A comprehensive study of mobility functioning information in clinical notes: Entity hierarchy, corpus annotation, and sequence labeling.
Background: Secondary use of Electronic Health Records (EHRs) has mostly focused on health conditions (diseases and drugs). Function is an important health indicator in addition to morbidity and mortality. Nevertheless, function has been overlooked in accessing patients' health status. The World Hea...
| Publicado en: | International Journal of Medical Informatics Vol. 147 |
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| Autores principales: | , , , , , , , , , , , , , |
| Formato: | equations & formulas research tables/charts Journal Article |
| Publicado: |
Elsevier B.V.
Mar2021
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=148168367&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 148168367 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 13865056 JR4 jtl: International Journal of Medical Informatics issn: 13865056 maglogo: N pubinfo: dt: Mar2021 vid: 147 pid: 467 pub: Elsevier B.V. place: New York, New York artinfo: ui: 148168367 148168367 NLM33401168 148168367 10.1016/j.ijmedinf.2020.104351 NLM33401169 148168367 ppct: 1 formats: tig: atl: A comprehensive study of mobility functioning information in clinical notes: Entity hierarchy, corpus annotation, and sequence labeling. aug: au: Miran, Seyed M. Nelson, Stuart J. Redd, Doug Zeng-Treitler, Qing Thieu, Thanh Maldonado, Jonathan Camacho Ho, Pei-Shu Ding, Min Marr, Alex Brandt, Diane Newman-Griffis, Denis Zirikly, Ayah Chan, Leighton Rasch, Elizabeth affil: Biomedical Informatics Center, School of Medicine and Health Sciences, George Washington University, Washington, D.C., USA sug: subj: Natural Language Processing Human Comparative Studies Multicenter Studies Evaluation Research Validation Studies Funding Source ab: Background: Secondary use of Electronic Health Records (EHRs) has mostly focused on health conditions (diseases and drugs). Function is an important health indicator in addition to morbidity and mortality. Nevertheless, function has been overlooked in accessing patients' health status. The World Health Organization (WHO)'s International Classification of Functioning, Disability and Health (ICF) is considered the international standard for describing and coding function and health states. We pioneer the first comprehensive analysis and identification of functioning concepts in the Mobility domain of the ICF.Results: Using physical therapy notes at the National Institutes of Health's Clinical Center, we induced a hierarchical order of mobility-related entities including 5 entities types, 3 relations, 8 attributes, and 33 attribute values. Two domain experts manually curated a gold standard corpus of 14,281 nested entity mentions from 400 clinical notes. Inter-annotator agreement (IAA) of exact matching averaged 92.3 % F1-score on mention text spans, and 96.6 % Cohen's kappa on attributes assignments. A high-performance Ensemble machine learning model for named entity recognition (NER) was trained and evaluated using the gold standard corpus. Average F1-score on exact entity matching of our Ensemble method (84.90 %) outperformed popular NER methods: Conditional Random Field (80.4 %), Recurrent Neural Network (81.82 %), and Bidirectional Encoder Representations from Transformers (82.33 %).Conclusions: The results of this study show that mobility functioning information can be reliably captured from clinical notes once adequate resources are provided for sequence labeling methods. We expect that functioning concepts in other domains of the ICF can be identified in similar fashion. pubtype: Academic Journal doctype: equations & formulas research tables/charts Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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