Enterprise-wide data services are available to help Mass General Brigham investigators and research groups expedite the process of obtaining data for analysis or to gauge study feasibility. Repositories of clinical samples and data, as well as public data sets, are accessible to researchers through the tools and processes outlined below.
A new initiative, the Mass General Brigham Big Data Commons, enables Big Data to be integrated with the RPDR and tighter integration of the RPDR with Epic. The specific areas of focus of the Big Data Commons are to create a Research Patient Portal for direct patient engagement in Epic, creating a distributed query system to allow more types of Partners Big Data to be integrated and become discoverable by researchers, and specific integration platforms such as the Biobank Portal which serve to researchers new forms of Big Data in easily consumable forms.
Click to learn more about the Complete PDSR Curated Data Set
Overview of the Complete PDSR Curated Data Set
The new Complete Patient Data Science Repository (PDSR) Curated Data Set increases the speed to research discovery and enables machine learning (ML) and artificial intelligence (AI) computation in a secure environment within the Mass General Brigham firewall. Access to the complete set of MGB patient population data with removed patient identifiers according to HIPAA-defined format within the Complete PDSR Curated Data Set helps researchers generate hypotheses and develop models. It facilitates the study of extensive populations of patients and clinical data without compromising patient privacy.
Direct access to this repository without the need to obtain an IRB-approved protocol broadens researchers’ opportunities for understanding, evaluating, and analyzing clinical data. Connecting to this repository within the secure MGB Data Enclave platform promotes collaboration for researchers working in teams with a shared set of computational resources and tools.
Visit the Complete PDSR Curated Data Set Home Page for more information.
Data Dictionaries for Digital Research Data Repositories
The RPDR has a new Daily Query Tool where users can query source systems which are updated in the RPDR on a daily basis.
This new functionality, allows users to query source systems that are updated in the RPDR on a daily basis. These include Encounter Detail, Demographic Detail, Laboratory Tests, Radiology Tests, Providers, Specimens, Transfusion Services, Biobank Patient Consents and perhaps the most powerful is the Notes Search (EPIC + LMR Ambulatory notes and Clinical Reports). Using the Notes Search in the Daily Query tool allows users to search for terms contained in notes without having to wait for delayed coded information.
In addition to having more patients available, the daily query tool is helpful for finding time-sensitive patients for enrollment in studies and clinical trials.
Identified detailed data (Demographic and Identifying Patient Information) can be requested through the Daily Query Tool.
*Note: http://rpdr.partners.org (this link is internal only and requires Internet Explorer; you must be logged on to a Mass General Brigham workstation or connected to the Mass General Brigham network via VPN)*
The Biobank Portal is a tool that links consented subjects from the MGB Biobank with their healthcare data.
The ACT Network is a real-time platform allowing researchers to explore and validate feasibility for clinical studies from their desktops.
mi2B2 Medical Image Access Tool
mi2b2 - Medical Image Access Tool
The Medical Imaging Informatics Bench to Bedside (mi2b2) workbench serves as a secure bridge between a researcher and the Mass General Brigham PACS systems, which aims to:
- Facilitate searching for, reviewing, and accessing clinically acquired images that are stored in several PACS (Picture Archive and Communication System) systems that serve the Mass General Brigham institutions
- Enable researchers to extend the use of the Research Patient Data Registry (RPDR) to access clinical images on patients of interest for enhanced research studies, with proper IRB approval
- Enable efficient retrieval of medical images (DICOM format) for lists of patients generated from research, teaching, and clinical activities in keeping with all regulatory guidelines
- Provide access to only patient images authorized by approved IRBs and provide audit trails for HIPAA compliance.
If using the RPDR Query tool and the RPDR Data Acquisition Engine (Image Request Wizard), a user can obtain aggregate numbers of patients with user-defined characteristics based on a query or upload a pre-defined list of Medical Record Numbers and then receive more detailed medical information about the queried patient cohort. Either way, the user is provided with a personalized mi2b2 workbench, directly configured to include the queried cohort information. It is delivered in a folder along with the encrypted RPDR data results. For instructions on how to use the RPDR to request mi2b2 workbench, please visit: (http://rpdr.partners.org) ->Help -> Request Images Help.
Detailed tutorial support for new users of the mi2b2 software is found at http://mi2b2help.partners.org.
The IDEA Platform hosts public data sets that research teams at Mass General Brigham can access using standard data analysis tools.
For research data queries, Investigators should use the RPDR, the Epic/Mass General Brigham eCare Reporting Workbench should not be used.
Use of the Epic/Mass General Brigham eCare Reporting Workbench for research is medical records research.
