scholarly journals Designing an openEHR-Based Pipeline for Extracting and Standardizing Unstructured Clinical Data Using Natural Language Processing

2020 ◽  
Vol 59 (S 02) ◽  
pp. e64-e78
Author(s):  
Antje Wulff ◽  
Marcel Mast ◽  
Marcus Hassler ◽  
Sara Montag ◽  
Michael Marschollek ◽  
...  
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Clinical Data ◽  
Expert Knowledge ◽  
Clinical Information ◽  
Structured Data ◽  
Unstructured Data ◽  
Mapping Rules ◽  
Medical Histories

Abstract Background Merging disparate and heterogeneous datasets from clinical routine in a standardized and semantically enriched format to enable a multiple use of data also means incorporating unstructured data such as medical free texts. Although the extraction of structured data from texts, known as natural language processing (NLP), has been researched at least for the English language extensively, it is not enough to get a structured output in any format. NLP techniques need to be used together with clinical information standards such as openEHR to be able to reuse and exchange still unstructured data sensibly. Objectives The aim of the study is to automatically extract crucial information from medical free texts and to transform this unstructured clinical data into a standardized and structured representation by designing and implementing an exemplary pipeline for the processing of pediatric medical histories. Methods We constructed a pipeline that allows reusing medical free texts such as pediatric medical histories in a structured and standardized way by (1) selecting and modeling appropriate openEHR archetypes as standard clinical information models, (2) defining a German dictionary with crucial text markers serving as expert knowledge base for a NLP pipeline, and (3) creating mapping rules between the NLP output and the archetypes. The approach was evaluated in a first pilot study by using 50 manually annotated medical histories from the pediatric intensive care unit of the Hannover Medical School. Results We successfully reused 24 existing international archetypes to represent the most crucial elements of unstructured pediatric medical histories in a standardized form. The self-developed NLP pipeline was constructed by defining 3.055 text marker entries, 132 text events, 66 regular expressions, and a text corpus consisting of 776 entries for automatic correction of spelling mistakes. A total of 123 mapping rules were implemented to transform the extracted snippets to an openEHR-based representation to be able to store them together with other structured data in an existing openEHR-based data repository. In the first evaluation, the NLP pipeline yielded 97% precision and 94% recall. Conclusion The use of NLP and openEHR archetypes was demonstrated as a viable approach for extracting and representing important information from pediatric medical histories in a structured and semantically enriched format. We designed a promising approach with potential to be generalized, and implemented a prototype that is extensible and reusable for other use cases concerning German medical free texts. In a long term, this will harness unstructured clinical data for further research purposes such as the design of clinical decision support systems. Together with structured data already integrated in openEHR-based representations, we aim at developing an interoperable openEHR-based application that is capable of automatically assessing a patient's risk status based on the patient's medical history at time of admission.

scholarly journals Latent Dirichlet Allocation in predicting clinical trial terminations

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Simon Geletta ◽  
Lendie Follett ◽  
Marcia Laugerman
Keyword(s):  
Clinical Trial ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Latent Dirichlet Allocation ◽  
Structured Data ◽  
Unstructured Data ◽  
Future Research ◽  
Funding Agencies ◽  
Dirichlet Allocation

Abstract Background This study used natural language processing (NLP) and machine learning (ML) techniques to identify reliable patterns from within research narrative documents to distinguish studies that complete successfully, from the ones that terminate. Recent research findings have reported that at least 10 % of all studies that are funded by major research funding agencies terminate without yielding useful results. Since it is well-known that scientific studies that receive funding from major funding agencies are carefully planned, and rigorously vetted through the peer-review process, it was somewhat daunting to us that study-terminations are this prevalent. Moreover, our review of the literature about study terminations suggested that the reasons for study terminations are not well understood. We therefore aimed to address that knowledge gap, by seeking to identify the factors that contribute to study failures. Method We used data from the clinicialTrials.gov repository, from which we extracted both structured data (study characteristics), and unstructured data (the narrative description of the studies). We applied natural language processing techniques to the unstructured data to quantify the risk of termination by identifying distinctive topics that are more frequently associated with trials that are terminated and trials that are completed. We used the Latent Dirichlet Allocation (LDA) technique to derive 25 “topics” with corresponding sets of probabilities, which we then used to predict study-termination by utilizing random forest modeling. We fit two distinct models – one using only structured data as predictors and another model with both structured data and the 25 text topics derived from the unstructured data. Results In this paper, we demonstrate the interpretive and predictive value of LDA as it relates to predicting clinical trial failure. The results also demonstrate that the combined modeling approach yields robust predictive probabilities in terms of both sensitivity and specificity, relative to a model that utilizes the structured data alone. Conclusions Our study demonstrated that the use of topic modeling using LDA significantly raises the utility of unstructured data in better predicating the completion vs. termination of studies. This study sets the direction for future research to evaluate the viability of the designs of health studies.

