Dataset Information

Core Data Elements in Acute Myeloid Leukemia: A Unified Medical Language System-Based Semantic Analysis and Experts' Review.

ABSTRACT: BACKGROUND:For cancer domains such as acute myeloid leukemia (AML), a large set of data elements is obtained from different institutions with heterogeneous data definitions within one patient course. The lack of clinical data harmonization impedes cross-institutional electronic data exchange and future meta-analyses. OBJECTIVE:This study aimed to identify and harmonize a semantic core of common data elements (CDEs) in clinical routine and research documentation, based on a systematic metadata analysis of existing documentation models. METHODS:Lists of relevant data items were collected and reviewed by hematologists from two university hospitals regarding routine documentation and several case report forms of clinical trials for AML. In addition, existing registries and international recommendations were included. Data items were coded to medical concepts via the Unified Medical Language System (UMLS) by a physician and reviewed by another physician. On the basis of the coded concepts, the data sources were analyzed for concept overlaps and identification of most frequent concepts. The most frequent concepts were then implemented as data elements in the standardized format of the Operational Data Model by the Clinical Data Interchange Standards Consortium. RESULTS:A total of 3265 medical concepts were identified, of which 1414 were unique. Among the 1414 unique medical concepts, the 50 most frequent ones cover 26.98% of all concept occurrences within the collected AML documentation. The top 100 concepts represent 39.48% of all concepts' occurrences. Implementation of CDEs is available on a European research infrastructure and can be downloaded in different formats for reuse in different electronic data capture systems. CONCLUSIONS:Information management is a complex process for research-intense disease entities as AML that is associated with a large set of lab-based diagnostics and different treatment options. Our systematic UMLS-based analysis revealed the existence of a core data set and an exemplary reusable implementation for harmonized data capture is available on an established metadata repository.

SUBMITTER: Holz C

PROVIDER: S-EPMC6709897 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

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Core Data Elements in Acute Myeloid Leukemia: A Unified Medical Language System-Based Semantic Analysis and Experts' Review.

Holz Christian C Kessler Torsten T Dugas Martin M Varghese Julian J

JMIR medical informatics 20190812 3

<h4>Background</h4>For cancer domains such as acute myeloid leukemia (AML), a large set of data elements is obtained from different institutions with heterogeneous data definitions within one patient course. The lack of clinical data harmonization impedes cross-institutional electronic data exchange and future meta-analyses.<h4>Objective</h4>This study aimed to identify and harmonize a semantic core of common data elements (CDEs) in clinical routine and research documentation, based on a systema ...[more]

PMID: 31407666

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Project description:ObjectiveThe study sought to evaluate the feasibility of using Unified Medical Language System (UMLS) semantic features for automated identification of reports about patient safety incidents by type and severity.Materials and methodsBinary support vector machine (SVM) classifier ensembles were trained and validated using balanced datasets of critical incident report texts (n_type = 2860, n_severity = 1160) collected from a state-wide reporting system. Generalizability was evaluated on different and independent hospital-level reporting system. Concepts were extracted from report narratives using the UMLS Metathesaurus, and their relevance and frequency were used as semantic features. Performance was evaluated by F-score, Hamming loss, and exact match score and was compared with SVM ensembles using bag-of-words (BOW) features on 3 testing datasets (type/severity: n_benchmark = 286/116, n_original = 444/4837, n_independent =6000/5950).ResultsSVMs using semantic features met or outperformed those based on BOW features to identify 10 different incident types (F-score [semantics/BOW]: benchmark = 82.6%/69.4%; original = 77.9%/68.8%; independent = 78.0%/67.4%) and extreme-risk events (F-score [semantics/BOW]: benchmark = 87.3%/87.3%; original = 25.5%/19.8%; independent = 49.6%/52.7%). For incident type, the exact match score for semantic classifiers was consistently higher than BOW across all test datasets (exact match [semantics/BOW]: benchmark = 48.9%/39.9%; original = 57.9%/44.4%; independent = 59.5%/34.9%).DiscussionBOW representations are not ideal for the automated identification of incident reports because they do not account for text semantics. UMLS semantic representations are likely to better capture information in report narratives, and thus may explain their superior performance.ConclusionsUMLS-based semantic classifiers were effective in identifying incidents by type and extreme-risk events, providing better generalizability than classifiers using BOW.

Dataset Information

Core Data Elements in Acute Myeloid Leukemia: A Unified Medical Language System-Based Semantic Analysis and Experts' Review.

Publications

Core Data Elements in Acute Myeloid Leukemia: A Unified Medical Language System-Based Semantic Analysis and Experts' Review.

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