NIH Requirement for a Data Management and Sharing Plan

As part of their effort to promote the management and sharing of data generated from NIH-funded research, the NIH will require all NIH-supported research generating scientific data to include a Data Management and Sharing Plan (DMSP). The policy applies to prospective grant/contract applications submitted on or after January 25, 2023.

For more information, please visit the NIH Data Sharing Policy Update posted by the UCSD Library

Health Data Oversight Committee

What is the Health Data Oversight Committee (HDOC)?

Health Technologies Services Partnership with Qualcomm Institute

The Health Technologies Service is a service offered by ACTRI in partnership with the UCSD Qi Health
Technology Group (Qi/HTG). The service provides purpose tailored system development conforming to
your health project requirements.

The Qi Health Technology Group has a rich history of implementing solutions for health researchers.

Qi/HTG is experienced with popular health technology platforms (e.g., EPIC/FHIR, REDCap, …) using
modern programming toolsets. Qi/HTG will engage with you to collect workflow, application and system
requirements for your project. Suitable technologies and system designs targeting the requirements will
be described. Development and project management services, in-whole or in-part, are available per
your timeline.

Qi Health Technology Group is an approved ACTRI IT Partner
ACTRI Health IT and data resources are available and will be coordinated for associated projects.

Development Services Include:
Web Systems
Design and implementation of web sites, apps, and backend systems tailored to the healthcare space.
Node.js, Apache, HTML5, Java, PHP, more.

Mobile Applications
Design and implementation of mobile applications tailored to the healthcare space.
Apple iOS and Android platforms.

Custom Applications
Windows/Linux/Mac

Request a project consultation, send questions about the QI program manager to Phil Rios here.

DocuSign - CFR Part 11 Electronic Signature Services

Departments with FDA studies or services requiring electronic signatures with CFR  Part 11 specifications may sign up for a DocuSign account.  There is a recharge fee of $7 per envelope for use of this service which is payable using your campus Oracle financial chart string. All users with studies requiring electronic consent or other related electronic methods should have their processes reviewed and approved by the IRB office and Compliance prior to implementation.

Sign up here and for further questions and please send email to ctri-support@health.ucsd.edu

ENACT is a network of sites from the National Clinical and Translation Science Award (CTSA) Consortium. ENACT network allows researchers to explore and validate feasibility for clinical studies across CTSA sites. ENACT network has been created to harmonize EHR of each site linked by the Shared Health Research Information Network (SHRINE). ENACT provides investigators the ability to design and obtain aggregated counts of patients to identify eligible participants under specific inclusion and exclusion criteria. The real-time query of ENACT network to diverse CTSA sites across the United States significantly increases efficiency of clinical studies.

The ENACT network currently connects 39 participated CTSA sites, including all 5 UC medical centers, and more than 100 million patients. More sites are joining and at staging status.

For more information visit the ACTRI ENACT Portal.

Access

To request access to the ENACT Network, visit the ACTRI ENACT Portal.

• Click the Register for ENACT button on the upper-right of the page.
• Complete all the fields required (*)
• Once approved, users can login to ENACT web client, https://shrine-act.ucsd.edu/shrine-webclient, using AD credentials to start exploring the platform.

The ENACT Interface

The user-friendly ENACT SHRINE query interface is shown as the following. It simply consists of 4 panels. The Terms panel allows investigators to search the information of Demographics, Diagnosis, Laboratory tests, Medications, Procedures, and Visit details. The defined inclusion/exclusion criteria can be dragged and dropped to numerous groups on the Query Tool panel. Each group enables independent criteria date range and times of occurrence. The current and previous query results are shown in the lower panels. In addition, ENACT allows aggregate count breakdown for patient age, race, gender, and vital status, and provides graphic reports.

Contact and Help

For any other questions regarding the ENACT Network, please contact the Application Support Team or phone (858) 534-0555.

ARMOR is a large-scale data registry designed to advance precision oncology. ARMOR aggregates clinicopathological and clinical genomics data from the Electronic Health Record using automated and real-time collection of both molecular and clinical information. This resource enables UCSD Health investigators to rapidly validate research findings in an independent, real world patient population, develop predictive models, test novel therapeutic paradigms and document patient trajectories.  

