The ICTR Informatics Core provides an integrated set of tools and services to help clinical researchers collect, extract, and analyze clinical data for research at every stage of the research lifecycle.
Prepare Your Study
Investigators with access to Epic can use Epic’s SlicerDicer to get rough patient counts. To find SlicerDicer in Epic, go to the Epic search bar and type in SlicerDicer. IRB approval is needed prior to using these data for recruitment or to conduct your research or publish.
Note that SlicerDicer has the following limitations:
– not all data in Epic are available for searching in SlicerDicer (most notably text data)
– patient data collected outside of the Johns Hopkins Epic system will not be available in SlicerDicer with the exception of some historical lab and encounter data.
To learn more about SlicerDicer visit http://slicerdicer.johnshopkins.edu/
TriNetX is a self-service tool launched broadly in January 2019. TriNetX has advanced analytic tools and a cleaner set of data then what is available in SlicerDicer. TriNetX is populated with data from Epic which have been cleaned, curated and more fully mapped to codes like LOINC to improve data quality and analysis. The date range of data in TriNetX is from July 2016 – present in order to reduce the problem of unexpected gaps in the data prior to the Johns Hopkins Medicine Epic enterprise go-live. Attend one of our training sessions to receive an account.
To learn more, visit: https://ictr.johnshopkins.edu/trinetx/
Accrural to Clinical Trials (ACT)
The ACT Network is a real-time platform allowing researchers to explore and validate feasibility for clinical studies across the NCATS Clinical and Translational Science Award (CTSA) consortium, from their desktops.
Core for Clinical Research Data Acquisition (CCDA)
When investigators have sophisticated inclusion and exclusion criteria that cannot be satisfied by using SlicerDicer or TriNetX, we recommend that they contact the CCDA for assistance. Investigators receive 2 initial hours of service subsidized by the ICTR, during which we are often able to complete simple feasibility queries. For more information, visit https://ictr.johnshopkins.edu/ccda
If you need a letter of support from the ICTR Informatics Core, please contact Diana Gumas, IT Senior Director at email@example.com or Christopher Chute so that we can better understand your proposed study, and provide you with a signed letter of support on official letterhead.
We offer 90 minute sessions attended by Dr. Christopher Chute, Diana Gumas, and invited guests (as required) to address the specific questions being posed by the study teams.
To apply for an informatics consult, please click on this application link.
The form requires:
- Email address
- Phone number
- Date of preferred informatics consult session
- IRB protocol number
- Study hypothesis and aims
- Questions you hope to have answered at the informatics consult
For more information, contact Diana Gumas at firstname.lastname@example.org.
Tools for Conducting Your Study
CRMS has the following main features:
- Protocol information from eIRB2
- Registry of study participants
- Management of study accruals
- Consent tracking
- Secure location for study-related documents
- Pre-configured and adhoc reports
- Multiple interfaces with Epic, including sending data to Epic about the study and the study participants
CRMS must be used by studies which could result in a patient bill. It may also be used by retrospective studies to define the study cohort in order to facilitate data extraction from Epic and other information systems.
If you are already a CRMS user, you can access the software at http://research-prod.jhmi.edu/.
For more information about CRMS, visit: https://cscop.jhmi.edu/confluence/display/RESRCH/CRMS+Home (This website requires that you are on campus or are using VPN.)
The ICTR Informatics Core provides multiple tools and services for study recruitment.
- With prior IRB approval, investigators may use SlicerDicer to get an identifiable list of patients for whom they have provided care who meet the inclusion and exclusion criteria for their study.
- With IRB approval, the Core for Clinical Data Acquisition (CCDA) can provide investigators with a list of patients that meeting their study’s inclusion and exclusion criteria. SlicerDicer cannot be used if the investigator needs to recruit patients who they have not previously had a treating relationship or if the inclusion and exclusion criteria for their study is more complex than what can be accomplished using SlicerDicer. Read more: https://ictr.johnshopkins.edu/ccda
- Investigators can contact potential candidates via the Epic MyChart patient portal. Read more here.
- Epic can be modified to alert the study team about patients who may be eligible for their study. For example, Epic can be programmed with a best practice advisory (BPA) decision support rule which sends a message to the study team when a patient is detected as being a candidate for their study. Examples of triggers that have been built in the past are patients who are admitted to the ED that meet a certain set of criteria, or who have a lab result that is in a desired range. Read more: https://ictr.johnshopkins.edu/PACE
For more general information about study recruitment, we recommend visiting our recruitment page.
OpenSpecimen is a Biospecimen Information Management System that is a scalable solution for a biorepository which meets the needs of a broad group of investigators and biobanks.
At Johns Hopkins, OpenSpecimen is currently used in multiple departments, including several Precision Medicine Centers of Excellence (PMCOE).
Watch the presentation below to learn about our services.
