Exploring Ancestors and Descendants of a Concept

Date: July 28 2021

Summary: How to explore ancestors and descendants of OHDSI concepts

Keywords: #ohdsi #sql #ancestor #descendant #r #archive

Bibliography

EHDEN Academy

Table of Contents

Setting Up Environment

Installation Requirements

We install the OHDSI dummy database, Eunomia, to write our queries:

install.packages(c("SqlRender", "DatabaseConnector", "remotes"))
remotes::install_github("ohdsi/Eunomia", ref = "v1.0.0")

We will also install the package knitr for viewing and working with resulting tables easily:

install.packages("knitr")

Making Connection to Eunomia

Here we load the DatabaseConnector library to connect to Eunomia:

library('DatabaseConnector')

And set a connection to Eunomia

connectionDetails <-Eunomia::getEunomiaConnectionDetails()
connection <- connect(connectionDetails)

Querying Ancestors from OHDSI

First we need to write our SQL query as follows:

sql <-	"
	SELECT max_levels_of_separation, concept.*
	FROM @cdm.concept_ancestor
	JOIN concept ON ancestor_concept_id = concept_id
	WHERE descendant_concept_id = 313217
	ORDER BY max_levels_of_separation
	"

And then we can run our SQL query and return the results as follows:

result <- renderTranslateQuerySql(connection, sql,cdm ="main")
knitr::kable(result)

Querying Descendants from OHDSI

First we need to write our SQL query as follows:

sql <-	"
	SELECT max_levels_of_separation, concept.*
	FROM @cdm.concept_ancestor
	JOIN concept ON descendant_concept_id = concept_id
	WHERE descendant_concept_id = 4478217
	ORDER BY max_levels_of_separation
	"

And then we can run our SQL query and return the results as follows:

result <- renderTranslateQuerySql(connection, sql,cdm ="main")
knitr::kable(result)

How To Cite

Zelko, Jacob. Exploring Ancestors and Descendants of a Concept. https://jacobzelko.com/07282021202459-exploring-ancestors-concept. July 28 2021.

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