ARMOR is available to UCSD investigators through a UCSD cBioportal instance hosting de-identified clinical genetic results and partial clinical information from patients who underwent tumor sequencing as part of their clinic care.  Source data can be accessed by approved users through the ACTRI Virtual Research Desktop. ARMOR is approved under the Molecular Oncology Registry protocol (UCSD IRB 200373) and maintained by the Center for Computational Biology & Bioinformatics with support from the Moores Cancer Center, Altman Clinical & Translational Research Institute and Vice Chancellor for Health Sciences.

Request Access to ARMOR

**Select Biomedical Informatics->ARMOR

Clinical Pipe is an EHR-to-EDC connector that securely pushes 50-80% of total trial data from one system to the other, with a few mouse clicks, without the need for manually transcribing it. The BMI team has established a workflow to build connections integrated with UCSD Epic EHR to streamline the secure data transfer for approved sponsored studies.

Clinical Pipe services bring many benefits to clinical research. Upon setup and configuration for integration with the UCSD Health EHR, benefits for sponsored studies include the following efficiencies:

• Faster, because data is typically transferred the same day it's entered into the EHR. You don’t have to wait for it to be transcribed into the EDC (which takes on average 2 weeks, but sometimes over a month).
• Data integrity, because there are no transcription errors.
• Compliance, because any data transferred via the validated application does not need to be source verified.

Data Types and Formats supported for Secure Transfer

Requesting Study Configuration

For study setup requests, please submit your service request below. An analyst from our team will be in touch to coordinate a consulation meeting and answer any questions you may have.

ACTRI – NIGHTINGALE Platform

Clinical research today often requires real world data (RWD) from electronic health record (EHR) systems.  In the 2021 calendar year, the UCSD ACTRI Data Concierge Extraction Service (DECS) securely provisioned over 96 data sets for IRB approved research totaling 100 billion data points from nearly a million unique individuals. The demand for data is so intense, request turnaround times have lengthened to over 12 weeks (Dec 2020).  

Clinical research often involves novel hypothesis generation and asking insightful scientific questions, but it is equally clear that rapid access to data is also an essential component for generating useful biomedical discoveries in a timely fashion. 

The UCSD Health Nightingale Initiative, has the goal of establishing the infrastructure and processes to allow rapid access to disease/device/drug cohort-based data sets to investigators within a secure HIPAA-compliant “research cloud” (enclave). We believe the benefits of providing rapid access to these data sets in a protected “enclave” will help accelerate biomedical research while incurring minimal risk.

Data Registries Available

UCSD_Research

The data sets are created as de-identified HIPAA Limited Data Sets.  Each patient record has a longitudinally preserved pseudo-identifier, preserved true dates, and zip codes. Addresses are redacted. The data is refreshed on a recurring basis and available to approved users in the UCSD Health Research Secure Cloud. Data is OMOP derived and stored in secure data repositories in AWS research cloud, and accessible from the Databricks and Amazon RDS PostgreSQL instances.

UCCORDS

Combined data from collected from all UC Health EHR records consisting of covid tested patients. This dataset follows contains COVID cohorts with various data phenotype standards. Updates are processed monthly as a refresh when data is collected in coordination with the UC Health Data Warehouse group. Many of the primary identifiers have been removed, however provisions within the data use agreement still need to be followed for protection of the limited dataset under HIPAA, state laws and local policies.

Data Analytics Applications

The Databricks application environment is a secure notebook-style development interface, that supports running R, Python, Scala as well as SQL code. Researchers can leverage the data registries made available as database schemas for direct analysis.  System users are automatically provisioned a compute cluster, for the notebook development application to execute custom analysis code. Each user’s notebook with custom code can also be shared with other users for collaboration. Notebook templates with pre-defined code snippets are also provided in consultation with the BIDS team, for efficient and seamless processing of common analysis routines.

Access the data registries from AWS a PostgreSQL server to execute custom SQL queries. Researchers can leverage elastic scaling with our datasets deployed to secure cloud services and output data for post-processing analysis. Resultant data can be integrated with ACTRI Virtual Research Desktop (VRD) applications pre-installed with compute images (R-Studio, Python, SPSS). All PostgresSQL compatible applications such as PGAdmin are supported for data query and management and included by default within the VRD for easy access.

