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Discoveries from Clinical Data

Large database collections of clinical data -- from longitudinal research projects, electronic medical records, and health information exchanges -- provide opportunities to examine controversial findings from smaller scale clinical studies and to conduct retrospective epidemiological studies in areas that lack clinical trials.

NLM established a goal to integrate biomedical, clinical, and public health information systems that promote scientific discovery and speed the translation of research into practice (NLM Long Range Plan, 2006-2016, Goal 3).  One of NLM's key recommendations to fulfill this goal is to "develop linked databases for discovering relationships between clinical data, genetic information, and environmental factors."

LHNCBC's biostatistician and clinicians are using MIT’s large longitudinal MIMIC-II database (33,000 patients with 40,000 intensive care unit (ICU) visits and 180 million rows of data) to answer clinical research questions. We also contributed standard clinical vocabulary code mappings to the latest MIMIC-II release (v 2.6).

We have completed a study on the impact of obesity on outcomes after critical illness, which was published in the journal Critical Care.

Ongoing studies include: 1) the relationship between vitamin B12 levels and mortality; and 2) the relationship between blood transfusions, feeds, and necrotizing enterocolitis (NEC) in newborns.

We developed and implemented Natural Language Processing algorithms to extract patients’ smoking status and discharge destinations from the MIMIC-II physician discharge summaries. We extracted information on episodes of neonatal apnea and bradycardia as well as maternal history from clinical notes for infants in the neonatal intensive care unit (NICU) for the NEC study. We also extracted data about hypertension and hypertensive medications from free-text notes, and used that data to compare to ICD-9 hypertension diagnosis codes in order to evaluate underreporting of certain common conditions after ICU admission.

To assist with integrating and analyzing the data, LHNCBC's researchers are using NLM-supported clinical vocabulary standards to improve the utility of the MIMIC-II database. We mapped the laboratory tests and medications to LOINC and RxNorm, respectively, and its radiology reports to the LOINC codes that describe the radiology study.

We are also developing the Maximum Likelihood (ML) statistical method -- to address measurement error in NLP-derived variables in order to reduce bias -- which could potentially increase the utility of NLP-derived data.

This LHNCBC research aligns closely with NIH's Big Data to Knowledge (BD2K) initiative, which "seeks to facilitate broad use of biomedical big data through new data sharing policies, catalogs of datasets, and enhanced training for early career scientists entering the new world of big data" by supporting "the management, analysis and integration of large-scale data and informatics."

Callaghan F, Demner-Fushman D, Abhyankar S, McDonald CJ. Addressing errors in a retrospective observational ICU database [poster]. AMIA 2011 Fall Symposium.
Abhyankar S, Callaghan FM, Demner-Fushman D, McDonald CJ. Using informatics tools to study obesity and outcomes after critical illness. NLM Informatics Training Conference 2011, National Institutes of Health (NIH) Campus, Natcher Conference Center, Bethesda, MD, June 28-30, 2011.
Overby CL, Tarczy-Hornoch P, Demner-Fushman D. The potential for automated question answering in the context of genomic medicine: An assessment of existing resources and properties of answers Summit on Translat Bioinforma. 2009 Mar 1;2009:1-25.
Hansen RA, Wanzhu T, Wang J, Ambuehl R, McDonald CJ, Murray MD. Risk of adverse gastrointestinal events from inhaled corticosteroids. 2008 Nov;28(11):1325-34.
Demner-Fushman D, Ananiadou S, Cohen KB, Pestian J, Tsujii J, Webber B. Themes in biomedical natural language processing: BioNLP08 BMC Bioinformatics. 2008 Nov 19;9 Suppl 11:S1.
Lin J, Demner-Fushman D. Semantic clustering of answers to clinical questions. AMIA Annu Symp Proc. 2007 Oct 11:458-62.
Zweigenbaum P, Demner-Fushman D, Yu H, Cohen KB. Frontiers of biomedical text mining: current progress Brief Bioinform. 2007 Sep;8(5):358-75. Epub 2007 Oct 30.
Huang X, Lin J, Demner-Fushman D. Evaluation of PICO as a knowledge representation for clinical questions AMIA Annu Symp Proc. 2006:359-63.
Demner-Fushman D, Hauser SE, Thoma GR. The role of title, metadata and abstract in identifying clinically relevant journal articles. AMIA Annu Symp Proc. 2005:191-5.
Lin J, Demner-Fushman D. "Bag of words" is not enough for strength of evidence classification AMIA Annu Symp Proc. 2005:1031.