Dataset Information

Protected Health Information filter (Philter): accurately and securely de-identifying free-text clinical notes.

ABSTRACT: There is a great and growing need to ascertain what exactly is the state of a patient, in terms of disease progression, actual care practices, pathology, adverse events, and much more, beyond the paucity of data available in structured medical record data. Ascertaining these harder-to-reach data elements is now critical for the accurate phenotyping of complex traits, detection of adverse outcomes, efficacy of off-label drug use, and longitudinal patient surveillance. Clinical notes often contain the most detailed and relevant digital information about individual patients, the nuances of their diseases, the treatment strategies selected by physicians, and the resulting outcomes. However, notes remain largely unused for research because they contain Protected Health Information (PHI), which is synonymous with individually identifying data. Previous clinical note de-identification approaches have been rigid and still too inaccurate to see any substantial real-world use, primarily because they have been trained with too small medical text corpora. To build a new de-identification tool, we created the largest manually annotated clinical note corpus for PHI and develop a customizable open-source de-identification software called Philter ("Protected Health Information filter"). Here we describe the design and evaluation of Philter, and show how it offers substantial real-world improvements over prior methods.

SUBMITTER: Norgeot B

PROVIDER: S-EPMC7156708 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Protected Health Information filter (Philter): accurately and securely de-identifying free-text clinical notes.

Norgeot Beau B Muenzen Kathleen K Peterson Thomas A TA Fan Xuancheng X Glicksberg Benjamin S BS Schenk Gundolf G Rutenberg Eugenia E Oskotsky Boris B Sirota Marina M Yazdany Jinoos J Schmajuk Gabriela G Ludwig Dana D Goldstein Theodore T Butte Atul J AJ

NPJ digital medicine 20200414

There is a great and growing need to ascertain what exactly is the state of a patient, in terms of disease progression, actual care practices, pathology, adverse events, and much more, beyond the paucity of data available in structured medical record data. Ascertaining these harder-to-reach data elements is now critical for the accurate phenotyping of complex traits, detection of adverse outcomes, efficacy of off-label drug use, and longitudinal patient surveillance. Clinical notes often contain ...[more]

PMID: 32337372

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Project description:BackgroundSymptoms are a core concept of nursing interest. Large-scale secondary data reuse of notes in electronic health records (EHRs) has the potential to increase the quantity and quality of symptom research. However, the symptom language used in clinical notes is complex. A need exists for methods designed specifically to identify and study symptom information from EHR notes.ObjectivesWe aim to describe a method that combines standardized vocabularies, clinical expertise, and natural language processing to generate comprehensive symptom vocabularies and identify symptom information in EHR notes. We piloted this method with five diverse symptom concepts: constipation, depressed mood, disturbed sleep, fatigue, and palpitations.MethodsFirst, we obtained synonym lists for each pilot symptom concept from the Unified Medical Language System. Then, we used two large bodies of text (clinical notes from Columbia University Irving Medical Center and PubMed abstracts containing Medical Subject Headings or key words related to the pilot symptoms) to further expand our initial vocabulary of synonyms for each pilot symptom concept. We used NimbleMiner, an open-source natural language processing tool, to accomplish these tasks and evaluated NimbleMiner symptom identification performance by comparison to a manually annotated set of nurse- and physician-authored common EHR note types.ResultsCompared to the baseline Unified Medical Language System synonym lists, we identified up to 11 times more additional synonym words or expressions, including abbreviations, misspellings, and unique multiword combinations, for each symptom concept. Natural language processing system symptom identification performance was excellent.DiscussionUsing our comprehensive symptom vocabularies and NimbleMiner to label symptoms in clinical notes produced excellent performance metrics. The ability to extract symptom information from EHR notes in an accurate and scalable manner has the potential to greatly facilitate symptom science research.

Project description:BackgroundText-based patient medical records are a vital resource in medical research. In order to preserve patient confidentiality, however, the U.S. Health Insurance Portability and Accountability Act (HIPAA) requires that protected health information (PHI) be removed from medical records before they can be disseminated. Manual de-identification of large medical record databases is prohibitively expensive, time-consuming and prone to error, necessitating automatic methods for large-scale, automated de-identification.MethodsWe describe an automated Perl-based de-identification software package that is generally usable on most free-text medical records, e.g., nursing notes, discharge summaries, X-ray reports, etc. The software uses lexical look-up tables, regular expressions, and simple heuristics to locate both HIPAA PHI, and an extended PHI set that includes doctors' names and years of dates. To develop the de-identification approach, we assembled a gold standard corpus of re-identified nursing notes with real PHI replaced by realistic surrogate information. This corpus consists of 2,434 nursing notes containing 334,000 words and a total of 1,779 instances of PHI taken from 163 randomly selected patient records. This gold standard corpus was used to refine the algorithm and measure its sensitivity. To test the algorithm on data not used in its development, we constructed a second test corpus of 1,836 nursing notes containing 296,400 words. The algorithm's false negative rate was evaluated using this test corpus.ResultsPerformance evaluation of the de-identification software on the development corpus yielded an overall recall of 0.967, precision value of 0.749, and fallout value of approximately 0.002. On the test corpus, a total of 90 instances of false negatives were found, or 27 per 100,000 word count, with an estimated recall of 0.943. Only one full date and one age over 89 were missed. No patient names were missed in either corpus.ConclusionWe have developed a pattern-matching de-identification system based on dictionary look-ups, regular expressions, and heuristics. Evaluation based on two different sets of nursing notes collected from a U.S. hospital suggests that, in terms of recall, the software out-performs a single human de-identifier (0.81) and performs at least as well as a consensus of two human de-identifiers (0.94). The system is currently tuned to de-identify PHI in nursing notes and discharge summaries but is sufficiently generalized and can be customized to handle text files of any format. Although the accuracy of the algorithm is high, it is probably insufficient to be used to publicly disseminate medical data. The open-source de-identification software and the gold standard re-identified corpus of medical records have therefore been made available to researchers via the PhysioNet website to encourage improvements in the algorithm.