Compliance and Security

• Data Use Agreement:
  UCSD Investigators must apply for access and attest a data use agreement (DUA) for access to the UCSD_Research, UCCORDS and future available registries, in which they agree to abide by a number of conditions, including not attempting to re-identify individuals even in the enclave. We have coordinated with UCSD IRB, which has determined the use of these de-identified limited data sets satisfy the definition of not human subjects research and their use in the enclave would not be regulated research.

• Not Sharable:
  Nightingale Registries available under these provisions (not regulated research, cohort-specific data sets furnished as a limited data set under an internal data use agreement) would not sharable outside of UCSD Health. If sharing is desired for research, or if further identification of participants is needed, the investigator must undertake the standard process of obtaining IRB and Health Data Oversight Committee (HDOC) approval for such sharing.

• Restricted Data Egress from Enclave
  Access to Nightingale Registries, as is also required with UC-Wide research data sets, can only be accessed within the UCSD Health Secure Research Cloud (the research enclave). This environment is sanctioned for PHI by the UCSD Health Chief Security Officer (CSO). Approved data platforms have been configured to restrict data download and other forms of exfiltration. Researchers are expected to comply with security guidelines and not attempt to circumvent access restrictions using any other technical methods.

Requesting Nightingale Data Services

For study setup requests, please submit a request below. A analyst from our team will be in touch to send you the necessary Data Use Agreements (DUAs) via DocuSign. Once your terms of use have been signed, account activation along with instructions will be sent to you for access to the services.

The Data Extraction Concierge Service (DECS) is a service that pulls data from the UCSD EPIC Electronic Medical Records system to provide UCSD patient and health data extracts for research purposes. This service allows to identifies specific patients, and extracts identified, de-identified, or limited patient-level datasets from electronic medical for clinical research projects. An approval by the Institutional Review Board (IRB) is required for extracting identified and limited datasets. Our support team will execute queries on the Clinical Data Warehouse for Research (CDWR) and return results to users.

Functionality

 The data extract can include many different types of information, such as:

• Patient demographics
• Visits
• Diagnoses
• Medications
• Lab results
• Procedures
• Insurance
• Radiology images

Any data visible in Epic can be included in an extraction request. Requests can be:

• simple: e.g., "All female patients diagnosed with lung cancer in 2016”
• very complex e.g., “Patients seen in 2012-2016 that presented with specific diagnoses within 3 months of an ER visit, including all culture labs, antibiotic medications, and surgeries”.

DECS delivers results to the requester through a dedicated Virtual Research Desktop (VRD). By default, requested data are provided in a Microsoft Excel workbook (.xlsx), but other data formats are supported.

Access

To request DECS services follow the request services button on top of the page.
Select "Biomedical Informatics" / "Data Extraction Concierge Services"

The following are needed:

• Details on the P.I. and the requester (if different).
• IRB# (unless proposed activities are not considered involving human research).
• A charge index for billing DECS service.

• The details of your request:

  • Inclusion criteria
  • Exclusion criteria
  • Date range for the data
  • What data you want retrieved – you can request multiple sets of related data (e.g., demographics for the matching patients, plus lists of medications administered in ED encounters, and notes from phone encounters).

Tips:

• For diagnosis criteria, please specify all of the ICD-9 and ICD-10 codes you need. Note that we do need ICD-9 as ICD-10 was only mandatory after 1 October 2015; earlier diagnoses will include ICD-9.

• For procedure criteria, please provide specific CPT codes.

• With procedures, medications, and labs there can be multiple EPIC entries for each name – your DECS analyst will likely need to review the lists with you to specify exactly which items should be part of your request.

• Be very specific about which data fields you require in the data results

Access to the DECS results VRD are only initially granted to the requester and/or PI. Only individuals listed in the IRB submission can be allowed access to the VRD. All VRD users require UCSD AD accounts.

Non-UCSD requests for DECS services normally require a UCSD P.I. sponsor, who will be responsible for the data generated. In addition, a legal data access agreement may be required.

