BIOMEDICAL INFORMATICS, BIOINFORMATICS & CYBERINFRACSTRUCTURE ENHANCEMENT CORE

Our Core goal is to strengthen and expand the tools and resources that supply real word data specific to Hispanic populations, and develop programs that prepare skilled informaticians. BiBEC will create a sustainable, team-based, multidisciplinary service to provide the cyber infrastructure needed to enable effective collaborative clinical and translational research while leveraging all available existing resources.

Our objectives are to strengthen and expand the Hispanic Collaborative Clinical Research Data Warehouse (HC²RDW), to intensify web-based technologies designed to promote clinical research among Hispanic populations, including increasing the number of Puerto Ricans registered to volunteer for clinical trials both within and outside of Puerto Rico (PR); and to strengthen our understanding of individual health status and its relationships with clinical care, drug efficacy and effectiveness, and healthcare delivery. Our central hypothesis is that informatics tools, and the necessary resources to fully utilize these tools, can advance Hispanic health and healthcare at all nodes along the clinical and translational research continuum.

• Specific Aim 1. Strengthen and expand existing health data infrastructure to improve clinical care and best practices (electronic health records/clinical research data warehouse known as HC²RDW.
• Specific Aim 2. Enhance the availability and recruitment opportunities of Puerto Rican and other Hispanic populations into clinical and translational research studies using technology-based innovations.
• Specific Aim 3. Develop training for clinicians and clinical and translational researchers which will enable their use and application of available biomedical, bioinformatic, and health informatics-related data and technologies.

• Alliance Web Portal in Spanish and English
• Interactive Alliance Request for Services Platform
• Innovative Uses of the HC2RDW
• REDCap (Research Electronic Data Capture)
• Community Volunteers participation in Clinical Trials and ResearchMatch
• Workshops and online resources
• Develop, implement, and monitor tools to support clinical research functions of the Alliance.
• Professional development and training opportunities in biomedical informatics for faculty, staff, and students of Consortium institutions
• Provide clinical and biomedical informatics support to cores within The Alliance

The Biomedical Informatics Core (BIC) under the PR-CTRC established critical infrastructure and systems designed to strengthen biomedical informatics within the clinical and translational research community in Puerto Rico and beyond. Originally a ‘service core’, BIC provided hardware/software support, maintenance of the organizational website, and training support in biomedical informatics and bioinformatics. In 2013, the core shifted it’s focus dramatically and saw a number of accomplishments during the funding period 2013 to 2018.

Under the new banner, The Hispanic Alliance for Clinical and Translational Research (Alliance), our core now operates as the Biomedical Informatics, Bioinformatics, and Cybersecurity Infrastructure Enhance (BiBEC) core. Going forward, BiBEC will continue providing excellence in services, increased access to informatics tools designed to further clinical and translational research, and seek to train clinicians and healthcare professionals in the tools and resources that enable and support excellence in clinical and translational research.

• Accessing REDCap
• Request BiBEC Technical Services
• Computer Cluster Facilities: access, technology, use, and security

The Alliance’s Biomedical Informatics, Bioinformatics, and Cyberinfrastructure Enhancement Core (BiBEC) is part of the national IDeA-CTR network, whose activities include involvement with the National COVID Cohort Collaborative (N3C) Data Enclave.  The Alliance has an executed Data Use Agreement with the National Institutes of Health, meaning that researchers wishing to conduct research in COVID-related research may request access to this data resource.  BiBEC is also involved with N3C research and education. The N3C Data Enclave was officially launched in September 2020 and is funded by the National Center for Advancing Translational Sciences (NCATS).

The National COVID Cohort Collaborative (N3C) data platform contains data on at least 1.6 COVID+ cases, representing almost 6 million persons.  In 2023, the Alliance will begin to contribute Puerto Rico-specific COVID data to the N3C Enclave.  COVID-19 clinical data is available for research through the new N3C analytics platform.