scholarly journals Latent Dirichlet Allocation in Predicting Clinical Trial Terminations

2019 ◽  
Author(s):  
Simon Geletta ◽  
Lendie Follett ◽  
Marcia R Laugerman
Keyword(s):  
Clinical Trial ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Latent Dirichlet Allocation ◽  
Structured Data ◽  
Unstructured Data ◽  
Future Research ◽  
Funding Agencies ◽  
Dirichlet Allocation

Abstract This study used natural language processing (NLP) and machine learning (ML) techniques to identify reliable patterns from within research narrative documents to distinguish studies that complete successfully, from the ones that terminate. Recent research findings have reported that at least ten percent of all studies that are funded by major research funding agencies terminate without yielding useful results. Since it is well-known that scientific studies that receive funding from major funding agencies are carefully planned, and rigorously vetted through the peer-review process, it was somewhat daunting to us that study-terminations are this prevalent. Moreover, our review of the literature about study terminations suggested that the reasons for study terminations are not well understood. We therefore aimed to address that knowledge gap, by seeking to identify the factors that contribute to study failures.Method: We used data from the clinicialTrials.gov repository, from which we extracted both structured data (study characteristics), and unstructured data (the narrative description of the studies). We applied natural language processing techniques to the unstructured data to quantify the risk of termination by identifying distinctive topics that are more frequently associated with trials that are terminated and trials that are completed. We used the Latent Dirichlet Allocation (LDA) technique to derive 25 “topics” with corresponding sets of probabilities, which we then used to predict study-termination by utilizing random forest modeling. We fit two distinct models – one using only structured data as predictors and another model with both structured data and the 25 text topics derived from the unstructured data.Results: In this paper, we demonstrate the interpretive and predictive value of LDA as it relates to predicting clinical trial failure. The results also demonstrate that the combined modeling approach yields robust predictive probabilities in terms of both sensitivity and specificity, relative to a model that utilizes the structured data alone.Conclusions: Our study demonstrated that the use of topic modeling using LDA significantly raises the utility of unstructured data in better predicating the completion vs. termination of studies. This study sets the direction for future research to evaluate the viability of the designs of health studies.

scholarly journals Latent Dirichlet Allocation in Predicting Clinical Trial Terminations

2019 ◽  
Author(s):  
Simon Geletta ◽  
Lendie Follett ◽  
Marcia R Laugerman
Keyword(s):  
Clinical Trial ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Latent Dirichlet Allocation ◽  
Structured Data ◽  
Unstructured Data ◽  
Future Research ◽  
Funding Agencies ◽  
Dirichlet Allocation

Abstract Background: This study used natural language processing (NLP) and machine learning (ML) techniques to identify reliable patterns from within research narrative documents to distinguish studies that complete successfully, from the ones that terminate. Recent research findings have reported that at least ten percent of all studies that are funded by major research funding agencies terminate without yielding useful results. Since it is well-known that scientific studies that receive funding from major funding agencies are carefully planned, and rigorously vetted through the peer-review process, it was somewhat daunting to us that study-terminations are this prevalent. Moreover, our review of the literature about study terminations suggested that the reasons for study terminations are not well understood. We therefore aimed to address that knowledge gap, by seeking to identify the factors that contribute to study failures.Method: We used data from the clinicialTrials.gov repository, from which we extracted both structured data (study characteristics), and unstructured data (the narrative description of the studies). We applied natural language processing techniques to the unstructured data to quantify the risk of termination by identifying distinctive topics that are more frequently associated with trials that are terminated and trials that are completed. We used the Latent Dirichlet Allocation (LDA) technique to derive 25 “topics” with corresponding sets of probabilities, which we then used to predict study-termination by utilizing random forest modeling. We fit two distinct models – one using only structured data as predictors and another model with both structured data and the 25 text topics derived from the unstructured data.Results: In this paper, we demonstrate the interpretive and predictive value of LDA as it relates to predicting clinical trial failure. The results also demonstrate that the combined modeling approach yields robust predictive probabilities in terms of both sensitivity and specificity, relative to a model that utilizes the structured data alone.Conclusions: Our study demonstrated that the use of topic modeling using LDA significantly raises the utility of unstructured data in better predicating the completion vs. termination of studies. This study sets the direction for future research to evaluate the viability of the designs of health studies.

