queryAnnotDB: Annotation Queries with Compound IDs

In yduan004/customCMPdb: Customize and Query Compound Annotation Database

Description

This function can be used to query compound annotations from the default resources as well as the custom resources stored in the SQLite annotation database. The default annotation resources are DrugAge, DrugBank, CMAP02 and LINCS. The customized compound annotations could be added/deleted by the customAnnot utilities.

Usage

queryAnnotDB(
  chembl_id,
  annot = c("drugAgeAnnot", "DrugBankAnnot", "cmapAnnot", "lincsAnnot")
)

Arguments

chembl_id	character vector of ChEMBL IDs or compound ids from other annotation system..
annot	character vector of annotation resources, such as drugAgeAnnot, DrugBankAnnot, cmapAnnot, lincsAnnot or names of the annotation tables added by users. The listAnnot function lists the available options for the annot argument names.

Details

The input of this query function could be a set of ChEMBL IDs, it returns a data.frame storing annotations of the input compounds from selected annotation resources defined by the annot argument.

Since in the SQLite annotation database, ID identifiers from different ID systems, such as DrugBank and LINCS, are connected by ChEMBL IDs, it is hard to tell whether two IDs, such as DB00341, BRD-A42571354, refer to the same compound if either of them lack ID mappings to ChEMBL. So for querying compounds that don't have ChEMBL IDs, only one isolated database where the compounds belong to are supported. For example, a compound with LINCS id as "BRD-A00150179" doesn't have the ChEMBL ID mapping, when it is passed to the 'chembl_id' argument, the 'annot' need only to be set as 'lincsAnnot' and the result will be the compound annotation table from the LINCS annotation.

Value

data.frame of annotation result

Examples

query_id <- c("CHEMBL1000309", "CHEMBL100014", "CHEMBL100109",
               "CHEMBL100", "CHEMBL1000", "CHEMBL10")
qres <- queryAnnotDB(query_id, annot=c("drugAgeAnnot", "lincsAnnot"))

# Add a custom compound annotation table
chembl_id <- c("CHEMBL1000309", "CHEMBL100014", "CHEMBL10",
               "CHEMBL100", "CHEMBL1000", NA)
annot_tb <- data.frame(compound_name=paste0("name", 1:6),
        chembl_id=chembl_id,
        feature1=paste0("f", 1:6),
        feature2=rnorm(6))
addCustomAnnot(annot_tb, annot_name="myCustom2")

# query custom annotation
qres2 <- queryAnnotDB(query_id, annot=c("lincsAnnot", "myCustom2"))

# query compounds that don't have ChEMBL IDs
query_id <- c("BRD-A00474148", "BRD-A00150179", "BRD-A00763758", "BRD-A00267231")
qres3 <- queryAnnotDB(chembl_id=query_id, annot=c("lincsAnnot"))
qres3

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