Cost

The current recharge rate for DECS services is available here.

Generally, the final cost of a DECS request is proportional to its complexity: Number of elements (variables) to retrieve, number of inclusion and exclusion criteria, and how easy it is to retrieve the requested data.

As part of the initial review meeting, your DECS analyst can generally provide an estimate for the time and cost. It’s difficult to provide a firm quote, as each DECS request is unique – as work proceeds we can generally improve the estimate.

Some broad guidelines:

• Very simple requests: 1-3 hours (<$400).
• Common requests: 4-6 hours ($450-$700).
• Complex requests: 7-9 hours ($800-$1,000)
• Very complex requests: 10+ hours ($1,100+)

If your data budget is very tight, we can often organize your request into multiple “phases”, to meet your key requirements first, and the rest if the budget allows.

Contact and Help

For any other questions regarding DECS, please contact the Application Support Team or phone (858) 534-0555.

 What are MarketScan databases?

• De-identified patient level medical, drug and dental data, productivity data (workplace absence, long-term disability), laboratory results, health risk assessments, and electronic medical records (a subset). It is a HIPAA Limited Data Set (LDS).​
• Data comes from large employers, health plans, state Medicaid programs ​
• Over 203 million commercially covered individuals annually, 48 million enrollees from Medicaid (locations not provided) ​
• Originally produced by Truven. IBM acquired Truven. MarketScandatabases are now an IBM product

Available MarketScan Data Sets:

Sign up here for access and send further questions to ctri-support@health.ucsd.edu.

Accelerate observational research with electronic medical records  in unstructured clinical documents,  an untapped rich source of additional data. Annotating this rich source of information using clinical natural language processing (cNLP) provides important additional data points for these activities.  Clinical NLP uses specialized content and techniques to extract valuable data from unstructured narrative clinical documents such as clinical notes, history and physicals, discharge summaries, pathology reports, and more.

The UCSD Health CTRI team has implemented a cNLP system in the UCSD Health Research Cloud. Researchers can now utilize the clinical NLP pipeline supplemented by medical terminology dictionaries and specialized processing as a powerful tool to enhance research discoveries.

• Apache cTAKES – a natural language processing system for extraction of information from electronic medical record clinical free-text. Accessible from VRD with no charge
• CLAMP – comprehensive clinical Natural Language Processing (NLP) software that enables recognition and automatic encoding of clinical information in narrative patient reports. Freeware as part of VRD avilable software packages.

• AWS Comprehend Medical - Secure HIPAA cloud access to pre-trained models (vendor fees apply)

Submit a request to the DSS team if you have interest in using NLP for a project. **Select Biomedical Informatics-Virtual Research Desktop. In the information textbox, enter which of the NLP platforms you're intersted in using.

Secure 21CFR11 compliant electronic data capture (EDC)

Build research forms using an industry leading software application, with a 21CFR11 compliant electronic data capture (EDC). Leverage a comprehensive electronic case report forms (eCRFs) platform for efficiency and secure data connection. The BMI team can also assist with data integrations with the UCSD Epic electronic health records (EHR) system for research form builds. Our instance of OpenClinica software securely connects to UC San Diego Health’s Epic EHR using the secure AppOrchard data integration services environment.

Starting your approved IRB research project requires a request to the BMI team. Project services will involve the following process:

• Initial consultation for IRB approved study
• Compliance verification with OIA office for
• Online training for study teams self-managed EDC services
• Creation of a Test/Production EDC project workspace

Data Integrations with UCSD Epic EHR

OpenClinca Unite automates source data acquisition from UCSD patient medical record systems (EHRs) to clinical trial research databases (EDCs) and case report forms (eCRFs). Data elements and APIs standards supported for integrations via Fast Healthcare Interoperability Resources (FHIR) with OpenClinica Unite EHR services.

REDCap (Research Electronic Data Capture) is a secure, web-based application for building and managing online surveys and databases.

REDCap provides automated export procedures for seamless data downloads to Excel and common statistical packages (SPSS, SAS, Stata, R), as well as a built-in project calendar, a scheduling module, ad hoc reporting tools, and advanced features, such as branching logic, file uploading, and calculated fields.

