Source and Concept Vocabularies: Single Site, Exploratory, Cross-Sectional Analysis


Created

2024-06-05

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Domain

Category

Parameters

Publisher

PEDSnet

Abstract

This check provides exploratory analyses at the level of a single site. It generates a single snapshot of a high-level summary of how the source system mappings may impact the data representation. This check may only be executed if both the source code and the represented code are provided.

Data Requirements

cohort , concept_set , omop_or_pcornet , domain_tbl , code_type , code_domain , multi_or_single_site , anomaly_or_exploratory , p_value , age_groups , time , time_span , time_period

Probe

Clinical Assessment

Access Package

# install.packages("devtools") devtools::install_github('ssdqa/sourceconceptvocabularies')

Visualization Output

Heatmaps of the top mappings (source_concept_id) for the top CDM codes (concept_id). The gradient is blue to red where red corresponds to the highest proportion of concept mapping (concept_prop) and blue corresponds to the lowest. Concept names can be identified by hovering over the heatmaps. A separate reference table, lists all concept_id, their corresponding concept_name and their respective total counts.

Raw Output

This check produces a raw data output containing nine columns of data:

Column Data Type Definition
site character the name of the site being targeted OR “combined” if multiple sites were provided
domain character the domain associated with the provided concept set
concept_id numeric / character the primary concept, native to the CDM and mapped from the source
source_concept_id numeric / character the source concept, from the source system and mapped to the CDM
ct numeric the number of times the concept_id / source_concept_id pair occurs in the data
denom_concept_ct numeric the number of times the concept_id appears in the data
denom_source_ct numeric the number of times the source_concept_id appears in the data
concept_prop numeric the proportion of concept_id appearences made up by the concept_id / source_concept_id pair
source_prop numeric the proportion of source_concept_id appearances made up by the concept_id / source_concept_id pair

Affiliation(s)

PEDSnet Data Coordinating Center

Funder(s)

This research was made possible through the generous support of Patient-Centered Outcomes Research Institute. The statements presented in this work are solely the responsibility of the author(s) and do not necessarily represent the views of PCORI, its Board of Governors, or its Methodology Committee.

Provenance

Description

Development Code

https://github.com/ssdqa/sourceconceptvocabularies/tree/main

Clinical Subjects Headings

Related Data Quality Result

Related Person

Related Code

Thumbnail Image
Study-Specific Quality, Utility, and Breadth Assessment
Created:2025-11Affiliation:PEDSnet Data Coordinating Center
This suite of R packages allows one to investigate multiple facets of data quality and customize analyses based on your study-specific needs. Each module allows up to 8 different analyses in either the OMOP or PCORnet CDM, all aimed at taking a different view of the data while still addressing the same data quality probe.

##### [View pkgdown summary here.](https://ssdqa.github.io/squba/)

Related Data Quality Check

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Creative Commons license

a CC-BY Attribution 4.0 License.
Except where otherwised noted, this item's license is described as a CC-BY Attribution 4.0 License.

Cite this Data Quality Check

PEDSnet Data Coordinating Center. (2024, June). Source and Concept Vocabularies: Single Site, Exploratory, Cross-Sectional Analysis. [D Q Check]. PEDSpace Knowledge Bank. https://doi.org/10.24373/pdsp-449