- Annotation of research and clinical data
- Specimen Information Interfaced with Precision Medicine
- Query capability
- Specimen and Derivative Tracking
- Specimen Event Tracking
- Epic Patient Lookup-Enabled
- Bulk Load Capability for Legacy Data
- Security (Enterprise Servers/JHED Login)
- Open Source with strong user community
- Extensible Architecture for Future Interfaces
- Considered a “Tier A” best practice for storing biospecimen metadata including PHI by the Data Trust’s Research Sub-council
- Support from the ICTR
Explanation of Charges– April 2021
Fee Schedule – effective July 1, 2021
If you are interested in using OpenSpecimen at Johns Hopkins, please contact Bob Lange at email@example.com.
Anaylsis Your Data
The Core for Clinical Research Data Acquisition (CCDA) assists researchers with accessing clinical data for research purposes. The CCDA is staffed with experienced data analysts who will assist you with access to data while also helping you comply with Data Trust privacy and security regulations.
Natural Language Processing (NLP) is a programming technique to find and extract data of interest from text documents.
NLP can sometimes involve a simple search for known text strings but is often more complex due to the ways that human beings use language. For example, the concept of smoking could be expressed in many different ways in a text document, such as “has never smoked”, “used to smoke 3 packs a day”, “recently quit smoking”, “is in a smoking cessation program”.
The Center for Clinical NLP, with faculty and staff from the Johns Hopkins School of Medicine, the Johns Hopkins Whiting School of Engineering, and the Johns Hopkins Applied Physics Laboratory (APL), are well versed in techniques and tools to assist you with your NLP needs.
The mission of the Johns Hopkins Precision Medicine Analytics Platform is to “revolutionize the capacity of health centers to continuously improve their patient and population health outcomes at more affordable costs through modern data science and rigorous systems engineering practices.”
The vision of PMAP is to:
- Accelerate biomedical discovery
- Accelerate translation of discovered knowledge to improve the delivery of patient-centered care
- Increase efficiency and effectiveness of clinical care and discovery
- Provide a platform for extending JHM excellence to expanded populations
The PMAP platform, as seen in the following diagram, pulls data from the Epic Medical Record and other data sources into a Data Commons, where the data are integrated together and available in a format that is operable by sophisticated machine learning and natural language processing technologies. With IRB approval, data from the PMAP Data Commons can be provisioned into a secure Research Environment for analysis by study teams and data scientists using tools like the Jupyter notebook and PMAP-developed cohort discovery tools. Validated algorithms and tools can be promoted to the Delivery Platform for use in clinical care or for commercialization.
PMAP is available to all Johns Hopkins Medicine researchers. A portion of the services are provided at no cost. To view the pricing structure, visit https://pm.jh.edu/pricing.
You can learn more about inHealth Precision Medicine activities at the following links:
SAFE, the Secure Analytic Framework Environment, is a virtual desktop that provides Johns Hopkins Medicine investigators (whether engaged in research or other data-intensive activities) with a secure environment to analyze and share sensitive data (e.g. PHI, PII) with colleagues.
- Software: the SAFE is installed with productivity software such as Microsoft Word and Excel, as well as statistical software, including SAS, Stata, R, R Studio, and Python. Other software applications can be installed for investigators willing to cover the licensing fees.
- Data sharing across study teams: the SAFE can be mapped to a secure file folder, where investigators can upload and share sensitive data. Data analytic teams can extract data and deliver to the SAFE so that investigators can analyze and view the data together. The SAFE’s basic file share stores up to 100 GB of data; storage can be expanded for an additional fee ($3/month per 100 GB).
- Security: In order to comply with federal and institutional requirements to protect patient data, the physical location of the data extracted, as well as the security of the data while in transit, must be protected against unauthorized access and use. Investigators who use the SAFE reduce the risk of copying data to an unencrypted desktop or device because the SAFE provides the tools to securely analyze and share PHI/PII all within the SAFE environment.
There is no cost for the “basic” SAFE, which includes use of the virtual desktop, 100 GB of storage space, and the licensing for SAS and Stata. Investigators can request additional software or increase the storage space on the file share for a fee. (Fees depend on the specific licensing fee for the software and the amount of storage space requested.)
Future features include batch processing for large analysis tasks to increase processing performance, support for genomic data, and a larger catalog of available applications.
Request Your SAFE
To request a SAFE for your study team or to request access to an existing SAFE folder, please submit the request using the SAFE Desktop Request Form. Please note that at this time, JH staff (not students) have access to submit the form. Students can receive SAFE desktops, but staff members must request them on behalf of the student.
The SAFE Desktop is managed and supported by IT@JH. Please contact the IT Help Desk at 410-955-HELP with any technical issues.
Office of Research Administration (ORA)
Institutional Review Board (IRB)
Data Trust Council
Biostatistics resources (links to Karen’s team and the BEAD Core)
Chesapeake Regional Information System for our Patients (CRISP)
Precision Medicine Analytic Platform (PMAP)
CADRE Committee for COVID-19 research