Welcome to the Institute for Biomedical Informatics (IBI) at the University of Kentucky. The Institute facilitates data-intensive, multidisciplinary team science to improve the health of patients and populations, in Kentucky and beyond. IBI provides services through the Center for Clinical and Translational Science's Biomedical Informatics Core and UK's College of Medicine provides its academic home.




IBI Launches New Center for Applied Artificial Intelligence

Sept 29, 2023

The Center for Applied Artificial Intelligence (CAAI) within the UK Institute for Biomedical Informatics launched today from the past two years of effort in the Artificial Intelligence in Medicine Alliance. The Alliance brought together researchers across campus to explore the potential of AI to transform healthcare. The establishment of CAAI will allow us to build on this foundation and accelerate AI innovation and translation.

CAAI will focus on developing AI tools for improving disease diagnosis, treatment personalization, clinical workflow optimization, and more. Potential high impact application areas include medical imaging, digital pathology, population health informatics, and precision medicine. We believe AI holds immense promise to augment clinician capabilities, increase access to care, reduce costs, and ultimately improve patient outcomes.

Under the leadership of Dr. Cody Bumgardner as Director, CAAI will host collaborative projects, share computing resources, provide educational opportunities, and foster an interdisciplinary community of AI researchers. We aim to develop strong partnerships between our clinicians, basic scientists, informaticians, and engineers to drive impactful work.

CAAI will build on existing strengths at our academic medical center while expanding the scope of AI application. We are excited by the breadth of talent and potential at UK to be leaders in validating, translating, and ethically implementing AI technologies. Please reach out if you are interested in learning more and participating in CAAI activities. Together we can harness AI to solve major challenges in 21st century medicine and healthcare.

The metabolomics workbench file status website: a metadata repository promoting FAIR principles of metabolomics data

Jul 23, 2023

Christian D. Powell & Hunter N. B. Moseley. BMC Bioinformatics volume 24, Article number: 299 (2023).

An updated version of the mwtab Python package for programmatic access to the Metabolomics Workbench (MetabolomicsWB) data repository was released at the beginning of 2021. Along with updating the package to match the changes to MetabolomicsWB’s ‘mwTab’ file format specification and enhancing the package’s functionality, the included validation facilities were used to detect and catalog file inconsistencies and errors across all publicly available datasets in MetabolomicsWB.

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MESSES: Software for Transforming Messy Research Datasets into Clean Submissions to Metabolomics Workbench for Public Sharing

Jul 12, 2023

P. Travis Thompson1 and Hunter N. B. Moseley. Metabolites 2023, 13(7), 842; https://doi.org/10.3390/metabo13070842

In recent years, the FAIR guiding principles and the broader concept of open science has grown in importance in academic research, especially as funding entities have aggressively promoted public sharing of research products. Key to public research sharing is deposition of datasets into online data repositories, but it can be a chore to transform messy unstructured data into the forms required by these repositories. To help generate Metabolomics Workbench depositions, we have developed the MESSES (Metadata from Experimental SpreadSheets Extraction System) software package, implemented in the Python 3 programming language and supported on Linux, Windows, and Mac operating systems. MESSES helps transform tabular data from multiple sources into a Metabolomics Workbench specific deposition format. The package provides three commands, extract, validate, and convert, that implement a natural data transformation workflow. Moreover, MESSES facilitates richer metadata capture than is typically attempted by manual efforts. The source code and extensive documentation is hosted on GitHub and is also available on the Python Package Index for easy installation.

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New faculty Yuan Wen joins IBI

Jul 01, 2023

We would like to welcome Dr. Yuan Wen, PhD, Assistant Professor in the Division of Biomedical Informatics, Department of Internal Medicine. Dr. Wen's career goal is to develop novel and effective tools and therapeutics so that more people can be cured faster. He started out as a chemist at the University of Pennsylvania before coming back to UK, where he graduated from the MD/PhD Program in 2020. Currently, Dr. Wen is focused on the application of computation and AI technologies to improve medical care for patients. His research program mainly includes molecular mechanisms of protein synthesis, cellular physiology, and animal models of health and disease. The plan is to extend the findings from these projects into translational and clinical applications to benefit patients in the ICU or suffering from genetic diseases such as muscular dystrophy.