Project description:ObjectivesUrinary tract infection (UTI) is common in home care but not easily captured with standard assessment. This study aimed to examine the value of nursing notes in detecting UTI signs and symptoms in home care.DesignThe study developed a natural language processing (NLP) algorithm to automatically identify UTI-related information in nursing notes.Setting and participantsHome care visit notes (n = 1,149,586) and care coordination notes (n = 1,461,171) for 89,459 patients treated in the largest nonprofit home care agency in the United States during 2014.MeasuresWe generated 6 categories of UTI-related information from literature and used the Unified Medical Language System (UMLS) to identify a preliminary list of terms. The NLP algorithm was tested on a gold standard set of 300 clinical notes annotated by clinical experts. We used structured Outcome and Assessment Information Set data to extract the frequency of UTI-related emergency department (ED) visits or hospitalizations and explored time-patterns in documentation of UTI-related information.ResultsThe NLP system achieved very good overall performance (F measure = 0.9, 95% CI: 0.87-0.93) based on the test results obtained by using the notes for patients admitted to the ED or hospital due to UTI. UTI-related information was significantly more prevalent (P < .01 for all the tests) in home care episodes with UTI-related ED admission or hospitalization vs the general patient population; 81% of home care episodes with UTI-related hospitalization or ED admission had at least 1 category of UTI-related information vs 21.6% among episodes without UTI-related hospitalization or ED admission. Frequency of UTI-related information documentation increased in advance of UTI-related hospitalization or ED admission, peaking within a few days before the event.Conclusions and implicationsInformation in nursing notes is often overlooked by stakeholders and not integrated into predictive modeling for decision-making support, but our findings highlight their value in early risk identification and care guidance. Health care administrators should consider using NLP to extract clinical data from nursing notes to improve early detection and treatment, which may lead to quality improvement and cost reduction.

Project description:BackgroundPhysician notes routinely recorded during patient care represent a vast and underutilized resource for human disease studies on a population scale. Their use in research is primarily limited by the need to separate confidential patient information from clinical annotations, a process that is resource-intensive when performed manually. This study seeks to create an automated method for de-identifying physician notes that does not require large amounts of private information: in addition to training a model to recognize Protected Health Information (PHI) within private physician notes, we reverse the problem and train a model to recognize non-PHI words and phrases that appear in public medical texts.MethodsPublic and private medical text sources were analyzed to distinguish common medical words and phrases from Protected Health Information. Patient identifiers are generally nouns and numbers that appear infrequently in medical literature. To quantify this relationship, term frequencies and part of speech tags were compared between journal publications and physician notes. Standard medical concepts and phrases were then examined across ten medical dictionaries. Lists and rules were included from the US census database and previously published studies. In total, 28 features were used to train decision tree classifiers.ResultsThe model successfully recalled 98% of PHI tokens from 220 discharge summaries. Cost sensitive classification was used to weight recall over precision (98% F10 score, 76% F1 score). More than half of the false negatives were the word "of" appearing in a hospital name. All patient names, phone numbers, and home addresses were at least partially redacted. Medical concepts such as "elevated white blood cell count" were informative for de-identification. The results exceed the previously approved criteria established by four Institutional Review Boards.ConclusionsThe results indicate that distributional differences between private and public medical text can be used to accurately classify PHI. The data and algorithms reported here are made freely available for evaluation and improvement.

Project description:BACKGROUND:Some medications carry increased risk of patient harm when they are given in error. In incident reports, names of the medications that are involved in errors could be found written both in a specific medication field and/or within the free text description of the incident. Analysing only the names of the medications implicated in a specific unstructured medication field does not give information of the associated factors and risk areas, but when analysing unstructured free text descriptions, the information about the medication involved and associated risk factors may be buried within other non-relevant text. Thus, the aim of this study was to extract medication names most commonly used in free text descriptions of medication administration incident reports to identify terms most frequently associated with risk for each of these medications using text mining. METHOD:Free text descriptions of medication administration incidents (n = 72,390) reported in 2016 to the National Reporting and Learning System for England and Wales were analysed using SAS® Text miner. Analysis included text parsing and filtering free text to identify most commonly mentioned medications, followed by concept linking, and clustering to identify terms associated with commonly mentioned medications and the associated risk areas. RESULTS:The following risk areas related to medications were identified: 1. Allergic reactions to antibacterial drugs, 2. Intravenous administration of antibacterial drugs, 3. Fentanyl patches, 4. Checking and documenting of analgesic doses, 5. Checking doses of anticoagulants, 6. Insulin doses and blood glucose, 7. Administration of intravenous infusions. CONCLUSIONS:Interventions to increase medication administration safety should focus on checking patient allergies and medication doses, especially for intravenous and transdermal medications. High-risk medications include insulin, analgesics, antibacterial drugs, anticoagulants, and potassium chloride. Text mining may be useful for analysing large free text datasets and should be developed further.

Dataset Information

Protected Health Information filter (Philter): accurately and securely de-identifying free-text clinical notes.

Publications

Protected Health Information filter (Philter): accurately and securely de-identifying free-text clinical notes.

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