scholarly journals Latent Dirichlet Allocation in Predicting Clinical Trial Failures

2019 ◽  
Author(s):  
Simon Geletta ◽  
Lendie Follett ◽  
Marcia R Laugerman
Keyword(s):  
Clinical Trial ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Latent Dirichlet Allocation ◽  
Peer Review Process ◽  
Structured Data ◽  
Unstructured Data ◽  
Funding Agencies ◽  
Dirichlet Allocation

Abstract Background : This study used natural language processing (NLP) and machine learning (ML) techniques to identify reliable patterns from within research narrative documents to distinguish studies that complete successfully, from the ones that terminate. Recent research findings have reported that at least ten percent of all studies that are funded by major research funding agencies terminate without yielding useful results. Since it is well-known that scientific studies that receive funding from major funding agencies are carefully planned, and rigorously vetted through the peer-review process, it was somewhat daunting to us that study-terminations are this prevalent. Moreover, our review of the literature about study terminations suggested that the reasons for study terminations are not well understood. We therefore aimed to address that knowledge gap, by seeking to identify the factors that contribute to study failures. Method : We used data from the clinicialTrials.gov repository, from which we extracted both structured data (study characteristics), and unstructured data (the narrative description of the studies). We applied natural language processing techniques to the unstructured data to quantify the risk of termination by identifying distinctive topics that are more frequently associated with trials that are terminated and trials that are completed. We used the Latent Dirichlet Allocation (LDA) technique to derived 25 “topics” with corresponding sets of probabilities, which we then used to predict study-termination by utilizing random forest modeling. We fit two distinct models – one using only structured data as predictors and another model with both structured data and the 25 text topics derived from the unstructured data. Results : In this paper, we demonstrate the interpretive and predictive value of LDA as it relates to predicting clinical trial failure. The results also demonstrate that the combined modeling approach yields robust predictive probabilities in terms of both sensitivity and specificity, relative to a model that utilizes the structured data alone. Conclusions : Our study demonstrated that the use of topic modeling using LDA significantly raises the utility of unstructured data in better predicating the completion vs. termination of studies.

scholarly journals Obtaining structured clinical data from unstructured data using natural language processing software

2017 ◽  
Vol 1 (1) ◽  
Author(s):  
Arron S Lacey ◽  
Beata Fonferko-Shadrach ◽  
Ronan A Lyons ◽  
Mike P Kerr ◽  
David V Ford ◽  
...  
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Age Of Onset ◽  
Focal Epilepsy ◽  
Clinical Information ◽  
Unstructured Data ◽  
Free Text ◽  
Epilepsy Diagnosis ◽  
Generalized Epilepsy

ABSTRACT BackgroundFree text documents in healthcare settings contain a wealth of information not captured in electronic healthcare records (EHRs). Epilepsy clinic letters are an example of an unstructured data source containing a large amount of intricate disease information. Extracting meaningful and contextually correct clinical information from free text sources, to enhance EHRs, remains a significant challenge. SCANR (Swansea University Collaborative in the Analysis of NLP Research) was set up to use natural language processing (NLP) technology to extract structured data from unstructured sources. IBM Watson Content Analytics software (ICA) uses NLP technology. It enables users to define annotations based on dictionaries and language characteristics to create parsing rules that highlight relevant items. These include clinical details such as symptoms and diagnoses, medication and test results, as well as personal identifiers.   ApproachTo use ICA to build a pipeline to accurately extract detailed epilepsy information from clinic letters. MethodsWe used ICA to retrieve important epilepsy information from 41 pseudo-anonymized unstructured epilepsy clinic letters. The 41 letters consisted of 13 ‘new’ and 28 ‘follow-up’ letters (for 15 different patients) written by 12 different doctors in different styles. We designed dictionaries and annotators to enable ICA to extract epilepsy type (focal, generalized or unclassified), epilepsy cause, age of onset, investigation results (EEG, CT and MRI), medication, and clinic date. Epilepsy clinicians assessed the accuracy of the pipeline. ResultsThe accuracy (sensitivity, specificity) of each concept was: epilepsy diagnosis 98% (97%, 100%), focal epilepsy 100%, generalized epilepsy 98% (93%, 100%), medication 95% (93%, 100%), age of onset 100% and clinic date 95% (95%, 100%). Precision and recall for each concept were respectively, 98% and 97% for epilepsy diagnosis, 100% each for focal epilepsy, 100% and 93% for generalized epilepsy, 100% each for age of onset, 100% and 93% for medication, 100% and 96% for EEG results, 100% and 83% for MRI scan results, and 100% and 95% for clinic date. Conclusions ICA is capable of extracting detailed, structured epilepsy information from unstructured clinic letters to a high degree of accuracy. This data can be used to populate relational databases and be linked to EHRs. Researchers can build in custom rules to identify concepts of interest from letters and produce structured information. We plan to extend our work to hundreds and then thousands of clinic letters, to provide phenotypically rich epilepsy data to link with other anonymised, routinely collected data.

