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Francis Ratsimbazafy
Project Personnel, Vanderbilt University Medical Center
11 active projects
test
Scientific Questions Being Studied
this is for tutorial and test. Every friday we need tutorial to show people how to work with the workbench. This tutorial is for these people.
Project Purpose(s)
- Educational
Scientific Approaches
this is for tutorial and test. Every friday we need tutorial to show people how to work with the workbench. This tutorial is for these people.
Anticipated Findings
this is for tutorial and test. Every friday we need tutorial to show people how to work with the workbench. This tutorial is for these people.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Registered TierResearch Team
Owner:
- Francis Ratsimbazafy - Project Personnel, Vanderbilt University Medical Center
Collaborators:
- Hiral Master - Project Personnel, Vanderbilt University Medical Center
- Thomas Rion - Project Personnel, Vanderbilt University Medical Center
How To Work With COPE Survey Data
Scientific Questions Being Studied
We recommend that all researchers explore the notebooks in this workspace to learn the basics of how to work with All of Us COPE data. What should you expect? This notebook will show what versions, topics, and questions are available for COPE, and teach you best practices on how to query them. It will also talk about key summary statistics about the data.
Project Purpose(s)
- Educational
- Methods Development
- Other Purpose (This is an All of Us Tutorial Workspace. It is meant to provide instruction for key Researcher Workbench components and All of Us data representation.)
Scientific Approaches
This Tutorial Workspace contains one Jupyter Notebook written in Python. The notebook contains information on how to use All of Us COPE data in the workbench to understand how participants lived through the pandemic. COPE survey data has been rolled out in different versions: May, June, July/Aug/Sep. Except from some minor adjustments, versions generally share the same set of questions. This notebook shows how to extract these information.
Anticipated Findings
By reading and running the notebook in this Tutorial Workspace, researchers will understand how to work with COPE survey data from the workbench. They will learn how to query information about how All of Us participants experienced anxiety, stress, physical activity, mood, general well-being, social distancing, etc. during the pandemic.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Registered TierResearch Team
Owner:
- Francis Ratsimbazafy - Project Personnel, Vanderbilt University Medical Center
Collaborators:
- John Carr - Project Personnel, Vanderbilt University Medical Center
How To Work With Fitbit Data
Scientific Questions Being Studied
We recommend that all researchers explore the notebooks in this workspace to learn the basics of how to work with All of Us Fitbit data. What should you expect? This notebook will show what types of data are available for Fitbit, and teach you best practices on how to query them. It will also talk about key summary statistics about each type of data.
Project Purpose(s)
- Educational
- Methods Development
- Other Purpose (This is an All of Us Tutorial Workspace. It is meant to provide instruction for key Researcher Workbench components and All of Us data representation.)
Scientific Approaches
This Tutorial Workspace contains one Jupyter Notebook written in Python. The notebook contains information on how to use All of Us Fitbit data in the workbench and how to extract information from it.
Anticipated Findings
By reading and running the notebook in this Tutorial Workspace, researchers will understand how to work with Fitbit CDR data from the workbench. They will learn how to query information about steps, heart rate, and daily activity summary.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Registered TierResearch Team
Owner:
- Francis Ratsimbazafy - Project Personnel, Vanderbilt University Medical Center
Collaborators:
- Kelsey Mayo - Other, Vanderbilt University Medical Center
- John Carr - Project Personnel, Vanderbilt University Medical Center
- Adrienne Roman - Project Personnel, Vanderbilt University Medical Center
Phenotype - Type 2 Diabetes
Scientific Questions Being Studied
The Notebooks in this Workspace can be used to implement well-known phenotype algorithms in one’s own research.
Project Purpose(s)
- Educational
- Methods Development
- Other Purpose (This is an All of Us Phenotype Library Workspace created by the Researcher Workbench Support team. It is meant to demonstrate the implementation of key phenotype algorithms within the All of Us Research Program cohort.)
Scientific Approaches
This is not applicable for the stable environment that is meant for QC and test. Any phenotype library in this environment is meant to test the data before it hits production.
Anticipated Findings
By reading and running the Notebooks in this Phenotype Library Workspace, researchers can implement the following phenotype algorithms: Jennifer Pacheco and Will Thompson. Northwestern University. Type 2 Diabetes Mellitus. PheKB; 2012 Available from: https://phekb.org/phenotype/18
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Registered TierResearch Team
Owner:
- Francis Ratsimbazafy - Project Personnel, Vanderbilt University Medical Center
Collaborators:
- John Carr - Project Personnel, Vanderbilt University Medical Center
Phenotype - Breast Cancer
Scientific Questions Being Studied
The Notebooks in this Workspace can be used to implement well-known phenotype algorithms in one’s own research.
