Leaf: an open-source, model-agnostic, data-driven web application for cohort discovery and translational biomedical research.
Objective: Academic medical centers and health systems are increasingly challenged with supporting appropriate secondary use of clinical data. Enterprise data warehouses have emerged as central resources for these data, but often require an informatician to extract meaningful information, limiting d...
| Publicado en: | Journal of the American Medical Informatics Association Vol. 27; no. 1; pp. 109 - 119 |
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| Autores principales: | , , , , , , , , , , , , |
| Formato: | Journal Article |
| Publicado: |
Oxford University Press / USA
Jan2020
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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=141218443&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 141218443 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 10675027 FZ9 jtl: Journal of the American Medical Informatics Association issn: 10675027 maglogo: N pubinfo: dt: Jan2020 vid: 27 iid: 1 pid: 622 pub: Oxford University Press / USA artinfo: ui: 141218443 141218443 NLM31592524 10.1093/jamia/ocz165 NLM31592524 141218443 ppf: 109 ppct: 10 formats: tig: atl: Leaf: an open-source, model-agnostic, data-driven web application for cohort discovery and translational biomedical research. aug: au: Dobbins, Nicholas J Spital, Clifford H Black, Robert A Morrison, Jason M Veer, Bas de Zampino, Elizabeth Harrington, Robert D Britt, Bethene D Stephens, Kari A Wilcox, Adam B Tarczy-Hornoch, Peter Mooney, Sean D de Veer, Bas affil: Department of Biomedical Informatics and Medical Education, UW Medicine Research IT, University of Washington, Seattle, Washington, USA sug: subj: Vocabulary, Controlled User-Computer Interface Information Retrieval Methods Research, Medical Databases Unified Medical Language System Internet Clinical Assessment Tools Scales ab: Objective: Academic medical centers and health systems are increasingly challenged with supporting appropriate secondary use of clinical data. Enterprise data warehouses have emerged as central resources for these data, but often require an informatician to extract meaningful information, limiting direct access by end users. To overcome this challenge, we have developed Leaf, a lightweight self-service web application for querying clinical data from heterogeneous data models and sources.Materials and Methods: Leaf utilizes a flexible biomedical concept system to define hierarchical concepts and ontologies. Each Leaf concept contains both textual representations and SQL query building blocks, exposed by a simple drag-and-drop user interface. Leaf generates abstract syntax trees which are compiled into dynamic SQL queries.Results: Leaf is a successful production-supported tool at the University of Washington, which hosts a central Leaf instance querying an enterprise data warehouse with over 300 active users. Through the support of UW Medicine (https://uwmedicine.org), the Institute of Translational Health Sciences (https://www.iths.org), and the National Center for Data to Health (https://ctsa.ncats.nih.gov/cd2h/), Leaf source code has been released into the public domain at https://github.com/uwrit/leaf.Discussion: Leaf allows the querying of single or multiple clinical databases simultaneously, even those of different data models. This enables fast installation without costly extraction or duplication.Conclusions: Leaf differs from existing cohort discovery tools because it does not specify a required data model and is designed to seamlessly leverage existing user authentication systems and clinical databases in situ. We believe Leaf to be useful for health system analytics, clinical research data warehouses, precision medicine biobanks, and clinical studies involving large patient cohorts. pubtype: Academic Journal doctype: Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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