Query UniChem for a compound. — queryUnichemCompound • AnnotationGx

This function queries the UniChem API for a compound based on the provided parameters.

Usage

queryUnichemCompound(
  compound,
  type,
  sourceID = NA_integer_,
  request_only = FALSE,
  raw = FALSE,
  progress = "Querying UniChem...",
  ...
)

Arguments

compound: character, integer, or a list of such values. When a vector or list is supplied, each element is queried and the results are returned as a named list.
type: character The type of compound identifier to search for. Valid types are "uci", "inchi", "inchikey", and "sourceID".
sourceID: integer The source ID to search for if the type is "sourceID". When querying multiple compounds, this can be a vector the same length as compound or a single value recycled to all queries. Defaults to NA.
request_only: boolean Whether to return the request only. Defaults to FALSE.
raw: boolean Whether to return the raw response. Defaults to FALSE.
progress: logical or character. Passed through to .perform_request_parallel() when multiple compounds are supplied. Use a character string to customise the progress label. Defaults to "Querying UniChem...".
...: Additional arguments.

Value

For a single query, a list with the external mappings and the UniChem mappings. For multiple queries, a named list of such results (one per compound). If raw = TRUE, raw responses are returned instead.

Examples

queryUnichemCompound(type = "sourceID", compound = "444795", sourceID = 22)
#> $External_Mappings
#>       compoundID             Name                            NameLong sourceID
#>           <char>           <char>                              <char>    <int>
#>   1:    CHEMBL38           chembl                              ChEMBL        1
#>   2:     DB00755         drugbank                            DrugBank        2
#>   3:         3KV         rcsb_pdb                            RCSB PDB        3
#>   4:         REA         rcsb_pdb                            RCSB PDB        3
#>   5:         REA             pdbe         Protein Data Bank in Europe        5
#>  ---                                                                          
#> 206: NCT06358677   clinicaltrials                     Clinical Trials       46
#> 207: NCT06439888   clinicaltrials                     Clinical Trials       46
#> 208: NCT06484920   clinicaltrials                     Clinical Trials       46
#> 209:    PD001430 probes_and_drugs                        Probes&Drugs       49
#> 210:      VITAAC             CCDC CSD (Cambridge Structural Database)       50
#>                                                                    sourceURL
#>                                                                       <char>
#>   1:                https://www.ebi.ac.uk/chembldb/compound/inspect/CHEMBL38
#>   2:                                   https://go.drugbank.com/drugs/DB00755
#>   3:                                         https://www.rcsb.org/ligand/3KV
#>   4:                                         https://www.rcsb.org/ligand/REA
#>   5:       https://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/REA
#>  ---                                                                        
#> 206:                            https://clinicaltrials.gov/study/NCT06358677
#> 207:                            https://clinicaltrials.gov/study/NCT06439888
#> 208:                            https://clinicaltrials.gov/study/NCT06484920
#> 209:                         https://www.probes-drugs.org/compounds/PD001430
#> 210: https://www.ccdc.cam.ac.uk/structures/search?sid=UNICHEM&pid=csd:VITAAC
#> 
#> $UniChem_Mappings
#> $UniChem_Mappings$UniChem.UCI
#> [1] 538323
#> 
#> $UniChem_Mappings$UniChem.InchiKey
#> [1] "SHGAZHPCJJPHSC-YCNIQYBTSA-N"
#> 
#> $UniChem_Mappings$UniChem.Inchi
#> [1] "InChI=1S/C20H28O2/c1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-20(18,4)5/h6,8-9,11-12,14H,7,10,13H2,1-5H3,(H,21,22)/b9-6+,12-11+,15-8+,16-14+"
#> 
#> $UniChem_Mappings$UniChem.formula
#> [1] "C20H28O2"
#> 
#> $UniChem_Mappings$UniChem.connections
#> [1] "1-15(8-6-9-16(2)14-19(21)22)11-12-18-17(3)10-7-13-20(18,4)5"
#> 
#> $UniChem_Mappings$UniChem.hAtoms
#> [1] "6,8-9,11-12,14H,7,10,13H2,1-5H3,(H,21,22)"
#> 
#>