buildDrugAgeDB: Build DrugAge Annotation Database

In yduan004/customCMPdb: Customize and Query Compound Annotation Database

Description

This function builds the DrugAge annotation SQLite database from the 'drugage_id_mapping' table stored in the 'inst/extdata' directory of this package. The 'drugage_id_mapping.tsv' table contains the DrugAge compounds annotation information (such as species, avg_lifespan_change etc) as well as the compound name to ChEMBL id and PubChem id mappings.

Usage

buildDrugAgeDB(
  da_path = system.file("extdata/drugage_id_mapping.tsv", package = "customCMPdb"),
  dest_path
)

Arguments

da_path	character(1), file path to the tabular file generated from processDrugage function and manually edited the missing IDs.
dest_path	character(1), destination path of the result DrugAge annotation SQLite database

Details

Part of the id mappings in the 'drugage_id_mapping.tsv' table is generated by the processDrugage function for compound names that have ChEMBL ids from the ChEMBL database (version 24). The missing IDs were added manually. A semi-manual approach was to use this web service: https://cts.fiehnlab.ucdavis.edu/batch. After the semi-manual process, the left ones were manually mapped to ChEMBL, PubChem and DrugBank ids. The mixed items were commented.

Value

DrugAge annotation SQLite database

Examples

buildDrugAgeDB(dest_path=tempfile(fileext="_drugage.db"))

yduan004/customCMPdb documentation built on Feb. 3, 2022, 2:10 p.m.