BMI Tools

Clinical Research Data Warehouse

Clinical Research Data Warehouse (CRDW)

CTSI’s CRDW provides no-cost self-service tools to CITI-trained research and QI teams for project feasibility, cohort discovery and data extraction.

CRDW tools include the i2b2 Cohort Discovery Tool, TriNetX cohort query and analysis tool, and the Honest Broker data extraction tool. Data sources include Epic, GE/IDX (legacy physician billing system), MCW Tissue Bank biospecimens, NAACCR tumor registry, and genetic testing vendors (e.g., Foundation Medicine).

This toolset is designed to help answer the question: “Does the CRDW contain a cohort of patients with certain characteristics?”


255 KBCRDW Access Instructions


Special Features of Query Tools & De-Identified Honest Broker:

  • You don’t need an approved IRB protocol to use our query tools.
  • All data is de-identified.
  • All dates are shifted.
  • No names or IDs are available.


The Honest Broker Data Dictionary contains detailed definitions for all our extractable tables.

2 MBCTSI Honest Broker Data Dictionary

The i2b2 query tool includes the following concept domains from which researchers can select criteria for cohort characterization.

  • Allergies
  • Biospecimens [Specimen Type, Tissue Site]
  • COVID Concepts [Diagnoses, Lab Results & Procedures]
  • Demographics [Age, Email, Ethnicity, Language, Race, Sex, Vital Status]
  • Diagnoses [ICD-9 & ICD-10]
  • Diagnostic Results [Clinical Labs, Cardiovascular/Pulmonary Diagnostics, Radiation]
  • Encounters (see Visit Details)
  • Genomics – genetic testing results from Foundation Medicine, Tempus, Invitae & Ambry
  • Immunizations
  • Medications [Ordered/Administered]
    • Pharmaceutical Class & Subclass
    • Ingredient
    • MAR Action, Route, Dose
    • Ordering Mode
  • NAACCR Tumor Registry from Froedtert Hospitals in Milwaukee, Menomonee Falls & West Bend
  • Procedures [CPT, HCPCS and custom codes from Epic Orders]
  • Procedures [CPT/HCPCS/ICD coding from Physician Billing & Hospital Billing]
  • Providers (searchable by name and specialty)
  • Social History [Alcohol, Contraceptives, Illicit Drug Use, Tobacco Use, SDOH]
  • Visit Details
    • Age at Visit
    • Department
    • Visit Type (e.g., AV=ambulatory, IP=inpatient)
  • Visit Vitals (outpatient only)


The TriNetX cohort query and analysis tool includes

  • Demographics, Medications, Diagnoses, Labs, Procedures, Visits, and Genomics

Terms of Use

  • This system was not designed, nor is it intended, to support any aspect of patient care and its use for any patient care purposes is prohibited.
  • The results returned by this system may not be distributed outside of Medical College of Wisconsin.
  • All searches executed within the system are recorded and will be examined, as part of routine compliance audits. The identity of the user is recorded along with information related to each search executed.
  • No person registered as a user of the system may share his/her login information with any other person for purposes of accessing this system. Only registered users who are Medical College of Wisconsin faculty, adjunct faculty, or academic staff may use the system.


  • CTSI membership
  • Current MCW-required Human Subjects Research CITI Training
  • CRDW Data Release Agreement from the PI with all named research team members
    • see Access Form section below
  • Medical College of Wisconsin network credentials (MCW username/password)
    • MCW faculty or adjunct faculty can sponsor:
      • CTSI academic faculty, postdocs, residents, fellows
      • CTSI staff and students
  • Access to the MCW network (MCW campus, remote VPN or


Read/Download Language to Include in IRB Applications

Citing the Clinical Research Data Warehouse

Investigators must cite both AHW and Medical College of Wisconsin CTSA Grant UL1TR001436.

This includes use of the self service cohort discovery tool, data consultations, clinical queries, and data extraction services made by our team.


“This project is funded in part by the Advancing a Healthier Wisconsin endowment at the Medical College of Wisconsin.”


Please acknowledge the Medical College of Wisconsin CTSA Grant UL1TR001436. All publications must comply with NIH Public Access Policy.

Researchers other than K Scholars (KL2) – Please cite Grant UL1TR001436, as follows:

“This publication [or project] was supported by the National Center for Research Resources and the National Center for Advancing Translational Sciences, National Institutes of Health, through Grant Number UL1TR001436. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIH.”

K Scholars (KL2) – Please cite Grant KL2TR001438, as follows:

“This publication [or project] was supported by the National Center for Research Resources, the National Center for Advancing Translational Sciences, and the Office of the Director, National Institutes of Health, through Grant Number KL2TR001438. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIH.”