The N3C aims to aggregate, harmonize, and make accessible vast amounts of data from healthcare providers nationwide to accelerate advances in COVID-19 research and clinical care. With the uncertainty of the COVID-19 global pandemic, the scientific community and Clinical and Translational Science Awards (CTSA) Program created the N3C partnership to overcome technical, regulatory, policy, and governance barriers to harmonizing and sharing individual-level clinical data.

In addition to the vast amounts of data available for coronavirus research, the N3C also aims to help scientists analyze these data to understand the disease and develop treatments.  The N3C enclave currently holds data related to roughly:

• 56 sites
• 5.9 million persons
• 1.6 million COVID+ cases
• 326 million procedures
• 582.8M million clinical observations
• 3.1 billion lab results
• …and more!

Benefits of Using the N3C Data Enclave!

• Generating sample data for pilot projects and grant proposals
• Training algorithms on a very large cohort of patients
• Opportunities to train junior researchers (the domain teams can offer support and a network for these investigators)
• Informatics and statistics opportunities for innovation and evaluation
• Opportunities for clinicians to investigate COVID-19 treatment patterns and disease progression

Three levels of data are available:

1. Synthetic data or a safe data derivative,
2. De-identified data; and
3. Limited data.

If you request limited data, you will need IRB approval from the UPRMSC and must provide documentation of human subject research protection training.

The Alliance has an executed Data Use Agreement with NIH for access to the N3C Data Enclave.  Interested investigators may REGISTER FOR ACCESS using their institutional email address.  After you register for an account, access is granted within 48 business hours.

One-on-one support for registering for access is available through Dr. Mary Helen Mays, Leader for BiBEC and N3C Navigator for the UPR/Alliance (mary.mays@upr.edu).

Data Use Requests

A Data Use Request (DUR) is an online application submitted by the researcher within the N3C Data Enclave that describes the scope and nature of the project and justifies the requested data access tier. Approval of the DUR by the Data Access Committee (DAC) is required before a researcher can access data within the enclave. (Approved DURs are valid for 1 year.) Please contact the Alliance N3C Navigator, Dr. Mary Helen Mays (mary.mays@upr.edu) for assistance.

 Domain teams are multidisciplinary research teams focusing on specific aspects of COVID-19 ranging from diabetes to pediatrics. These teams collaboratively submit data access requests to avoid duplication of efforts and to ensure appropriate expertise while answering questions about the pandemic.  Joining a Clinical Domain Team also gives Investigators the opportunity to connect with other researchers currently working within the N3C Data Enclave in common areas of interest, opening up opportunities for collaboration.  See the list of clinical domain teams.

 Learn More about the N3C Initiative and the N3C Data Enclave at these Links

• Read a complete overview of the N3C enclave.
• Review the webinar slides or watch a recording of the October 28, 2020 presentation, “Building a COVID-19 Analytics Platform to Turn Clinical Data into Knowledge: Introducing N3C”
• More information on the N3C Data Enclave and general information about N3C are found in these tutorials.   Additional can be found at these links:  webinars and information sessions.
• Read the JAMIA paper: “The National COVID Cohort Collaborative (N3C): Rationale, Design, Infrastructure, and Deployment”.

REDCap is a secure web application for building and managing online surveys and databases. While REDCap can be used to collect virtually any type of data in any environment (including compliance with 21 CFR Part 11, FISMA, HIPAA, and GDPR), it is specifically geared to support online and offline data capture for research studies and operations. The REDCap Consortium, a vast support network of collaborators, is composed of thousands of active institutional partners in over one hundred countries who utilize and support their own individual REDCap systems.  The Alliance is proud to be one of the long-time, active partners with Vanderbilt University, offering this important research tool to the faculty, researchers, and students of the UPRMSC.

Click this link to view a list of informational REDCap videos that can help you get started and gain a better understanding of the REDCap application and its functionality. NOTE: New versions of REDCap are released frequently, so the videos and other training resources below may reflect earlier software versions and thus may look slightly different than your system.  To go directly to an introductory video of REDCap, you may want to watch a brief 5 minute video or a more detailed overview (14 minutes)

REDCap has multiple and flexible uses that will support different types of research studies.  Should you have any questions about REDCap and if it is the right system to use for your particular research study, please contact Ms. Magaly Torres at magaly.torres@uccaribe.edu.

