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README.md

ClinicalCodes: An online clinical codes repository to improve the validity and reproducibility of research using electronic medical records

David A Springate, Evangelos Kontopantelis, Darren M Ashcroft, Ivan Olier, Rosa Parisi, Edmore Chamapiwa, David Reeves

Repository for the open publication of the paper on http://www.Clinicalcodes.org

This paper has now been published in PLoS ONE.

The data is available on Figshare.

The R code for programatically interacting with the database is available on Github and CRAN.

Abstract

Lists of clinical codes are the foundation for research undertaken using electronic medical records (EMRs). If clinical code lists are not available, reviewers are unable to determine the validity of research, full study replication is impossible, researchers are unable to make effective comparisons between studies and the construction of new code lists is subject to much duplication of effort. Despite this, the publication of clinical codes is rarely if ever a requirement for obtaining grants, validating protocols or publishing research. In a representative sample of 450 EMR primary research articles indexed on PubMed, we found that only 19 (5.1%) were accompanied by a full set of published clinical codes and 32 (8.6%) stated that code lists were available on request. To help address these problems, we have built an online repository where researchers using EMRs can upload and download lists of clinical codes. The repository will enable clinical researchers to better validate EMR studies, build on previous code lists and compare disease definitions across studies. It will also assist health informaticians in replicating database studies, tracking changes in disease definitions or clinical coding practice through time and sharing clinical code information across platforms and data sources as research objects.