2023 Precision Medicine SymposiumRegister
The Precision Medicine Analytics Platform was created to help Johns Hopkins realize the promise of precision medicine: to reduce waste and improve patient outcomes, by using sophisticated new analytical tools and data; by discovering clinically-relevant subgroups of patients; and by bringing those discoveries back into the clinical setting.
Our Precision Medicine Centers of Excellence are leading the way in:
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A growing array of precision medicine tools and resources are available to help your clinical research team. Through the Precision Medicine Analytics Platform (PMAP) and other machine learning tools, you can draw insights on your own protected data. Want to learn more? Check these categories for more information.
Explore the advantages of working with the Precision Medicine Analytics Platform and discover the resources available to precision medicine researchers.
Johns Hopkins is seeing improvements in research and clinical care delivery through precision medicine. PMAP allows insights to be made more efficient–faster and with less trial and error.
Research is accelerated in PMAP by combining Epic data with research databases and other data collection tools (radiology, wearables, monitors, etc.) into one place.
PMAP cross-links this data to create a super record for our patients. The data is stored in the PMAP Data Lake and a slice of that data can be cut for projections and researcher use.
Leverage our precision medicine expertise and find ways to improve your data skills.
The PMAP Cookbook is a textbook of computational notebooks to help investigators at Johns Hopkins conduct clinical research.
The Cookbook provides examples of how to work with clinical data within PMAP using a combination of R and Python programming languages and modern data science libraries.
Data from each PMCOE is ingested into PMAP and stored in the same location with all other Johns Hopkins data. PMAP is secure and HIPAA-compliant. Access controls (based on JHED IDs) limit clinicians and researchers to the data defined by their IRB approval.
You’ll need to fill the skill set of two key roles:
Options include finding expertise in your team or department, or working with partners in CCDA, School of Public Health, APL, or others.
inHealth is continuously ingesting new data sources into PMAP. Review the Data Catalog (in the SAFE Desktop environment). If your data source is not listed, there is a process in place to present your case for inclusion. You can work with your PMCOE project manager or someone on the Precision Medicine team to submit a request for consideration. We formally evaluate, rank, and weigh new data sources according to the following criteria:
Yes, find this glossary of common terms here.
The PMAP Data Catalog contains information about the data that are available in the PMAP. The research community can browse and search the contents of the Data Catalog that includes sources such as Epic, REDCap, open specimen data set, imaging data set, etc.
The Data Catalog does not show the actual patient data. Rather, it provides information about the available data to guide subsequent requests for that data. It is THE place to look for the most up-to-date information on PMAP data.
Don't be intimidated when it comes to data science tooling. A great way to grow your data science skills is to learn from others. inHealth is expanding its team and resources in order to support researchers.
The Precision Medicine website was set up as a portal for all your clinical research needs in PMAP.
A pilot is underway to establish an institution-wide eConsent process. If successful, this process will be implemented and available to all clinical research protocols approved by JH IRB (anticipated Q1 2021).
Before beginning the IRB Approval Process, the following steps must be completed:
You can find the new IRB application flow here.
Learn more about the tools available to you in the world of precision medicine research. Discover how the IRB approval process works and follow the steps to access data.
inHealth is a strategic initiative to advance precision medicine at Johns Hopkins. By leveraging university-wide assets from the disciplines of medicine, engineering, nursing, public health, and our Applied Physics Laboratory, our team is developing patient-level insights that will improve health care.
The inHealth program is a part of the Johns Hopkins Medicine Strategic Plan to use data and technology in innovative ways to guide decision making in every corner of the Johns Hopkins organization.
The Precision Medicine Analytics Platform (PMAP) is a system that lets you obtain comprehensive clinical research data sets. The platform ingests disparate clinical and research data sources and provides machine learning tools to draw insights. In PMAP, the data collected for your studies is protected.
In the analysis layer of precision medicine at Johns Hopkins, several different environments are available:
To request a SAFE desktop for your study team or to request access to an existing SAFE folder, please submit the request using the SAFE Desktop Request Form.
Go to Johns Hopkins Precision Medicine Analytics Platform (PMAP) Cookbook for detailed instructions on how to get to the crunchr website.
There are several learning resources available while getting started on PMAP.
The Johns Hopkins PMAP Cookbook has links to many important FAQs and How To’s including:
Access the various analytic environments here:
Access crunchr Support through SAFE Desktop here.
With the Precision Medicine Analytics Platform (PMAP), you can combine data from multiple sources, including REDCap. Researchers can bring in data from a REDCap database, and enrich it with data from Epic, or from other systems such as imaging or genomics.
When projects use SAFE Desktop or PMAP as intended, they’re considered Tier 1 Risk (lowest risk) by the Johns Hopkins Data Trust. This low-risk tier waives the need for a review by the Data Trust, unless data is being shared outside the institution. For this reason, most researchers don’t need separate approval from the Data Trust when they get IRB approval, skipping a step that sometimes takes months.
If you would like access to an existing research project in PMAP, you MUST request access through the PI.*. The PI needs to fill out this form and submit for access request: https://t.jh.edu/pmap-edit-team.
*The PI has a legal requirement to control access to study data for his/her research team.
If you are a researcher or a member of a study team and would like additional information, please visit the Support Resources on the PM Portal.
A de-identified dataset of asthma and diabetes patient records are available for PMAP training.
Submit this request form for access to the Training Dataset.