Project Purpose(s)
- Educational
- Methods Development
- Other Purpose (This is an All of Us Phenotype Library Workspace created by the Researcher Workbench Support team. It is meant to demonstrate the implementation of key phenotype algorithms within the All of Us Research Program cohort.)
Scientific Approaches
This question is not applicable for a phenotype library. This is meant for an internal study to QC the data. It is not meant for publication.
Anticipated Findings
By reading and running the Notebooks in this Phenotype Library Workspace, researchers can implement the following phenotype algorithms: Ning Shang, George Hripcsak, Chunhua Weng, Wendy K. Chung, & Katherine Crew. Breast Cancer. Retrieved from https://phekb.org/phenotype/breast-cancer.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Registered TierResearch Team
Owner:
- Francis Ratsimbazafy - Project Personnel, Vanderbilt University Medical Center
Collaborators:
- John Carr - Project Personnel, Vanderbilt University Medical Center
Phenotype - Dementia
Scientific Questions Being Studied
The Notebooks in this Workspace can be used to implement well-known phenotype algorithms in one’s own research.
Project Purpose(s)
- Educational
- Methods Development
- Other Purpose (This is an All of Us Phenotype Library Workspace created by the Researcher Workbench Support team. It is meant to demonstrate the implementation of key phenotype algorithms within the All of Us Research Program cohort.)
Scientific Approaches
This is not applicable for a phenotype library meant to be run internally. This phenotype library is used to QC the data.
Anticipated Findings
By reading and running the Notebooks in this Phenotype Library Workspace, researchers can implement the following phenotype algorithms: Ritchie, M., Denny, J., Crawford, D., Ramirez, A., Weiner, J., … Roden, D. (2010). Robust replication of genotype-phenotype associations across multiple diseases in an electronic medical record. American Journal of Human Genetics. 87(2):310 doi: 10.1016/j.ajhg.2010.03.003
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Registered TierResearch Team
Owner:
- Francis Ratsimbazafy - Project Personnel, Vanderbilt University Medical Center
Collaborators:
- John Carr - Project Personnel, Vanderbilt University Medical Center
Phenotype - Depression
Scientific Questions Being Studied
The Notebooks in this Workspace can be used to implement well-known phenotype algorithms in one’s own research.
Project Purpose(s)
- Educational
- Methods Development
- Other Purpose (This is an All of Us Phenotype Library Workspace created by the Researcher Workbench Support team. It is meant to demonstrate the implementation of key phenotype algorithms within the All of Us Research Program cohort.)
Scientific Approaches
This is not applicable for a phenotype library at the stable environment. The workspace is meant to be run for QC purposes.
Anticipated Findings
By reading and running the Notebooks in this Phenotype Library Workspace, researchers can implement the following phenotype algorithms: This Workspace contains an implementation of a phenotype algorithm for depression: This algorithm was obtained from the eMERGE network. Citation: TBA. KPWA/UW. Depression. PheKB; 2018 Available from: https://phekb.org/phenotype/1095
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Registered TierResearch Team
Owner:
- Francis Ratsimbazafy - Project Personnel, Vanderbilt University Medical Center
Collaborators:
- John Carr - Project Personnel, Vanderbilt University Medical Center
Phenotype - Ischemic Heart Disease
Scientific Questions Being Studied
The Notebooks in this workspace can be used to implement well-known phenotype algorithms in one’s own research.
Project Purpose(s)
- Educational
- Methods Development
- Other Purpose (This is an All of Us Phenotype Library Workspace created by the Researcher Workbench Support team. It is meant to demonstrate the implementation of key phenotype algorithms within the All of Us Research Program cohort.)
Scientific Approaches
Not Applicable because this is a phenotype library. This does not have scientific approaches.
Anticipated Findings
By reading and running the Notebooks in this Phenotype Library Workspace, researchers can implement the following phenotype algorithms: Christianne L. Roumie; Jana Shirey-Rice, Sunil Kripalani. Vanderbilt University. MidSouth CDRN - Coronary Heart Disease Algorithm. PheKB; 2014. Available from https://phekb.org/phenotype/234.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Registered TierResearch Team
Owner:
- Francis Ratsimbazafy - Project Personnel, Vanderbilt University Medical Center
Collaborators:
- John Carr - Project Personnel, Vanderbilt University Medical Center
How to Work with All of Us Survey Data
Scientific Questions Being Studied
We recommend that all researchers explore the notebooks in this workspace to learn the basics of All of Us Program Data. What should you expect? By running the notebooks in this workspace, you should get familiar with how to query PPI questions/surveys, what the frequencies of answers for each question in each PPI module are.
