keyword
https://read.qxmd.com/read/38180139/natural-language-processing-to-extract-snomed-ct-codes-from-pathological-reports
#21
JOURNAL ARTICLE
Giorgio Cazzaniga, Albino Eccher, Enrico Munari, Stefano Marletta, Emanuela Bonoldi, Vincenzo Della Mea, Moris Cadei, Marta Sbaraglia, Angela Guerriero, Angelo Paolo Dei Tos, Fabio Pagni, Vincenzo L'Imperio
OBJECTIVE: The use of standardized structured reports (SSR) and suitable terminologies like SNOMED-CT can enhance data retrieval and analysis, fostering large-scale studies and collaboration. However, the still large prevalence of narrative reports in our laboratories warrants alternative and automated labeling approaches. In this project, natural language processing (NLP) methods were used to associate SNOMED-CT codes to structured and unstructured reports from an Italian Digital Pathology Department...
December 2023: Pathologica
https://read.qxmd.com/read/38147848/representation-of-environmental-concepts-associated-with-health-impacts-in-computer-standardized-clinical-terminologies
#22
JOURNAL ARTICLE
Lorraine J Block, Erika Lozada-Perezmitre, Hwayoung Cho, Shauna Davies, Jisan Lee, Zerina Lokmic-Tomkins, Laura-Maria Peltonen, Lisiane Pruinelli, Lisa Reid, Jiyoun Song, Maxim Topaz, Hanna von Gerich, Pankaj Vyas
OBJECTIVE: To evaluate the representation of environmental concepts associated with health impacts in standardized clinical terminologies. METHODS: This study used a descriptive approach with methods informed by a procedural framework for standardized clinical terminology mapping. The United Nations Global Indicator Framework for the Sustainable Development Goals and Targets was used as the source document for concept extraction. The target terminologies were the Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT) and the International Classification for Nursing Practice (ICNP)...
August 2023: Yearbook of Medical Informatics
https://read.qxmd.com/read/38146537/using-natural-language-processing-to-explore-characteristics-and-management-of-patients-with-axial-spondyloarthritis-and-psoriatic-arthritis-treated-under-real-world-conditions-in-spain-spainet-study
#23
JOURNAL ARTICLE
Diego Benavent, Santiago Muñoz-Fernández, Isabel De la Morena, Antonio Fernández-Nebro, Judith Marín-Corral, Eva Castillo Rosa, Miren Taberna, Cristina Sanabra, Carlos Sastre
BACKGROUND: Spondyloarthritis (SpA) is a group of related but phenotypically distinct inflammatory disorders that include axial SpA (axSpA) and psoriatic arthritis (PsA). Information on the characteristics and management of these patients in the real world remains scarce. OBJECTIVES: To explore the characteristics and management [disease activity assessment and treatment with secukinumab (SEC) or other biologic disease-modifying antirheumatic drugs (bDMARDs)] of axSpA and PsA patients using natural language processing (NLP) in Electronic Health Records (EHRs)...
2023: Therapeutic Advances in Musculoskeletal Disease
https://read.qxmd.com/read/38135303/why-it-is-hard-to-use-proms-and-prems-in-routine-health-and-care
#24
REVIEW
Tim Benson
Patient-reported outcome measures (PROMs) and patient-reported experience measures (PREMs) show the results of healthcare activities as rated by patients and others. Patients or their proxies record feedback using questionnaires. These can enhance quality for all and tailored care for individuals. This paper describes obstacles that inhibit widespread use of PROMs and PREMs and some potential solutions.Implementation is a prerequisite for any innovation to succeed. Health and care services are complex and people need to be engaged at every level...
December 21, 2023: BMJ Open Quality
https://read.qxmd.com/read/38133917/the-necessity-of-interoperability-to-uncover-the-full-potential-of-digital-health-devices
#25
JOURNAL ARTICLE
Julian D Schwab, Silke D Werle, Rolf Hühne, Hannah Spohn, Udo X Kaisers, Hans A Kestler
Personalized health care can be optimized by including patient-reported outcomes. Standardized and disease-specific questionnaires have been developed and are routinely used. These patient-reported outcome questionnaires can be simple paper forms given to the patient to fill out with a pen or embedded in digital devices. Regardless of the format used, they provide a snapshot of the patient's feelings and indicate when therapies need to be adjusted. The advantage of digitizing these questionnaires is that they can be automatically analyzed, and patients can be monitored independently of doctor visits...
