The MIMIC Code Repository: enabling reproducibility in critical care research.
Objective: Lack of reproducibility in medical studies is a barrier to the generation of a robust knowledge base to support clinical decision-making. In this paper we outline the Medical Information Mart for Intensive Care (MIMIC) Code Repository, a centralized code base for generating reproducible s...
| Publicado en: | Journal of the American Medical Informatics Association Vol. 25; no. 1; pp. 32 - 40 |
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| Autores principales: | , , , , |
| Formato: | Journal Article |
| Publicado: |
Oxford University Press / USA
Jan2018
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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=127021675&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 127021675 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: Jan2018 vid: 25 iid: 1 pid: 622 pub: Oxford University Press / USA artinfo: ui: 127021675 127021675 NLM29036464 10.1093/jamia/ocx084 NLM29036464 127021675 ppf: 32 ppct: 8 formats: tig: atl: The MIMIC Code Repository: enabling reproducibility in critical care research. aug: au: Johnson, Alistair E W Stone, David J Celi, Leo A Pollard, Tom J Johnson, Alistair Ew affil: Massachusetts Institute of Technology, Cambridge, MA, USA sug: subj: Resource Databases Critical Care Research, Medical ROC Curve Sepsis Health Status Indicators Comorbidity Therapeutics Data Mining Access to Information Severity of Illness Indices Reproducibility of Results Critical Care Family Needs Inventory Scales ab: Objective: Lack of reproducibility in medical studies is a barrier to the generation of a robust knowledge base to support clinical decision-making. In this paper we outline the Medical Information Mart for Intensive Care (MIMIC) Code Repository, a centralized code base for generating reproducible studies on an openly available critical care dataset.Materials and Methods: Code is provided to load the data into a relational structure, create extractions of the data, and reproduce entire analysis plans including research studies.Results: Concepts extracted include severity of illness scores, comorbid status, administrative definitions of sepsis, physiologic criteria for sepsis, organ failure scores, treatment administration, and more. Executable documents are used for tutorials and reproduce published studies end-to-end, providing a template for future researchers to replicate. The repository's issue tracker enables community discussion about the data and concepts, allowing users to collaboratively improve the resource.Discussion: The centralized repository provides a platform for users of the data to interact directly with the data generators, facilitating greater understanding of the data. It also provides a location for the community to collaborate on necessary concepts for research progress and share them with a larger audience. Consistent application of the same code for underlying concepts is a key step in ensuring that research studies on the MIMIC database are comparable and reproducible.Conclusion: By providing open source code alongside the freely accessible MIMIC-III database, we enable end-to-end reproducible analysis of electronic health records. pubtype: Academic Journal doctype: Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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