azza_Shoaibi (Peer reviewer )
- P4 Neutropenia - Anna Ostropolets MD PhD @aostropolets (Peer reviewer )
Week 2: Evaluation and Peer review
- P5 Systemic Lupus Erythematous - (Evaluator) @jswerdel , (Peer reviewer ) @Daniel_Prieto
- P6 Acute Hepatic Failure - (Evaluator) @Christian_Reich , (Peer reviewer) @Patrick_Ryan
- P7 Idiopathic Inflammatory Myopathies (Evaluator) @Christopher_Mecoli (Peer reviewer) @agolozar
Week 3:
- P8 Parkinsons Disease - Need to run network study, (Evaluator) @allanwu, (peer reviewer) pending
- P9 Myocardial Infarction (Evaluator) @mirza_khan, @atifadam
Week 4:
- Hypoxic Ischemic Encephalopathy - @Khyzer_Aziz
Thanks @Gowtham_Rao and @Azza_Shoaibi for organizing this year’s 2023 Phenotype Phebruary, and thanks to all the volunteers who have taken on leading some part of the fun (@Evan_Minty @Andrea_Noel @Azza_Shoaibi @aostropolets @jswerdel @Daniel_Prieto @Christian_Reich @Christopher_Mecoli @agolozar @allanwu @mirza_khan @atifadam @Khyzer_Aziz )
There’s a lot going on during Phenotype Phebruary this year, and I’ve received a few folks asking: "how can I get involved?’
The answer is simple: Join the Journey! Read and post on the discussions here on the Forums, participate in a Phenotype WG meeting each Friday or listen to the weekly updates on our OHDSI community calls on Tuesday. Share your thoughts, ask your questions, solicit collaboration for developing or evaluating a phenotype. Everyone is welcome and encouraged to engage in this fun community collaboration opportunity, so we can all share, learn, and advance together.
‘Phenotype Phebruary’ is just an excuse to have our community put focused attention for a few weeks on an important topic that touches every study that everyone of us conducts every single day when trying to generate reliable evidence from observational data. The science of phenotyping is still very much unsettled (I would even contend that its still in its infancy, and more of an art than a real science at this point). There are still lots of disease targets that haven’t been phenotyped and lots of other diseases that have candidate algorithms but little-to-no proper validation. So there’s a lot of opportunities for us to work together to move this field forward. Let’s do it!
We are looking for volunteers to help with phenotype development activities for week 3 and 4. ie if you are familiar with atlas and would like to help with development of Cohort definitions for phenotype phebruary please message me.
This will require 1 to 2 hour session with either @Christopher_Mecoli @allanwu @mirza_khan or @Khyzer_Aziz to develop, review or improve the cohort definitions.
Today February 8th 2022, we are planning to have three interactive work sessions.
9am EST to 10 am EST - Inflammatory Myopathies - Dermatomyositis
- This cohort definition was previously developed by @Christopher_Mecoli at JHU.
- Purpose: assist running CohortDiagnostics, perform evaluation of the developed cohort definitions.
- Meeting invite
10am EST to 11am EST - ST Elevated Myocardial Infarction
- Input cohort definitions proposed here Phenotype Phebruary post 2022
- Purpose: Clarify clinical idea, determine if we need to develop additional cohort definition, execute a network study @mirza_khan
- Meeting invite
11am EST to 12pm EST - Parkinson’s disease
- Purpose: develop cohort definitions, execute network study, evaluate results @allanwu
- Meeting invite
Please join if you are avaiable.
For Phenotype Phebruary 2023 EHDEN Academy is delighted to launch a 3 module course on the ‘Phenotyping Problem’ from basic concepts to hands on example with relevant OHDSI tools, and best practice in phenotype development and evaluation.
The modules are facilitated by @Gowtham_Rao, @Azza_Shoaibi and @nigehughes.
This course is also the first in a series of, ‘One hour of your time’, courses to support quick learning and upskilling.
In this first module of three, available now, Gowtham Rao and Azza Shoaibi outline the ‘Phenotyping Problem’.
In the module we cover:
-
Outlining that phenotyping is more complex than ‘code picking’ and in some ways has not progressed as a discipline compared to other methodological innovation
-
It is critical for phenotyping to be undertaken with a best practice approach, outlined in this and subsequent modules
-
There are various stages to phenotyping:
- The research question and clinical definition of the disease or clinical event to be phenotyped
- Phenotype development within ATLAS
- Phenotype evaluation via Cohort Diagnostics and PheValuator
-
Ultimately, without a consistent, rigorous and reproducible approach to phenotyping errors and bias will impact on the study outcomes, reducing confidence also in the study and method
In module 2 we examine a best practice approach to phenotyping utilising the tools described above, and in module 3 we will wrap up with some best practice takeaways for your own phenotyping work. These modules will follow soon.
All our content is free and require a simple account set up via https://academy.ehden.eu!
@Gowtham_Rao @Patrick_Ryan @Azza_Shoaibi is there a Phenotype Phebruary meeting today (Fri Feb 10, 2023)? What time EST/CST? I see a Teams link above, but its not on my calendar so have to check my availability.
Yes, we’re meeting today at 9 am EST (very soon). I am afraid I don’t know how to obtain the link… @Gowtham_Rao should know how.
@allanwu Today we have the standing meeting of the OHDSI Phenotype Development and Evaluation Workgroup
To access meeting information - please use the OHDSI MS teams as shown in screenshot
Proposed agenda
Sorry I have a conflict at that time; I will see if I can join at the end. I see the Phea discussion coming up near the end; I’ll reply to @fabkury logic of the Phea SQL addition to tiered consensus in that thread to contribute.
Hi, are there instructions anywhere for how to do this? I have executed CohortDiagnostics and got results but I do not know how to make them available on data.ohdsi.org. Thanks!
Great question.
If the data object is <100mb and you want to make a shiny app on data.ohdsi.org, then the steps are:
- Go to the Shiny repo: https://github.com/OHDSI/ShinyDeploy
- Log in to your github account
- Create a fork:
- Select your user account name as the place to create the fork
- Clone your fork
- Create a folder in your clone for your shiny, e.g. “SLECohortDiagnostics”
- [Important] Download the latest version of CohortDiagnostics as zip from https://github.com/OHDSI/CohortDiagnostics/ .
1.Unzip and find the folder CohortDiagnostics\inst\shiny\DiagnosticsExplorer folder - Copy all files, as is, from the folder above to the folder you created in Step 6
- Create a new folder in your folder (created in step 6) – rename it as “data”
- Add your .sqlite file to the ‘data’ folder
- Test your app: Click on the below file object in your folder to open Rstudio and run app locally by clicking on RunApp after opening server.R file.
- Commit your work to github
- Create a Pull Request
a. Click
b. Click
- Enter the information for your pull request and save
- Notify a repo administrator (erica, Gowtham Patrick, Jenna, Martijn) of your pull request
- Will be available at https://data.ohdsi.org/SLECohortDiagnostics
If your .sqlite file > 100mb, then you cannot host it on github because of file size limitation - you will have to load to a postgres server exposed to the internet and data.ohdsi.org shiny server should know how to talk to it. Thats more complicated.
Thank you, really appreciate this. Will work on these steps.