December 22, 2023: JMIR Medical Informatics
https://read.qxmd.com/read/38094031/colorectal-serrated-lesions-and-polyps-in-the-danish-population-a-large-nationwide-register-based-cohort-study
#26
JOURNAL ARTICLE
Mille Andrea, Rikke Karlin Jepsen, Mads Falk Klein, Ismail Gögenur, Tine Plato Kuhlmann
Background and study aims Colorectal serrated lesions and polyps (SPs) include hyperplastic polyps (HP), sessile serrated lesions-/+dysplasia (SSL/SSL-D), and traditional serrated adenomas (TSA). From 20% to 30% of colorectal cancers (CRC) develop from SP. We present incidence and baseline characteristics of SP in a Danish cohort. Patients and methods We used The Danish Pathology Registry to include all SPs in the Danish population from January 1, 2000 to December 31, 2021. Based on the unique Danish personal identification number and SNOMED-codes, combined with the age and sex of patients, and date of procedure, we determined the incidence of the SP subtypes, anatomical location, and changes over time...
December 2023: Endoscopy International Open
https://read.qxmd.com/read/38070816/obtaining-clinical-term-embeddings-from-snomed-ct-ontology
#27
JOURNAL ARTICLE
Fuad Abu Zahra, Rohit J Kate
Clinical term embeddings are traditionally obtained using corpus-based methods, however, these methods cannot incorporate knowledge about clinical terms which is already present in medical ontologies. On the other hand, graph-based methods can obtain embeddings of clinical concepts from ontologies, but they cannot obtain embeddings for clinical terms and words. In this paper, a novel method is presented to obtain embeddings for clinical terms and words from the SNOMED CT ontology. The method first obtains embeddings of clinical concepts from SNOMED CT using a graph-based method...
December 7, 2023: Journal of Biomedical Informatics
https://read.qxmd.com/read/38058679/transforming-estonian-health-data-to-the-observational-medical-outcomes-partnership-omop-common-data-model-lessons-learned
#28
JOURNAL ARTICLE
Marek Oja, Sirli Tamm, Kerli Mooses, Maarja Pajusalu, Harry-Anton Talvik, Anne Ott, Marianna Laht, Maria Malk, Marcus Lõo, Johannes Holm, Markus Haug, Hendrik Šuvalov, Dage Särg, Jaak Vilo, Sven Laur, Raivo Kolde, Sulev Reisberg
OBJECTIVE: To describe the reusable transformation process of electronic health records (EHR), claims, and prescriptions data into Observational Medical Outcome Partnership (OMOP) Common Data Model (CDM), together with challenges faced and solutions implemented. MATERIALS AND METHODS: We used Estonian national health databases that store almost all residents' claims, prescriptions, and EHR records. To develop and demonstrate the transformation process of Estonian health data to OMOP CDM, we used a 10% random sample of the Estonian population ( n  = 150 824 patients) from 2012 to 2019 (MAITT dataset)...
December 2023: JAMIA Open
https://read.qxmd.com/read/38034661/a-novel-approach-for-standardizing-clinical-laboratory-categorical-test-results-using-machine-learning-and-string-distance-similarity
#29
JOURNAL ARTICLE
Syed Ahmmed, M Rubaiyat Hossain Mondal, Md Raihan Mia, Mohammad Adibuzzaman, Abu Sayed Md Latiful Hoque, Sheikh Iqbal Ahamed
Standardizing clinical laboratory test results is critical for conducting clinical data science research and analysis. However, standardized data processing tools and guidelines are inadequate. In this paper, a novel approach for standardizing categorical test results based on supervised machine learning and the Jaro-Winkler similarity algorithm is proposed. A supervised machine learning model is used in this approach for scalable categorization of the test results into predefined groups or clusters, while Jaro-Winkler similarity is used to map text terms into standard clinical terms within these corresponding groups...