scholarly journals Latent Dirichlet Allocation in Predicting Clinical Trial Terminations

2019 ◽  
Author(s):  
Simon Geletta ◽  
Lendie Follett ◽  
Marcia R Laugerman
Keyword(s):  
Clinical Trial ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Latent Dirichlet Allocation ◽  
Peer Review Process ◽  
Structured Data ◽  
Unstructured Data ◽  
Funding Agencies ◽  
Dirichlet Allocation

Abstract Background : This study used natural language processing (NLP) and machine learning (ML) techniques to identify reliable patterns from within research narrative documents to distinguish studies that complete successfully, from the ones that terminate. Recent research findings have reported that at least ten percent of all studies that are funded by major research funding agencies terminate without yielding useful results. Since it is well-known that scientific studies that receive funding from major funding agencies are carefully planned, and rigorously vetted through the peer-review process, it was somewhat daunting to us that study-terminations are this prevalent. Moreover, our review of the literature about study terminations suggested that the reasons for study terminations are not well understood. We therefore aimed to address that knowledge gap, by seeking to identify the factors that contribute to study failures. Method : We used data from the clinicialTrials.gov repository, from which we extracted both structured data (study characteristics), and unstructured data (the narrative description of the studies). We applied natural language processing techniques to the unstructured data to quantify the risk of termination by identifying distinctive topics that are more frequently associated with trials that are terminated and trials that are completed. We used the Latent Dirichlet Allocation (LDA) technique to derived 25 “topics” with corresponding sets of probabilities, which we then used to predict study-termination by utilizing random forest modeling. We fit two distinct models – one using only structured data as predictors and another model with both structured data and the 25 text topics derived from the unstructured data. Results : In this paper, we demonstrate the interpretive and predictive value of LDA as it relates to predicting clinical trial failure. The results also demonstrate that the combined modeling approach yields robust predictive probabilities in terms of both sensitivity and specificity, relative to a model that utilizes the structured data alone. Conclusions : Our study demonstrated that the use of topic modeling using LDA significantly raises the utility of unstructured data in better predicating the completion vs. termination of studies.

scholarly journals Natural language processing methods for knowledge management—Applying document clustering for fast search and grouping of engineering documents

2021 ◽  
pp. 1063293X2098297
Author(s):  
Ivar Örn Arnarsson ◽  
Otto Frost ◽  
Emil Gustavsson ◽  
Mats Jirstrand ◽  
Johan Malmqvist
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Domain Knowledge ◽  
Clustering Algorithms ◽  
Document Clustering ◽  
Unstructured Data ◽  
Free Text ◽  
Engineering Change ◽  
Engineering Documents

Product development companies collect data in form of Engineering Change Requests for logged design issues, tests, and product iterations. These documents are rich in unstructured data (e.g. free text). Previous research affirms that product developers find that current IT systems lack capabilities to accurately retrieve relevant documents with unstructured data. In this research, we demonstrate a method using Natural Language Processing and document clustering algorithms to find structurally or contextually related documents from databases containing Engineering Change Request documents. The aim is to radically decrease the time needed to effectively search for related engineering documents, organize search results, and create labeled clusters from these documents by utilizing Natural Language Processing algorithms. A domain knowledge expert at the case company evaluated the results and confirmed that the algorithms we applied managed to find relevant document clusters given the queries tested.