New faculty Cody Steely joins IBI

Jul 01, 2023

We would like to welcome Dr. Cody Steely, PhD, Assistant Professor in the Division of Biomedical Informatics, Department of Internal Medicine. His work is focused on using sequencing data and bioinformatics to study age-related disorders like neurodegeneration and cancer. Dr. Steely is currently working to understand how the genome changes as individuals age and how the somatic mutations accrued over time might impact disease risk. Dr. Steely is also interested in the role of repetitive DNA (transposable elements and tandem repeats) in Alzheimer’s Disease and cancer. 

A Case for Accelerating Standards to Achieve the FAIR Principles of Environmental Health Research Experimental Data

Jun 23, 2023

    Rance Nault, Matthew C. Cave, Gabriele Ludewig, Hunter N.B. Moseley, Kelly G. Pennell, and Tim Zacharewski

    Funding agencies, publishers, and other stakeholders are pushing environmental health science investigators to improve data sharing; to promote the findable, accessible, interoperable, and reusable (FAIR) principles; and to increase the rigor and reproducibility of the data collected. Accomplishing these goals will require significant cultural shifts surrounding data management and strategies to develop robust and reliable resources that bridge the technical challenges and gaps in expertise.

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    A proposed FAIR approach for disseminating geospatial information system maps

    Jun 16, 2023

    P. Travis Thompson, Sweta Ojha, Christian D. Powell, Kelly G. Pennell & Hunter N. B. Moseley. Scientific Data volume 10, Article number: 389 (2023).

    We present a draft Minimum Information About Geospatial Information System (MIAGIS) standard for facilitating public deposition of geospatial information system (GIS) datasets that follows the FAIR (Findable, Accessible, Interoperable and Reusable) principles. The draft MIAGIS standard includes a deposition directory structure and a minimum javascript object notation (JSON) metadata formatted file that is designed to capture critical metadata describing GIS layers and maps as well as their sources of data and methods of generation. The associated miagis Python package facilitates the creation of this MIAGIS metadata file and directly supports metadata extraction from both Esri JSON and GEOJSON GIS data formats plus options for extraction from user-specified JSON formats. We also demonstrate their use in crafting two example depositions of ArcGIS generated maps. We hope this draft MIAGIS standard along with the supporting miagis Python package will assist in establishing a GIS standards group that will develop the draft into a full standard for the wider GIS community as well as a future public repository for GIS datasets.

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    Students@SC Chair Sally Ellingson Shines Her Guiding Light

    Apr 11, 2023

    The Students@SC program is a perfect example of what SC is all about – bringing people together to talk tech. Open to everyone from high school to graduate students, the program provides vital career-growing tools, such as a job fair, alumni networking event, various workshops and skill-building activities, and so much more.

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    Rama Kavuluru receives best paper award at IEEE ICHI

    Mar 29, 2023

    The 11th IEEE International Conference on Healthcare Informatics awarded Dr. Kavuluru's article entitled, "End-to-End n-ary Relation Extraction for Combination Drug Therapies" as best paper.

    Relations linking various biomedical entities constitute a crucial resource that enables biomedical data science applications and knowledge discovery. Relational information spans the translational science spectrum going from biology (e.g., protein–protein interactions) to translational bioinformatics (e.g., gene–disease associations), and eventually to clinical care (e.g., drug–drug interactions). Scientists report newly discovered relations in nat- ural language through peer-reviewed literature and physicians may communicate them in clinical notes. More recently, patients are also reporting side-effects and adverse events on social media. With exponential growth in textual data, advances in biomedical natural language processing (BioNLP) methods are gaining prominence for biomedical relation extraction (BRE) from text.

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    Sally Ellingson, Ph.D., is a computational scientist working at the intersection of computational biology and high-performance computing.

