Coronavirus disease 2019 (COVID-19) was declared as a pandemic by the World Health Organization (WHO) on March 11th 2020 and it has raised a serious global health crisis since then. As stated by Science - “it is more important than ever for scientists around the world to openly share their knowledge, expertise, tools, and technology” [1].
To efficiently conduct clinical studies across different institutions within a network, one requirement is to normalize clinical data to common data models (CDM) and standard terminologies. Among different types of clinical data, COVID-19 diagnostic testings are extremely important for all the following analyses, as they are the primary means to identify the confirmed COVID-19 cases. To address the urgency of the pandemic, individual institutions have created local names and local codes for those new COVID-19 testings in their EHRs. Meanwhile, LOINC (The standard code system for laboratory observations), a widely used international standard for lab tests, has responded quickly by developing a new set of standard codes for COVID-19 testings, to guide standard coding of COVID-19 testings in clinical settings.
This repository contains supplementary data and code to the tool: COVID-19 TestNorm - A tool to normalize COVID-19 testing names to LOINC codes.
Figure 1 shows an overview of the modules of the COVID-19 TestNorm system, mainly including entity recognition and LOINC mapping, with inputs from knowledge components such as lexicons and coding rules.
Figure 2 shows the flow chart of coding rules for COVID-19 LOINC mapping.
TestNorm
This folder contains COVID19 TestNorm codes for rules-based method including entity recognition and LOINC mapping.
data
This folder contains the full list of LOINC SARS CoV 2 lab tests (from https://loinc.org/sars-coronavirus-2/), and IVD testkits data (from https://www.cdc.gov/csels/dls/sars-cov-2-livd-codes.html and https://loinc.org/sars-cov-2-and-covid-19/), and Covid19 lexicons file (mannually annotated from multi-sites data). Please note that the data files will be updated dynamically according to the frequently updated data from LOINC and CDC websites.
Run
The following steps briefly describe how to run the TestNorm tool.
Install requirement packages in requirement.txt: pip install -r requirements.txt. Please note that TestNorm tool is tested using python 3.
Run the test.py: python test.py 'NOVEL CORONAVIRUS 2019 rRT PCR, NASOPHAR'.
The mapping LOINC codes together with long common name will be displayed as: '94759-8' and 'SARS coronavirus 2 (COVID19) RNA [Presence] in Nasopharynx by NAA with probe detection'
References
[1] Barton CM, Alberti M, Ames D, Atkinson J-A, Bales J, Burke E, et al. Call for transparency of COVID-19 models. Science. 2020 01;368(6490):482–3.