REMINDER: The Epic/Mass General Brigham eCare Reporting Workbench tool is for use in clinical care.
For research data queries, Investigators should use the Research Patient Data Registry (RPDR); the Epic/Mass General Brigam eCare Reporting Workbench tool should not be used.
If RPDR is insufficient for your research, you may use the Epic/Mass General Brigham eCare Reporting Workbench if:
- you have IRB approval AND
- use is in accordance with specific restrictions as outlined in the FAQs.
Use of medical records and protected health information (PHI) for research must be compliant with the HIPAA Privacy Rule, the Common Rule, and other laws that regulate patient and study subject privacy, in addition to Mass General Brigham policies on encryption and Information Security.
Paul J. Anderson, MD, PhD, Chief Academic Officer, Brigham and Women’s Hospital
O’Neil Britton, MD, CHIO, Partners HealthCare
Shelly Greenfield, MD, MPH, Chief Academic Officer, McLean Hospital
Jigar Kadakia, Chief Information Security and Privacy Officer, Partners HealthCare
Anne Klibanski, MD, Chief Academic Officer, Partners HealthCare
Janet (Jodi) Larson, MD, Acting Associate Chief Medical Officer, Newton Wellesley Hospital
Gregg S. Meyer, MD, Chief Clinical Officer, Partners HealthCare
Harry W. Orf, PhD, Senior Vice President for Research, Massachusetts General Hospital
Kerry Ressler, MD, PhD, Chief Scientific Officer, McLean Hospital
Ross Zafonte, DO, Senior Vice President of Medical Affairs, Research and Education, Spaulding Rehabilitation Network
The Defined Exam Retrieval Service enables Mass General Brigham investigators to obtain radiologic imaging studies for research purposes.
The Enterprise Medical Imaging team within the Data Science Office recently launched the Medical Imaging Data As A Service (MIDAS) that enables MGB investigators to obtain radiologic imaging studies for research purposes.
The Defined Exam Retrieval enables Mass General Brigham investigators to obtain radiologic imaging studies for research purposes. Researchers may request retrieval of large batches up to 1,000 imaging studies per request. Studies will be automatically retrieved from clinical imaging archives and stored in a temporary location that has security and access control based on IRB permissions. To use this service, the list of studies must contain three data elements for each study: the site where the study was performed; the site MRN; and, the accession number. There is an option for images to be de-identified if required for the research protocol. The de-identification process follows the DICOM standard for de-identification and replaces/removes/modifies PHI following a standard workflow. A key to the de-identification will be provided so that the study staff can identify the studies as needed. Estimated image retrieval time is 3-5 business days, once the PAS Group is created, however please note, customization requests may delay turnaround time.
ImageMover is a self-service tool that allows Mass General Brigham investigators to keep their dataset current by requesting a limited number of individual exams (small batches <200 exams) to be extracted and added to a project dedicated ERIS storage space. Should you require this service for pulling limited exams, please request ImageMover on your form.
Step 1: Use the link to request a Personnel Authorization System (PAS) group for your research team. A PAS group is required for granting access to the directory where retrieved data will be temporarily stored. It ensures that only those members of your research group (per your approved IRB) will have access to your data. Please allow time for approval of your PAS request if you do not already have one. The same PAS group can be used for multiple requests if the group members are on the IRB protocol governing the request.
Step 2: Complete the Medical Imaging Data As A Service (MIDAS) Request Form and prepare a .csv or .xls file (eg, Microsoft Excel Spread Sheet) of the imaging studies you want to retrieve with the following information for each study (3 columns, 1 row per study):
- Patient Medical Record Number (MRN) from site where images were obtained; DFCI studies should use BWH MRNs
- Accession Number (unique radiologic imaging study identifier)
- Site where the images were obtained (e.g., BWH, DFCI, MGH)
To retrieve this information, you can use the RPDR Query Tool - Data Request Wizards. (RPDR Query Tool) from within the MGB Firewall. For detailed instruction click the document below.
Optional Step 2a: If De-Identification is required, this needs to be requested on the form. The specifications for the DICOM fields that will be automatically de-identified is available at this link. If there are specific DICOM tags that should not be de-identified and maintaining that specific information is approved per the IRB protocol, please specify that on the form.
Step 3: When the requested imaging studies are available, you will be notified via email with instructions for how to access the files. Files may be stored in the assigned location without cost for up to 180 days, after which the research team must move the files to their own permanent storage location.
Fee-for-service storage options may be found on the Digital Research website.
For more information, please review the MIDAS Defined Exam Retrieval FAQs