November 2023: Heliyon
https://read.qxmd.com/read/37981455/a-knowledge-graph-based-data-harmonization-framework-for-secondary-data-reuse
#30
JOURNAL ARTICLE
Francisco Abad-Navarro, Catalina Martínez-Costa
BACKGROUND AND OBJECTIVE: The adoption of new technologies in clinical care systems has propitiated the availability of a great amount of valuable data. However, this data is usually heterogeneous, requiring its harmonization to be integrated and analysed. We propose a semantic-driven harmonization framework that (1) enables the meaningful sharing and integration of healthcare data across institutions and (2) facilitates the analysis and exploitation of the shared data. METHODS: The framework includes an ontology-based common data model (i...
November 10, 2023: Computer Methods and Programs in Biomedicine
https://read.qxmd.com/read/37964450/review-of-the-2023-korean-society-of-medical-informatics-summer-camp-on-snomed-ct
#31
EDITORIAL
Hyeoun-Ae Park
No abstract text is available yet for this article.
October 2023: Healthcare Informatics Research
https://read.qxmd.com/read/37900712/multiple-emergency-department-encounters-for-acute-musculoskeletal-presentation-with-an-existing-mental-health-diagnosis
#32
Priya Arora, James M Elliott, Fereshteh Pourkazemi, Roxanna Nasseri Pebdani
Reconceptualising acute Musculoskeletal (MSK) injuries with both stress- and tissue- based factors is required to consider prior influences of mental health disorders on acute persistent MSK pain presentations. This report describes repeated emergency presentations of an individual with acute persistent MSK pain in their twenties living with mental health. Their mental health diagnoses included depression, mood disorders, and anorexia nervosa. This person also had mental health related inpatient admissions that were not captured under the retrospective record review for a large district hospital emergency department using the Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT) classification system...
November 2023: Clinical Case Reports
https://read.qxmd.com/read/37898795/extracting-cancer-concepts-from-clinical-notes-using-natural-language-processing-a-systematic-review
#33
JOURNAL ARTICLE
Maryam Gholipour, Reza Khajouei, Parastoo Amiri, Sadrieh Hajesmaeel Gohari, Leila Ahmadian
BACKGROUND: Extracting information from free texts using natural language processing (NLP) can save time and reduce the hassle of manually extracting large quantities of data from incredibly complex clinical notes of cancer patients. This study aimed to systematically review studies that used NLP methods to identify cancer concepts from clinical notes automatically. METHODS: PubMed, Scopus, Web of Science, and Embase were searched for English language papers using a combination of the terms concerning "Cancer", "NLP", "Coding", and "Registries" until June 29, 2021...
October 29, 2023: BMC Bioinformatics
https://read.qxmd.com/read/37853326/mapping-hungarian-procedure-codes-to-snomed-ct
#34
JOURNAL ARTICLE
Ágota Mészáros, Sándor Kovács, Tibor Héja, Zsolt Bagyura, Antal Zemplényi
BACKGROUND: Data harmonisation is essential in real-world data (RWD) research projects based on hospital information systems databases, as coding systems differ between countries. The Hungarian hospital information systems and the national claims database use internationally known diagnosis codes, but data on medical procedures are recorded using national codes. There is no simple or standard solution for mapping the national codes to a standard coding system. Our aim was to map the Hungarian procedure codes (OENO) to SNOMED CT as part of the European Health Data Evidence Network (EHDEN) project...
October 18, 2023: BMC Medical Research Methodology
https://read.qxmd.com/read/37741862/towards-interoperability-in-infection-control-a-standard-data-model-for-microbiology
#35
JOURNAL ARTICLE
Eugenia Rinaldi, Cora Drenkhahn, Benjamin Gebel, Kutaiba Saleh, Hauke Tönnies, Friederike D von Loewenich, Norbert Thoma, Claas Baier, Martin Boeker, Ludwig Christian Hinske, Luis Alberto Peña Diaz, Michael Behnke, Josef Ingenerf, Sylvia Thun
The COVID-19 pandemic has made it clear: sharing and exchanging data among research institutions is crucial in order to efficiently respond to global health threats. This can be facilitated by defining health data models based on interoperability standards. In Germany, a national effort is in progress to create common data models using international healthcare IT standards. In this context, collaborative work on a data set module for microbiology is of particular importance as the WHO has declared antimicrobial resistance one of the top global public health threats that humanity is facing...