Functionality

• Electronic Data Capture
•     Design of forms for electronic data capture
•     Import/export of data
•     Secure storage of data, documents, and files
•     Online surveys
•     Mobile, offline collection of data
•     Reporting/data analysis

While REDCap may be used to store PHI, it is not CFR 21 Part 11 compliant. If your project requires compliance with CFR 21 Part 11, you will need to use the Velos system.

Access

REDCap is available to all UC San Diego faculty and staff, and to users outside the organization who have sponsorship from UC San Diego faculty. To gain access, all REDCap users must have UC San Diego Active Directory (AD) system credentials (contact ITS Service Desk for credentials)

To request access to REDCap, follow the request services button on top of the page.
Select "Biomedical Informatics"/ "REDCap Access"

Training

Once granted access to the REDCap application, all users have access to extensive training videos, located on the REDCap home page.

The REDCap Wiki is a tool available to all REDCap users to post questions to the UCSD REDCap community.

Contact and Help

For any other questions regarding REDCap, please contact the REDCap Application Support Team or phone (858) 534-0555.

TriNetX is a platform that is used to assess the feasibility of clinical trials by testing criteria against patients receiving care at UC San Diego Health. TriNetX utilizes data from electronic health records including demographics, diagnoses, procedures, medications, and labs that can be used to create queries so researchers can forecast the expected size of the patient population that might meet the study criteria. Search queries will include all research eligible patients from the UCSD Health electronic health records system.

Getting Started

This section describes how users access their TriNetX account begin using the application. Access will allow users to define data variables for the search criteria and explore different dimensions of the UC San Diego Health’s research eligible patient population.

Requirements

To access TriNetX you will need:

• Request a new account using ACTRI service form link below

• A computer
• An Internet browser

 *Please note that TriNetX is optimized for Google Chrome

Logging into TriNetX

To access TriNetX, open your browser and type the following URL into the address bar: https://live.trinetx.com. The TriNetX page will display.

 When your account is created, you will receive an email to reset your password. Follow the link in the email to set your password.

1. Enter your UCSD email address (@ucsd.edu) and assigned your password
2. Click the Login button. A successful login will direct you to the TriNetX homepage.

Building a Query

Select your inclusion and exclusion criteria under ‘Must Have’ and ‘Cannot Have’. Your criteria can include the following:

• Demographics
• Diagnoses
• Procedures
• Medications
• Labs
• Visits

Define a patient cohort criteria and explore the demographics of the UCSD Health research eligible patients.

Online Training

Click the Training Center Option, in the top right-hand corer of the login page. Browse the Training Program to display the different selections available for various tutorials on usage of the application.

The UC Health Data Warehouse (UCHDW) pulls a subset of the data from the Electronic Health Record system and allows investigators to query patient information in a HIPAA-compliant manner.

The UCHDW currently holds data on nearly 6 million patients seen at a UC facility since 2012. These patients received care from nearly 100,000 health care providers in over 200 million encounters, with nearly 200 million procedures, more than half a billion medication orders, and with over 2 billion vital signs measurements and test results. Over 600,000 of these patients are primary care patients.

Access to this information requires technical familiarity and ability to write code in R, Python, or Spark SQL, that queries the deidentified clinical data. The BMI team may assist to provision access directly to the UCHDW data. If assistance is needed in preparing the customized queries, there will be a recharge fee.

To request access, please sign up here and send questions to the Application Support Team.

Tableau is a powerful and fast-growing data visualization tool widely used in the Business Intelligence Industry. It helps its users to simplify raw data into an easily understandable format.

Analysis is very fast with Tableau — using worksheets and dashboards to create charts and diagrams. Tableau makes it easy to present data in a way that can be readily understood by professionals at any level in an organization.

Tableau has many features including:

• Data Blending
• Real time analysis
• Collaboration of data

Best of all, the Tableau application does not require of its users any technical or programming skills to operate.

• What is Tableau?  - Uses and Applications
• To learn more about Tableau or to sign-up for access, please contact Application Support Team.

