Annotating longitudinal clinical narratives for de-identification: The 2014 i2b2/UTHealth corpus.

Journal of Biomedical Informatics
Amber Stubbs, Özlem Uzuner

Abstract

The 2014 i2b2/UTHealth natural language processing shared task featured a track focused on the de-identification of longitudinal medical records. For this track, we de-identified a set of 1304 longitudinal medical records describing 296 patients. This corpus was de-identified under a broad interpretation of the HIPAA guidelines using double-annotation followed by arbitration, rounds of sanity checking, and proof reading. The average token-based F1 measure for the annotators compared to the gold standard was 0.927. The resulting annotations were used both to de-identify the data and to set the gold standard for the de-identification track of the 2014 i2b2/UTHealth shared task. All annotated private health information were replaced with realistic surrogates automatically and then read over and corrected manually. The resulting corpus is the first of its kind made available for de-identification research. This corpus was first used for the 2014 i2b2/UTHealth shared task, during which the systems achieved a mean F-measure of 0.872 and a maximum F-measure of 0.964 using entity-based micro-averaged evaluations.

References

Jun 30, 2007·Journal of the American Medical Informatics Association : JAMIA·Ozlem UzunerPeter Szolovits
Jul 26, 2008·BMC Medical Informatics and Decision Making·Ishna NeamatullahGari D Clifford
Apr 25, 2009·Journal of the American Medical Informatics Association : JAMIA·Ozlem Uzuner
Aug 18, 2009·Journal of Biomedical Informatics·Dina Demner-FushmanClement J McDonald
Aug 3, 2011·Journal of the American Medical Informatics Association : JAMIA·Chunhua WengStephen B Johnson
Mar 1, 2012·Journal of the American Medical Informatics Association : JAMIA·Robert J CarrollJoshua C Denny
May 1, 2012·Journal of the American Medical Informatics Association : JAMIA·Kavishwar B WagholikarRajeev Chaudhry
Jul 27, 2015·Journal of Biomedical Informatics·Amber StubbsÖzlem Uzuner
Oct 4, 2015·Journal of Biomedical Informatics·Vishesh KumarÖzlem Uzuner

❮ Previous
Next ❯

Citations

Sep 1, 2015·Journal of Biomedical Informatics·Bin HeWenlan Hua
Oct 31, 2015·Journal of Biomedical Informatics·Özlem Uzuner, Amber Stubbs
Sep 27, 2015·Journal of Biomedical Informatics·Tao ChenMarshall Godwin
Jul 27, 2015·Journal of Biomedical Informatics·Azad DehghanGoran Nenadic
Jul 27, 2015·Journal of Biomedical Informatics·Amber StubbsÖzlem Uzuner
Oct 4, 2015·Journal of Biomedical Informatics·Vishesh KumarÖzlem Uzuner
May 26, 2015·Journal of Biomedical Informatics·Amber Stubbs, Özlem Uzuner
Mar 30, 2016·Journal of Biomedical Informatics·Muqun LiBradley A Malin
Mar 29, 2018·BMC Medical Informatics and Decision Making·Yue-Shu ZhaoKun Li
Jul 10, 2019·Journal of the American Medical Informatics Association : JAMIA·Youngjun Kim, Stéphane M Meystre
Dec 1, 2017·Journal of the American Medical Informatics Association : JAMIA·Ergin SoysalHua Xu
Dec 6, 2019·BMC Medical Informatics and Decision Making·Xi YangYonghui Wu
May 18, 2018·JMIR Medical Informatics·Yingxiang HuangXiaoqian Jiang
Feb 1, 2020·BMC Medical Informatics and Decision Making·Tzvika HartmanYossi Matias
Apr 2, 2020·JMIR Medical Informatics·Irena Spasic, Goran Nenadic
Jun 6, 2017·Journal of Biomedical Informatics·Zengjian LiuQingcai Chen
Jun 15, 2017·Journal of Biomedical Informatics·Amber StubbsÖzlem Uzuner
Jun 9, 2018·Vaccine·Matthew FosterTaxiarchis Botsis
Oct 9, 2021·Scientific Reports·Jitendra JonnagaddalaChandini Nekkantti

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.