You are here

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."

Publications/Tools: 
Hume S, Aerts J, Sarnikar S, Huser V. Current applications and future directions for the CDISC Operational Data Model standard: A methodological review. J Biomed Inform. 2016 Apr;60:352-62. doi: 10.1016/j.jbi.2016.02.016. Epub 2016 Mar 2.
Kilicoglu H, Demner-Fushman D. Bio-SCoRes: A Smorgasbord Architecture for Coreference Resolution in Biomedical Text. PLoS One. 2016 Mar 2;11(3):e0148538. doi: 10.1371/journal.pone.0148538. eCollection 2016.
Driessen J, Baik SH, Zhang Y. Explaining Improved Use of High-Risk Medications in Medicare Between 2007 and 2011. J Am Geriatr Soc. 2016 Mar;64(3):674-6. doi: 10.1111/jgs.14000.
Baik SH, Hernandez I, Zhang Y. Evaluating the Initiation of Novel Oral Anticoagulants in Medicare Beneficiaries. J Manag Care Spec Pharm. 2016 Mar;22(3):281-92. doi: 10.18553/jmcp.2016.22.3.281.
Demner-Fushman D, Kohli MD, Rosenman MB, Shooshan SE, Rodriguez L, Antani S, Thoma GR, McDonald CJ. Preparing a collection of radiology examinations for distribution and retrieval. J Am Med Inform Assoc. 2016 Mar;23(2):304-10. doi: 10.1093/jamia/ocv080. Epub 2015 Jul 1.
Cimino JJ, Huser V. Characterization of the Context of Drug Concepts in Research Protocols: An Empiric Study to Guide Ontology Development. AMIA Annu Symp Proc. 2015 Nov 5;2015:441-7. eCollection 2015.
Pan X, Cimino JJ. Identifying the Clinical Laboratory Tests from Unspecified "Other Lab Test" Data for Secondary Use. AMIA Annu Symp Proc. 2015 Nov 5;2015:1018-23. eCollection 2015.
Drawz PE, Archdeacon P, McDonald CJ, Powe NR, Smith KA, Norton J, Williams DE, Patel UD, Narva A. CKD as a Model for Improving Chronic Disease Care through Electronic Health Records. Clin J Am Soc Nephrol. 2015 Aug 7;10(8):1488-99. doi: 10.2215/CJN.00940115. Epub 2015 Jun 25.
Roberts K, Simpson M, Demner-Fushman D, Voorhees E, Hersh W. State-of-the-art in biomedical literature retrieval for clinical cases: A survey of the TREC 2014 CDS Track. Inf Retrieval J. 2015.
Ayvas S, Horn J, Hassanzadeh O, Zhu Q, Stan J, Tatonetti NP, Vilar S, Brochhausen M8, Samwald M, Rastegar-Mojarad M, Dumontier M, Boyce RD. Toward a complete dataset of drug-drug interaction information from publicly available sources. J Biomed Inform. 2015 Jun;55:206-17. doi: 10.1016/j.jbi.2015.04.006. Epub 2015 Apr 24.

Pages