disease_id_to_omop: Human Phenotype Ontology: Disease ID to OMOP

In neurogenomics/HPOExplorer: Analysis and Visualisation of the Human Phenotype Ontology

Human Phenotype Ontology: Disease ID to OMOP

Description

Mapping of HPO disease IDs (disease_id) to OMOP concepts (OMOP_ID).

Usage

disease_id_to_omop

Format

An object of class data.table (inherits from data.frame) with 5354 rows and 3 columns.

Source

annot <- load_phenotype_to_genes(3) input_col <- "disease_id" ## NOTE: must keep batch_size=1 as the OARD API returns results only for ## the IDs it can map. This leads to a mismatch between the input and output ## which is exacerbated that the concept_id is automatically converted to ## MONDO IDs for some reason, without any way to map back to the original ## input ID... disease_id_to_omop <- oard_query_api(ids = annot$disease_id, workers=10, batch_size=1) data.table::setnames(disease_id_to_omop, toupper(gsub("concept_","OMOP_",names(disease_id_to_omop))) ) data.table::setnames(disease_id_to_omop,"QUERY",input_col) disease_id_to_omop <- disease_id_to_omop[,c(input_col,"OMOP_ID","OMOP_NAME"), with=FALSE] usethis::use_data(disease_id_to_omop, overwrite = TRUE) @format data.table @usage data("disease_id_to_omop")

neurogenomics/HPOExplorer documentation built on July 17, 2024, 3:12 p.m.