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The MIMIC Code Repository: enabling reproducibility in critical care research.

ABSTRACT: 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.

SUBMITTER: Johnson AE

PROVIDER: S-EPMC6381763 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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The MIMIC Code Repository: enabling reproducibility in critical care research.

Johnson Alistair Ew AE Stone David J DJ Celi Leo A LA Pollard Tom J TJ

Journal of the American Medical Informatics Association : JAMIA 20180101 1

<h4>Objective</h4>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.<h4>Materials and methods</h4>Code is provided to load the data into a relational structure, create extractions of the data, and reproduce en ...[more]

PMID: 29036464

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Project description:BackgroundThe ability to reproduce experiments is a defining principle of science. Reproducibility of clinical research has received relatively little scientific attention. However, it is important as it may inform clinical practice, research agendas, and the design of future studies.MethodsWe used scoping review methods to examine reproducibility within a cohort of randomized trials examining clinical critical care research and published in the top general medical and critical care journals. To identify relevant clinical practices, we searched the New England Journal of Medicine, The Lancet, and JAMA for randomized trials published up to April 2016. To identify a comprehensive set of studies for these practices, included articles informed secondary searches within other high-impact medical and specialty journals. We included late-phase randomized controlled trials examining therapeutic clinical practices in adults admitted to general medical-surgical or specialty intensive care units (ICUs). Included articles were classified using a reproducibility framework. An original study was the first to evaluate a clinical practice. A reproduction attempt re-evaluated that practice in a new set of participants.ResultsOverall, 158 practices were examined in 275 included articles. A reproduction attempt was identified for 66 practices (42%, 95% CI 33-50%). Original studies reported larger effects than reproduction attempts (primary endpoint, risk difference 16.0%, 95% CI 11.6-20.5% vs. 8.4%, 95% CI 6.0-10.8%, P = 0.003). More than half of clinical practices with a reproduction attempt demonstrated effects that were inconsistent with the original study (56%, 95% CI 42-68%), among which a large number were reported to be efficacious in the original study and to lack efficacy in the reproduction attempt (34%, 95% CI 19-52%). Two practices reported to be efficacious in the original study were found to be harmful in the reproduction attempt.ConclusionsA minority of critical care practices with research published in high-profile journals were evaluated for reproducibility; less than half had reproducible effects.

Project description:In the UK care homes are one of the main providers of long term care for older people with dementia. Despite the recent increase in care home research, residents with dementia are often excluded from studies. Care home research networks have been recommended by the Ministerial Advisory Group on Dementia Research (MAGDR) as a way of increasing research opportunities for residents with dementia. This paper reports on an evaluation of the feasibility and early impact of an initiative to increase care home participation in research.A two phase, mixed methods approach was used; phase 1 established a baseline of current and recent studies including the National Institute for Health Research portfolio. To explore the experiences of recruiting care homes and research participation, interviews were conducted with researchers working for the Dementia and Neurodegenerative Diseases Research Network (DeNDRoN) and care home managers. In phase 2, four DeNDRoN area offices recruited care homes to a care home network for their region. The care home networks were separate from the DeNDRoN research network. Diaries were used to document and cost recruitment; DeNDRoN staff were interviewed to understand the barriers, facilitators and impact of the care home networks.Thirty three current or recent studies were identified as involving care homes as care home specific studies or those which included residents. Further details of care home recruitment were obtained on 20 studies by contacting study teams. Care home managers were keen to be involved in research that provided staff support, benefits for residents and with minimal disruption. In phase 2, 141 care homes were recruited to the care home research networks, through corporate engagement and individual invitation. Pre-existing relationships with care homes facilitated recruitment. Sites with minimal experience of working with care homes identified the need for care home training for researchers.Phase 1 review revealed a small but increasing number of studies involving care homes. Phase 2 demonstrated the feasibility of care home research networks, their potential to increase recruitment to research and develop partnerships between health services and care homes, but highlighted the need for care home training for researchers.

Project description:ObjectiveTo characterise the research profile of UK critical care physiotherapists including experience, training needs, and barriers and enablers to engagement in critical care research. 'Research' was defined broadly to encompass activities related to quantitative and qualitative studies, service evaluations, clinical audit and quality improvements.DesignClosed-question online survey, with optional free-text responses.SettingUK critical care community.ParticipantsUK critical care physiotherapists, regardless of clinical grade or existing research experience.Results268 eligible survey responses were received during the 12-week study period (21 incomplete, 7.8%). Respondents were based in university-affiliated (n=133, 49.6%) and district general (n=111, 41.4%) hospitals, and generally of senior clinical grade. Nearly two-thirds had postgraduate qualifications at master's level or above (n=163, 60.8%). Seven had a doctoral-level qualification. Respondents reported a range of research experience, predominantly data acquisition (n=144, 53.7%) and protocol development (n=119, 44.4%). Perceived research training needs were prevalent, including topics of research methods, critical literature appraisal, protocol development and statistical analysis (each reported by ≥50% respondents). Multiple formats for delivery of future research training were identified. Major barriers to research engagement included lack of protected time (n=220, 82.1%), funding (n=177, 66.0%) and perceived experience (n=151, 56.3%). Barriers were conceptually categorised into capability, opportunity and motivation themes. Key enabling strategies centred on greater information provision about clinical research opportunities, access to research training, secondment roles and professional networks.ConclusionsUK critical care physiotherapists are skilled, experienced and motivated to participate in research, including pursuing defined academic research pathways. Nonetheless wide-ranging training needs and notable barriers preclude further involvement. Strategies to harness the unique skills of this profession to enhance the quality, quantity and scope of critical care research, benefiting from a multiprofessional National Clinical Research Network, are required.

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The MIMIC Code Repository: enabling reproducibility in critical care research.

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The MIMIC Code Repository: enabling reproducibility in critical care research.

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