In meerapatelmd/mOMOP: What the Package Does (One Line, Title Case)

knitr::opts_chunk$set(
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  fig.path = "man/figures/README-",
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mOMOP

The goal of mOMOP is to crosswalk the Minimal Common Oncology Data Elements (mCode) with the OMOP Vocabularies. mCode and the mCode Initiative provides a common data language and model for data exchange between entities while the OMOP Vocabularies integrate data elements into the OMOP Common Data Model to serve analytics use cases. A crosswalk using the terminology service will bridge the gap between data interoperability and analytical application.

Installation

You can install mOMOP with:

library(devtools)
install_github("meerapatelmd/mOMOP")

Examples

library(mOMOP)

mCode Class Hierarchy

The end-product of this package is the MCODE_CLASS_HIERARCHY dataset, which is a flattened taxonomy that serves a variety of use cases. For example, it can be used to incorporate mCode into a lookup table in a relational database such as the retrieval of a certain class of data elements or it can be incorporated into an ontology.

head(MCODE_CLASS_HIERARCHY)

Crosswalks from mCode to OMOP

The crosswalk between mCode value sets and OMOP concepts used to create the MCODE_CLASS_HIERARCHY dataset can be accessed with the following pre-packaged dataframes: CANCER_STAGING, GENOMICS, ICD10CM, LOINC, SNOMED, SPECIMEN, UNITS_OF_MEASUREMENT.

Cancer Staging

head(CANCER_STAGING)

Genomics

head(GENOMICS)

ICD-10-CM

head(ICD10CM)

LOINC

head(LOINC)

SNOMED

head(SNOMED)

Specimen

head(SPECIMEN)

Units of Measurement

head(UNITS_OF_MEASUREMENT)

Code of Conduct

Please note that the mOMOP project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

meerapatelmd/mOMOP documentation built on June 15, 2021, 3:01 p.m.