Velos eResearch is an integrated software system for managing clinical trials. The software links to the UCSD Health's Epic Electronic Medical Record System to provide improved information and integration for clinical research projects.

One module within this platform, called eSample, will track biological samples and link them to the Electronic Health Record.

A robust support team assists investigators in implementing their protocols, study budgets, and calendars.

Functionality

Velos eResearch is a web-based system that supports:

• Creation of budgets
• Creation of protocols with calendars
• Scheduling of subjects
• Electronic case report forms
• Tracking visits and events
• Creation of invoices
• Reporting

Access

It is mandatory that all new users attend Velos CRB training session, upcoming training schedule is available on the Velos Wiki. To reserve a space for the Training, please e-mail ctri-velos@ucsd.edu.   Once users have attended a training session and submitted a completed and signed access request form, access to the Velos Application will be granted.

To request access for Velos Application follow the request services button on top of the page.
Select "Biomedical Informatics" / "Velos Access"

Velos CRB Training

The Application Support Team conducts detailed in-depth hands-on Velos CRB training sessions twice a month.

Once granted Velos access, the Velos CRB training manuals are accessible within the Velos application under the question mark (?) icon in the upper right corner.

Training material (manuals and videos) are also available on the Velos Wiki webpage.

Custom trainings tailored to your study needs can be provided: eSampling, budgeting, reporting etc.

Contact and Help

For any questions regarding Velos (general inquiries, custom trainings etc),  please contact the Velos Application Support Team or phone (858) 534-0555.

The Virtual Research Desktop (VRD) offers researchers a secure way to store and access their research data.  It allows the hosting of a desktop operating system on a centralized HIPAA-compliant server that is managed by the BIDS Unit. VRD access is limited to users with a valid UCSD Active Directory account and multi-factor authentication through Duo. For extra security, the VRD environment is self-contained and allows no access to printers, internet, email or external drives.

VRD can also be customized to include your own licenses and/or applications.

Functionality

• Increased productivity with access to the data from anywhere.
• HIPAA data is stored at the UCSD data center where security can protect against leaks.
• Centralizing desktop execution in the data center reduces the number of data paths that security must inspect and streamlines compliance with audit reporting requirements for the use of personal health information (PHI) and other regulated data. Since the data that is accessed from the VRD is never stored on the end user’s device, the need for data protection is lessened.
• Easy to setup secure group-level access to PHI.
• Upon request, data may also be backed up and archived.

Access

Currently VRD is a free service provided by the BIDS Unit. To request VRD access please submit a BIDS Request and select "Biomedical Informatics" / "Virtual Research Desktop". Registration to the UC San Diego Health Duo is also needed in order to log in to your VRD.

BIDS Service Request

Data

Data in the VRD shared folder is removed after 30 days – this shared folder is used to deliver results (such as DECS) to the end user and is not intended for long-term storage; users are expected to move the data to the VRD personal folder. Data in the VRD personal folder is preserved for the lifetime of the VRD account.

Data Import/Export

For all data migration requests, please email the Application Support Team with the “VRD:” in the subject.

For import please include:

• File names to import
• File types (Excel, text, etc.)
• File sizes
• Where is the data from? (Ex. University of Wisconsin)

For export please include:

• File names to export
• Computer IP or Hostname
• Justification for the export

Data exports will only be allowed onto UCSD Health System controlled computers which are secure and encrypted.

Resources

CTRI VRD- Access Instructions

Connecting to CTRI SFTP Server

Contact and Help

For any other questions regarding the VRD, please contact the Application Support Team or phone (858) 534-0555.

Contact the IT Support Team at:

• Main Line Phone: (858) 534-0555
• Email: ctri-support@ucsd.edu
• Hardware service request form

Weekly Office Hours  - Data Extraction Concierge Service (DECS)

Thursdays 1:00PM - 2:00PM

Zoom link:   https://uchealth.zoom.us/j/81732217241?pwd=Yk9rc0NPTGRTMnFxQkxhSTFaVEo2UT09&from=addon

• Get questions answered for a new project
• Discuss and follow up on an existing data request
• Q&A and guidance from data team on general electronic health data needs

Nguyen Trieu, MHIM
Chief Technology Officer
Phone: (858) 822-0111