Project Purpose(s)
- Educational
- Methods Development
- Other Purpose (This is an All of Us Tutorial Workspace created by the Researcher Workbench Support team. It is meant to provide instruction for key Researcher Workbench components and All of Us data representation. )
Scientific Approaches
We recommend that all researchers explore the notebooks in this workspace to learn the basics of All of Us Program Data. What should you expect? By running the notebooks in this workspace, you should get familiar with how to query PPI questions/surveys, what the frequencies of answers for each question in each PPI module are.
Anticipated Findings
By reading and running the notebooks in this Tutorial Workspace, researchers will learn the following: - how to query the survey data, - how to summarize PPI modules, and questions.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Registered TierResearch Team
Owner:
- Francis Ratsimbazafy - Project Personnel, Vanderbilt University Medical Center
Collaborators:
- Kelsey Mayo - Other, Vanderbilt University Medical Center
- John Carr - Project Personnel, Vanderbilt University Medical Center
- Adrienne Roman - Project Personnel, Vanderbilt University Medical Center
How to Get Started with Registered Tier Data
Scientific Questions Being Studied
We recommend that all researchers explore the notebooks in this workspace to learn the basics of All of Us Program Data. What should you expect? This notebook will give you an overview of what data is available in the current Curated Data Repository (CDR). It will also teach you how to retrieve information about Electronic Health Record (EHR), Physical Measurements (PM), and Survey data.
Project Purpose(s)
- Educational
Scientific Approaches
This Tutorial Workspace contains two Jupyter Notebooks (one written in Python, the other in R). Each notebook is divided into the following sections: 1. Setup: How to set up this notebook, install and import software packages, and select the correct version of the CDR. 2. Data Availability Part 1: How to summarize the number of unique participants with major data types: Physical Measurements, Survey, and EHR; 3. Data Availability Part 2: How to delve a little deeper into data availability within each major data type; 4. Data Organization: An explanation of how data is organized according to our common data model. 5. Example Queries: How to directly query the CDR, using two examples of SQL queries to extract demographic data. 6. Expert Tip: How to access the base version of the CDR, for users that want to do their own cleaning.
Anticipated Findings
By reading and running the notebooks in this Tutorial Workspace, you will understand the following: All of Us data are made available in a Curated Data Repository. Participants may contribute any combination of survey, physical measurement, and electronic health record data. Not all participants contribute all possible data types. Each unique piece of health information is given a unique identifier called a concept_id and organized into specific tables according to our common data model. You can use these concept_ids to query the CDR and pull data on specific health information relevant to your analysis. See our support article Learning the Basics of the All of Us Dataset for more info.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Registered TierResearch Team
Owner:
- Francis Ratsimbazafy - Project Personnel, Vanderbilt University Medical Center
Collaborators:
- Kelsey Mayo - Other, Vanderbilt University Medical Center
- Adrienne Roman - Project Personnel, Vanderbilt University Medical Center
- John Carr - Project Personnel, Vanderbilt University Medical Center
How to Work with All of Us Physical Measurements Data
Scientific Questions Being Studied
How to navigate around physical measurements? This workspace shows how researchers can start working on physical measurements data. These measurements (PM) were taken at signup time and include height, weight, hip circumference, bmi, bood pressure.
The workspace contains snippets of code that show how to manipulate PM data, how to clean them and remove potential outliers. The codes are written in both R and Python.
Project Purpose(s)
- Educational
- Methods Development
Scientific Approaches
There is no anticipated approach for this study because this is not a research project.
The approach is to use the Physical measurements data from the measurement table, plot them, and show how to clean them.
Anticipated Findings
There is no anticipated findings from this study, because this is an operational work.
However, researchers new to the workbench will find here all the resources needed to start working with the AoU data.
Demographic Categories of Interest
This study will not center on underrepresented populations.
Data Set Used
Registered TierResearch Team
Owner:
- Francis Ratsimbazafy - Project Personnel, Vanderbilt University Medical Center
Collaborators:
- Kelsey Mayo - Other, Vanderbilt University Medical Center
- John Carr - Project Personnel, Vanderbilt University Medical Center
- Adrienne Roman - Project Personnel, Vanderbilt University Medical Center
Request a Review of this Research Project
You can request that the All of Us Resource Access Board (RAB) review a research purpose description if you have concerns that this research project may stigmatize All of Us participants or violate the Data User Code of Conduct in some other way. To request a review, you must fill in a form, which you can access by selecting ‘request a review’ below.