    Mar 15, 2023

    Throughout March, the University of Kentucky is spotlighting Women Making History during Women’s History Month. These women are leading their fields of research and impacting the lives of Kentuckians.

    Their work addresses key issues impacting the Commonwealth, like cancer, Alzheimer’s disease and diabetes. They also offer new perspectives on history by finding ways to preserve our collective memory and better understand it.

    When you think of how scientists test new drugs to fight cancers, you probably think of a traditional lab setting. However, one UK researcher is using computers to evaluate how those drugs work in the body.

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    kegg_pull: a software package for the RESTful access and pulling from the Kyoto Encyclopedia of Gene and Genomes

    Mar 4, 2023

    Erik Huckvale & Hunter N. B. Moseley. BMC Bioinformatics volume 24, Article number: 78 (2023).

    The Kyoto Encyclopedia of Genes and Genomes (KEGG) provides organized genomic, biomolecular, and metabolic information and knowledge that is reasonably current and highly useful for a wide range of analyses and modeling. KEGG follows the principles of data stewardship to be findable, accessible, interoperable, and reusable (FAIR) by providing RESTful access to their database entries via their web-accessible KEGG API. However, the overall FAIRness of KEGG is often limited by the library and software package support available in a given programming language. While R library support for KEGG is fairly strong, Python library support has been lacking. Moreover, there is no software that provides extensive command line level support for KEGG access and utilization.

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    New faculty Yasminka Jakubek Swartzlander joins 3rd cohort of the Research Scholars Program

    Mar 01, 2023

    We welcome Yasminka Jakubek Swartzlander to the third cohort of the Research Scholars Program (RSP). The program is aimed at ensuring diversity, equity and inclusion in research by promoting faculty success.

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    Eric Durbin's research seeks to understand Appalachia’s childhood cancer disparity

    Feb 07, 2023

    When Eric Durbin, Dr.PH., director of the Cancer Research Informatics Shared Resource Facility at the University of Kentucky Markey Cancer Center, began mapping childhood cancer incidence rates, he noticed a troubling trend: Brain cancer rates appeared to be higher in the Appalachian region of Kentucky. That led Durbin, who is also the director of the Kentucky Cancer Registry, to conduct a broader study that looked at all childhood brain cancers across the U.S. The goal of this study was to see if there were differences between Appalachian children and children outside Appalachia.

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    Kavuluru becomes chartered member of NIH study section

    Jul 05, 2022

    Ramakanth (Rama) Kavuluru, PhD, Associate Professor, has become a chartered member of the National Institute of Health’s Clinical Data Management and Analysis (CDMA) Study Section.  This study section meets three times a year to review grant applications that "develop computing technology, simulation/data models, data analytics, and technical software intended for eventual translation of research or novel findings for clinical use.”  His term will expire in 2026.

    Dr. George Shih delivers keynote address at AIM Summit 2022

    May 17, 2022

    On April 20, 2022, the AIM Alliance hosted the inaugural AIM Summit, a half-day conference focusing on AI in Medicine. Dr. George Shih from Weill Cornell Medicine addressed the inaugural AIM Summit as the keynote speaker and delivered his presentation "AI Bias and Fairnes"

    AI in Medicine Alliance announces AIM Summer Undergraduate Research Fellowship

    Mar 11, 2022

    The AIM Fellowship, sponsored by the AI in Medicine (AIM) Alliance, Institute for Biomedical Informatics (IBI), and UK Center for Clinical and Translational Science (CCTS) seeks to ensure the inclusion of a diverse population of undergraduate students pursuing mentored research in artificial intelligence and medicine.

    Clarkson awarded NIH grant to develop standardized graphic libraries for anatomy

    Jul 01, 2021

    Dr. Melissa Clarkson has been awarded four years of funding from the National Institute of Dental and Craniofacial Research for her project "Developing standardized graphic libraries for anatomy: A focus on human craniofacial anatomy and phenotypes". Her team will be developing "semantically-enabled" graphics depicting anatomy of the human head, including developmental stages, phenotypes, and malformations. You can preview their work at the Endless Forms Studio website.

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