Software access and training for REDCap are available through the Biomedical Informatics, Bioinformatics, and Cybersecurity Infrastructure Enhancement (BiBEC) Core of the Alliance.  Any faculty member or student of the University of Puerto Rico Medical Sciences Campus AND any researcher who is receiving services from the Alliance may have access to REDCap.

You can request access to REDCap by completing and submitting the Alliance’s Online Request for Services Platform . Once your request is processed and approved, the applicant will be contacted by a BiBEC staff member to discuss the steps required in establishing a REDCap account for the researcher and their study coordinator and staff, including recommended training. Download our Accessing REDCap SOP

For consultation services regarding setting up a database using REDCap or analyzing data collected using REDCap, please contact Mrs. Lorena Gonález at lorena.gonzalez2@upr.edu with the Biostatistics, Epidemiology, and Research Design (BERD) Core.

To determine if REDCap is right for you, contact Dr. Mary Helen-Mays, BiBEC Leader at mary.mays@upr.edu,  or Ms. Magaly Torres, REDCap Administrator at magaly.torres@uccaribe.edu.

Please note that this “trial session” is not to be used for storing any real data. ALL DATA ENTERED BY YOU WILL BE DELETED EVERY EVENING. Project information (e.g., forms, reports, etc.) will be deleted after three months. You can request login credentials for a trial period by contacting (need to set this email address).  Requests for ‘trial session’ access will be answered within 48 hours of the request.

If you visit the REDCap trial site and are still unsure if REDCap is an appropriate solution for your research study data management needs, you may email the Alliance REDCap team at hispanicalliance.rcm@upr.edu

There are many, many training resources on how to use the basic functions of REDCap to be the more complex features of the software.  Many of these training materials are available in Spanish as well!  Many are in YouTube videos, Power Point Presentations, or print materials.

We recommend that you check out the REDCap Shared Library for these available materials.

The REDCap Shared Library is a repository for REDCap data collection instruments and forms that can be downloaded and used by researchers at REDCap partner institutions. Curated instruments have been approved for inclusion by the REDCap Library Oversight Committee (REDLOC) after review for research relevance, accuracy in function and coding (see guidelines), and copyright issues.

You may search available data collection instruments (click here). If you got to this site directly, you will be able to view the shared instruments as they would appear in REDCap or view a PDF version that can be downloaded and/or printed. If you wish, you may download a list of all library instruments in Excel/CSV format. If you download and utilize an instrument from the REDCap Shared Library, please cite the RSL manuscript. If you have questions or are experiencing issues, please contact redcap@vumc.org

And, there are numerous informational REDCap videos that can help you get started and gain a better understanding of the REDCap application and its functionality. You can access this ‘quick list’ of informational videos through this link.

The Hispanic Collaborative Clinical Research Data Warehouse (HC²RDW), also known as i2b2 is a project sponsored by the NIH Roadmap National Centers for Biomedical Computing. The i2b2 software is the backbone of the Alliance Hispanic Collaborative Clinical Research Data Warehouse (HC²RDW) clinical data warehouse and serves two important purposes:

• Support de-identified browsing of patient data to allow easy identification of patient cohorts
• Allow for creation of limited sets of patient data (“Data Marts”), containing only the data needed for a particular research project.

For additional information, please contact Dr. Mary Helen Mays at mary.mays@upr.edu

Researchers interested in using the Hispanic Collaborative Clinical Research Data Warehouse (HC²RDW)  for a clinical study will first need to complete the Online Request for Services: Application Form.

The request will be sent to the BiBEC Core Leader for review. If the request is research-oriented and involves Personal Health Information (PHI), IRB approval will be needed. After approval, the Core team will begin processing the data request, communicating preliminary results to the researcher(s) to facilitate data quality and validation assessments. The Biomedical Informatics and Biostatistic, Epidemiology, and Research Design Core teams will provide follow-up support to researchers on issues such as data management and use.

To request BiBEC technical services please click here