JMIR Publications

ABSTRACT

Background:

Data standardization is essential in electronic health records (EHRs) for both clinical practice and retrospective research. However, it is still not easy to standardize EHR data because of nonidentical duplicates, typographical errors, or inconsistencies. To overcome this drawback, standardization efforts have been undertaken for collecting data in a standardized format as well as for curating the stored data in EHRs. To perform clinical big data research, the stored data in EHR should be standardized, starting from laboratory results, given their importance. However, most of the previous efforts have been based on labor-intensive manual methods.

Objective:

We aimed to develop an automatic standardization method for eliminating the noises of categorical laboratory data, grouping, and mapping of cleaned data using standard terminology.

Methods:

We developed a method called Standardization Algorithm for Laboratory Test–Categorical result (SALT-C) that can process categorical laboratory data, such as “pos +,” “250 4+ (urinalysis results),” and “reddish (urinalysis color results).” SALT-C consists of five steps. First, it applies data cleaning rules to categorical laboratory data. Second, it categorizes the cleaned data into five predefined groups (urine color, urine dipstick, blood type, presence finding, and pathogenesis tests). Third, all data in each group are vectorized. Fourth, similarity is calculated between the vectors of data and those of each value in the predefined value sets. Finally, the value closest to the data is assigned. The source code of SALT-C can be downloaded via https://github.com/rpmina/SALT_C.

Results:

The performance of SALT-C was validated using 59,213,696 data points (167,938 unique values) generated over 23 years from a tertiary hospital. Apart from the data whose original meaning could not be interpreted correctly (e.g., “**” and “_^”), SALT-C mapped unique raw data to the correct reference value for each group with accuracy of 97.62% (urine color tests), 97.54% (urine dipstick tests), 94.64% (blood type tests), 99.68% (presence finding tests), and 99.61% (pathogenesis tests).

Conclusions:

The proposed SALT-C successfully standardized the categorical laboratory test results with high reliability. SALT-C can be beneficial for clinical big data research by reducing laborious manual standardization efforts.