Each project includes the following training and support:

  • 1 hour training (no charge)
  • 1 hour project support (no charge)
  • Any project needs beyond the complimentary 2 hours, as outlined above, is considered out of scope and may affect your data delivery timeline and/or budget



Additional project support is billed hourly at a rate of $100 per hour. No project work can begin until a signed Letter of Agreement and Statement of Work has been fully executed. To achieve this state, the Biomedical Informatics team must receive a well-formed service request including but not limited to project description, scope of work, cohort definition, comprehensive data element manifest with accompanying code sets, IRB approval documentation, external data use/sharing agreement(s), expected timeline, funding sources, and billing details.


No work on scope changes will be done before both parties agree on cost and timeline changes and are client authorized with approval of a written change order.

Fees last updated June 30, 2017


Validate or test a project hypothesis by using a de-identified CRDW query tool

No, an IRB protocol is not required to use CRDW query tools

Extract de-identified data from Honest Broker for a known cohort or a query-generated cohort 

No, an IRB protocol is not required to use fully de-identified data

Extract identified data (real MRNs/real dates) from Honest Broker for a known cohort or a query-generated cohort

Yes, IRB approval is required

Extract identified data from Honest Broker for a QA/QI project

Yes, approval is required from the IRB or a designated QI authority in your department. If your department/division/center does not have a QA/QI review process, contact Froedtert’s OCRICC team or MCW’s IRB for advice on next steps.


Research teams may use the CRDW’s self-service de-identified cohort discovery query tools to curate and iteratively refine cohorts for hypothesis development. Researcher teams may also extract and review de-identified clinical data as a preliminary step before requesting identified data for a research project.

The CTSI Biomedical Informatics team will provide up to 2 hours of complimentary consultation and training to develop queries and/or extracts that meet the specific needs of each research project.

Research teams should define specific inclusion and/or exclusion criteria to build a study cohort within one of the CRDW query tools. This curated cohort can then be used to export various data tables from the Honest Broker extract tool in CSV format. CSV files are compatible for import into many data analysis tools.

De-Identified data extracts should be treated as if they contain real patient data – they must be stored on a secure device or network drive.

Teams who wish to identify the patients in their cohort must apply to the IRB for study approval in order to extract identified patient data.


Research projects wanting to use identified data or a limited data set must have an approved IRB protocol to extract identified data from Honest Broker. Project teams are encouraged to use the de-identified query tools to inform protocol content, i.e. validating the cohort size for Section 3F.

Simply receiving IRB approval does not guaranty Honest Broker approval. There are 5 IRB checkpoints that must be in place on the eBridge SmartForm for a successful Honest Broker submission: Sections 2.1 (team members), 3F (both dates and counts), 19.7/30.1 (process language), and 26.2 (link to CRDW bank).

Existing protocols should be reviewed to ensure all IRB checkpoints are covered. In some cases, the researcher must submit an IRB amendment to include additional elements and/or language. To request a protocol review, please contact


The Medical College of Wisconsin’s Clinical & Translational Research Informatics team offers a number of research data management options in support of clinical research, including: REDCap, and Secure ResearchWiki. We strongly encourage researchers to consult with a biostatistician from the CTSI, CAPS, or MCW’s Institute for Health & Society before beginning the analysis of their clinical data.


Inquiries and consultations on new research projects are offered free of charge to CTSI community researchers. In general, we will provide one hour of labor working on a project before we need to discuss setting up a payment plan.

When additional payment is required, you will be responsible for covering a standard billing rate on an hourly basis for the time spent working on your project.

In projects where Biomedical Informatics expertise is required, we may engage in a collaborative partnership leading to co-authorship on related publications. In such a collaboration, and particularly where the work is of shared interest, we may be able to extend a cost-sharing of services.


We ask that all research related to your consultation include appropriate citations to the resources used. Please see our citation information for details.


To gain access to the Clinical Research Data Warehouse, a PI (or PI delegate) must complete the following form. The PI must be a registered CTSI member and be designated as Faculty or Adjunct Faculty. In order to grant access to research team members, the PI must provide a name, contact information and project role for each team member on the Project Team form.

Only MCW employees/students/adjunct faculty or CTSI community partners with an MCW Network ID (e.g., an email address) can be given access to the CRDW.


NIH Funding Acknowledgment: Important Reminder – Please acknowledge the NIH when publishing papers, patents, projects, and presentations resulting from the use of CTSI resources by including the NIH Funding Acknowledgement.


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