Cancer Research Informatics Shared Resource (CRI SR)
CRI SR Overview
The mission of the Cancer Research Informatics (CRI) Shared Resource (SR) is to develop and sustain biomedical informatics expertise and resources needed to enable and accelerate Markey Cancer Center (MCC) research. In accordance with MCC’s Strategic Plan, CRI efforts are aligned to meet the needs of an aspiring Comprehensive Cancer Center serving Kentucky’s high cancer burden. CRI aims are achieved through exceptional faculty and staff who provide integrated local and statewide cancer data from the Surveillance, Epidemiology and End Results (SEER) Kentucky Cancer Registry (KCR), and develop innovative informatics methods and computational resources widely utilized by all Research Programs and multiple SRs. CRI provides data and resources to assist the Cancer Prevention and Control Research Program and other partners in cancer prevention and control initiatives throughout the state.
Specific Aims
- Provide the cancer data ecosystem that empowers MCC investigators with integrated datasets from diverse sources ranging from molecular biomarkers to population-based SEER patient data.
- Develop artificial intelligence (AI) and high throughput computational methods that elevate MCC Research Program science.
- Provide secure computational resources, biomedical informatics applications and expertise to facilitate interoperability among MCC SRs and Research Programs.
The CRI SR facilitates collaborative research among members of the cancer center through the optimal application of informatics technologies and methods that maximize the accessibility and usability of data, information, and knowledge. The primary goal of CRI is to provide comprehensive and centralized data acquisition and informatics support that is readily available to cancer center members.
RESEARCH
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Did you acknowledge
the CRI SR?
CRI services are broadly categorized into three areas:
- Curate, harmonize, integrate and deliver the clinical and moleculardata ecosystem for scientific discovery.
- Design and develop informatics methods for molecular, clinical and data mining and drug discovery.
- Develop and deploy secure computational resources and applications.
CRI serves as a key gateway to Surveillance, Epidemiology, and End Results (SEER) Kentucky Cancer Registry (KCR) data to inform and enable MCC catchment-relevant research.
To request services from CRI SR, please complete the Service Request Form.
Directors and Faculty
Staff
Cancer Research Informatics Shared Resource (CRI SR)
2365 Harrodsburg Road, Suite A230
Lexington KY 40504-3381
CRISRF-requests@uky.edu
The CRI SR covers operational costs through salary support for personnel from grants and contracts, CCSG funds, as well as state and institutional support from UK. For projects that require significant staff effort, CRI works with investigators to estimate total costs for grant proposals.
What molecular data is available through CRI?
Molecular data at CRI is currently available from 4 different providers:
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Providers |
Available Features |
Notes for Users |
| Caris |
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Foundation Medicine |
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| Tempus |
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ORIEN |
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How do I get access to Molecular Data at CRI?
Molecular data can be accessed in multiple ways depending on the requested study type:
- MCC cBioPortal provides deidentified molecular and clinical reports. please fill out MCC cBioPortal account request form
- Foundation Medicine and Caris data provide clinically approved molecular data including BAM/CRAM, XML, JSON, and PDF. Please fill out CRI service request form
- For ORIEN data, please fill out ORIEN data request form
How do I access UK Healthcare data, SEER cancer registry data, or other CRI hosted data sets?
CRI can help facilitate access to research data sets, please fill out our service request form depending on the source of the data you are requesting:
- For SEER cancer registry data, please fill out KCR service request form: https://redcap.uky.edu/redcap/surveys/?s=NL8TRLK3HM
- For other CRI-facilitated data, please fill out the CRI service request form: https://redcap.uky.edu/redcap/surveys/?s=PT79FME9MK
What data variables are available?
Please review the data dictionaries at the websites below, depending on the data source:
- SEER KY cancer registry data: https://confluence.kcr.uky.edu/display/KAM
- cBioportal molecular data: https://wp.kcr.uky.edu/cbioportal/
What computational and data storage resources are available from CRI?
CRI provides a secure virtual environment, a PII-secured HPC Cluster, and extensive data storage resources. CRI personnel have the capability to create servers within the virtual environment and host them for investigators. CRI’s data storage capacity exceeds 1.3PB. Additionally, CRI operates a PII-secured HPC cluster comprising five compute nodes incorporating multiple GPU nodes.
Please visit the following links for public software and additional information.
- Cancer Research Data Commons/cBioPortal Portal
- The Markey Cancer Center's Cancer Research Informatics Shared Resource (CRI SR) has developed a cBioPortal instance to allow investigators to quickly review Foundation Medicine reports with clinical and outcome data from the SEER Kentucky Cancer Registry and other sources.
- A login account is required to access the portal. Please complete the REDCap form (https://redcap.uky.edu/redcap/surveys/?s=AL8THNDHA3) to request access to this online service.
- Kentucky Cancer Registry
- NIH Data sharing Policies
- UK Institute for Biomedical Informatics
- Center for Data-Driven Discovery in Biomedicine at CHOP
- ORIEN Avatar Program
Acknowledge the CRI SR
Investigators are required to acknowledge the Markey Cancer Center Cancer Research Informatics Shared Resource (CRI SR) in any publications, research papers and/or grant applications that result from services or CRI member-provided intellectual input or collaborative support received through the CRI SR. Please use the following statement to acknowledge the CRI SR.
“This research was supported by the Cancer Research Informatics Shared Resource of the University of Kentucky Markey Cancer Center (P30CA177558).”