September 23, 2023: Scientific Data
https://read.qxmd.com/read/37722859/trends-in-consultations-and-prescribing-for-rheumatic-and-musculoskeletal-diseases-an-electronic-primary-care-records-study
#36
JOURNAL ARTICLE
Victoria K Welsh, Kayleigh J Mason, James Bailey, Ram Bajpai, Kelvin P Jordan, Christian D Mallen, Claire Burton
BACKGROUND: Rheumatic and musculoskeletal diseases (RMDs) are common and generally managed in primary care through supported self-care, physiotherapy, analgesia, and specialist referral where indicated. The COVID-19 pandemic led to abrupt changes in primary care delivery, including moves to remote consulting, pauses on group-based self-care, and restricted referrals. AIM: To describe how patterns of UK primary healthcare consultations and analgesic prescribing relating to RMDs changed during the COVID-19 pandemic...
May 23, 2023: British Journal of General Practice
https://read.qxmd.com/read/37697861/design-and-implementation-of-an-etl-process-to-transfer-wound-related-data-into-a-standardized-common-data-model
#37
JOURNAL ARTICLE
Mareike Przysucha, Jens Hüsers, Daniil Liberman, Oliver Kersten, Aphrodite Schlüter, Sebastian Fraas, Dorothee Busch, Maurice Moelleken, Cornelia Erfurt-Berge, Joachim Dissemond, Ursula Hübner
For observational studies, which are relevant especially for chronic conditions like chronic wounds, the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) offers a standardized database schema. In this study an ETL process for the transition of wound related data was developed. After understanding the data in general and mapping the relevant codes to concepts available in OMOP, the ETL process was implemented. In a first step, a generic algorithm to convert data to a csv format was implemented in Java...
September 12, 2023: Studies in Health Technology and Informatics
https://read.qxmd.com/read/37697860/evaluating-interoperability-in-german-critical-incident-reporting-systems
#38
JOURNAL ARTICLE
Laura Tetzlaff, Anne-Maria Purohit, Jacob Spallek, Christine Holmberg, Thomas Schrader
INTRODUCTION: In industrialised countries, one in ten patients suffers harm during hospitalization. Critical Incident Reporting Systems (CIRS) aim to minimize this by learning from errors and identifying potential risks. However, a lack of interoperability among the 16 CIRS in Germany hampers their effectiveness. METHODS: This study investigates reports' syntactic and semantic interoperability across seven different reporting systems. Syntactic interoperability was examined using WHO's Minimal Information Models (MIM), while semantic interoperability was evaluated with SNOMED concepts...
September 12, 2023: Studies in Health Technology and Informatics
https://read.qxmd.com/read/37691103/identifying-populations-with-chronic-pain-in-primary-care-developing-an-algorithm-and-logic-rules-applied-to-coded-primary-care-diagnostic-and-medication-data
#39
REVIEW
Nasrin Hafezparast, Ellie Bragan Turner, Rupert Dunbar-Rees, Amoolya Vusirikala, Alice Vodden, Victoria de La Morinière, Katy Yeo, Hiten Dodhia, Stevo Durbaba, Siddesh Shetty, Mark Ashworth
BACKGROUND: Estimates of chronic pain prevalence using coded primary care data are likely to be substantially lower than estimates derived from community surveys. Most primary care studies have estimated chronic pain prevalence using data searches confined to analgesic medication prescriptions. Increasingly, following recent NICE guideline recommendations, patients and doctors opt for non-drug treatment of chronic pain thus excluding these patients from prevalence estimates based on medication codes...
September 11, 2023: BMC Prim Care
https://read.qxmd.com/read/37652265/machine-translation-of-standardised-medical-terminology-using-natural-language-processing-a-scoping-review
#40
JOURNAL ARTICLE
Richard Noll, Lena S Frischen, Martin Boeker, Holger Storf, Jannik Schaaf
Standardised medical terminologies are used to ensure accurate and consistent communication of information and to facilitate data exchange. Currently, many terminologies are only available in English, which hinders international research and automated processing of medical data. Natural language processing (NLP) and Machine Translation (MT) methods can be used to automatically translate these terms. This scoping review examines the research on automated translation of standardised medical terminology. A search was performed in PubMed and Web of Science and results were screened for eligibility by title and abstract as well as full text screening...
August 29, 2023: New Biotechnology
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