queryAnnotDB: Annotation Queries with Compound IDs
In customCMPdb: Customize and Query Compound Annotation Database

Description Usage Arguments Details Value Examples

View source: R/query_fcts.R

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.

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

`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.

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.

data.frame of annotation result

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