scholarly journals Natural Language Processing for Rapid Response to Emergent Diseases: Case Study of Calcium Channel Blockers and Hypertension in the COVID-19 Pandemic

10.2196/20773 ◽  
2020 ◽  
Vol 22 (8) ◽  
pp. e20773 ◽  
Author(s):  
Antoine Neuraz ◽  
Ivan Lerner ◽  
William Digan ◽  
Nicolas Paris ◽  
Rosy Tsopra ◽  
...  
Keyword(s):  
Natural Language Processing ◽  
Text Mining ◽  
Natural Language ◽  
Calcium Channel ◽  
Language Processing ◽  
Calcium Channel Blockers ◽  
Structured Data ◽  
Channel Blockers ◽  
Knowledge Model ◽  
Long Term Treatment

Background A novel disease poses special challenges for informatics solutions. Biomedical informatics relies for the most part on structured data, which require a preexisting data or knowledge model; however, novel diseases do not have preexisting knowledge models. In an emergent epidemic, language processing can enable rapid conversion of unstructured text to a novel knowledge model. However, although this idea has often been suggested, no opportunity has arisen to actually test it in real time. The current coronavirus disease (COVID-19) pandemic presents such an opportunity. Objective The aim of this study was to evaluate the added value of information from clinical text in response to emergent diseases using natural language processing (NLP). Methods We explored the effects of long-term treatment by calcium channel blockers on the outcomes of COVID-19 infection in patients with high blood pressure during in-patient hospital stays using two sources of information: data available strictly from structured electronic health records (EHRs) and data available through structured EHRs and text mining. Results In this multicenter study involving 39 hospitals, text mining increased the statistical power sufficiently to change a negative result for an adjusted hazard ratio to a positive one. Compared to the baseline structured data, the number of patients available for inclusion in the study increased by 2.95 times, the amount of available information on medications increased by 7.2 times, and the amount of additional phenotypic information increased by 11.9 times. Conclusions In our study, use of calcium channel blockers was associated with decreased in-hospital mortality in patients with COVID-19 infection. This finding was obtained by quickly adapting an NLP pipeline to the domain of the novel disease; the adapted pipeline still performed sufficiently to extract useful information. When that information was used to supplement existing structured data, the sample size could be increased sufficiently to see treatment effects that were not previously statistically detectable.

scholarly journals Implementation of a Cohort Retrieval System for Clinical Data Repositories Using the Observational Medical Outcomes Partnership Common Data Model: Proof-of-Concept System Validation (Preprint)

2019 ◽  
Author(s):  
Sijia Liu ◽  
Yanshan Wang ◽  
Andrew Wen ◽  
Liwei Wang ◽  
Na Hong ◽  
...  
Keyword(s):  
Information Retrieval ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Data Model ◽  
Structured Data ◽  
Common Data Model ◽  
Concept System ◽  
Unstructured Text ◽  
Electronic Health

BACKGROUND Widespread adoption of electronic health records has enabled the secondary use of electronic health record data for clinical research and health care delivery. Natural language processing techniques have shown promise in their capability to extract the information embedded in unstructured clinical data, and information retrieval techniques provide flexible and scalable solutions that can augment natural language processing systems for retrieving and ranking relevant records. OBJECTIVE In this paper, we present the implementation of a cohort retrieval system that can execute textual cohort selection queries on both structured data and unstructured text—Cohort Retrieval Enhanced by Analysis of Text from Electronic Health Records (CREATE). METHODS CREATE is a proof-of-concept system that leverages a combination of structured queries and information retrieval techniques on natural language processing results to improve cohort retrieval performance using the Observational Medical Outcomes Partnership Common Data Model to enhance model portability. The natural language processing component was used to extract common data model concepts from textual queries. We designed a hierarchical index to support the common data model concept search utilizing information retrieval techniques and frameworks. RESULTS Our case study on 5 cohort identification queries, evaluated using the precision at 5 information retrieval metric at both the patient-level and document-level, demonstrates that CREATE achieves a mean precision at 5 of 0.90, which outperforms systems using only structured data or only unstructured text with mean precision at 5 values of 0.54 and 0.74, respectively. CONCLUSIONS The implementation and evaluation of Mayo Clinic Biobank data demonstrated that CREATE outperforms cohort retrieval systems that only use one of either structured data or unstructured text in complex textual cohort queries.

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