Querying ChEMBL Database
Jermiah Joseph, Shahzada Muhammad Shameel Farooq, and Christopher Eeles
ChEMBL.RmdIntroduction to ChEMBL API
WARNING: This vignette is a work in progress. If you have questions or would like to see more features, please open an issue at bhklab/AnnotationGx
The ChEMBL database contains information on bioactive drug-like small molecules. The information includes 2-D structures, calculated properties; logP, Molecular Weight, Lipinski Parameters, and abstracted bioactivities; binding constants and ADMET data. The data is curated from primary scientific literature. The ChEMBL API allows for the data to be made available for retrieval in a programmatic fashion. We can use the API to query CHEMBL ID of a compound, retrieve all molecule mechanisms of action, query compound_record resource and molecule resource from the ChEMBL database.
Retrieve molecule mechanisms of action from ChEMBL
Given a ChEMBL ID, we can retrieve the molecule mechanisms of action
from the ChEMBL database using the getChemblMechanism()
function.
NOTE: This is a specialized function that queries the API for the mechanism resource only. To query other resources, please see the Custom Queries section.
mechs <- getChemblMechanism("CHEMBL1413")
mechs
#> action_type binding_site_comment direct_interaction disease_efficacy
#> <char> <lgcl> <int> <int>
#> 1: CHELATING AGENT NA 1 1
#> 2: CHELATING AGENT NA 1 1
#> max_phase mec_id
#> <int> <int>
#> 1: 4 2200
#> 2: 4 2224
#> mechanism_comment
#> <char>
#> 1: Trivalent metal cations chelating agent; inhibition of the metal-dependent enzymes that are responsible for the degradation of peroxides within the fungal cell
#> 2: Trivalent metal cations chelating agent; inhibition of the metal-dependent enzymes that are responsible for the degradation of peroxides within the fungal cell
#> mechanism_of_action mechanism_refs molecular_mechanism
#> <char> <list> <int>
#> 1: Iron chelating agent <data.frame[3x3]> 1
#> 2: Aluminium chelating agent <data.frame[3x3]> 1
#> molecule_chembl_id parent_molecule_chembl_id record_id selectivity_comment
#> <char> <char> <int> <lgcl>
#> 1: CHEMBL1413 CHEMBL1413 1343970 NA
#> 2: CHEMBL1413 CHEMBL1413 1343970 NA
#> site_id target_chembl_id variant_sequence
#> <lgcl> <char> <lgcl>
#> 1: NA CHEMBL2363058 NA
#> 2: NA CHEMBL2366381 NAIn the above example, multiple mechanisms of action are returned.
Custom Queries
The ChEMBL API allows for a wide range of queries. We have specialized one function, but are open to incorporating more. Please open an issue at bhklab/AnnotationGx with an idea of a specialized function that meets a use case.
A query to the API follows the following format:
https://www.ebi.ac.uk/chembl/api/data/[resource]?[field]__[filter_type]=[value]&format=[format]More information can be found at the API Documentation
In summary, the requirements for a query are:
- The
resourceto be queried - The reource
fieldto be queried - The
filter_typeto be used - The
valueto be used for the filter - (optional) The
formatof the returned data (default is JSON)
For example, the query for the example in the above section would be: “https://www.ebi.ac.uk/chembl/api/data/mechanism?molecule_chembl_id__in=CHEMBL1413&format=json” where:
-
resourceis “mechanism” -
fieldis “molecule_chembl_id” -
filter_typeis “in” -
valueis “CHEMBL1413” -
formatis “json”
These parameters can be used in the
queryChemblAPI(resource, field, filter_type, value, format = "json")
function to query the ChEMBL API.
NOTE: unlike the getChemblMechanism() function
which returns a data.table, the
queryChemblAPI() function returns the raw data
unformatted
queryChemblAPI("mechanism", "molecule_chembl_id", "in", "CHEMBL1413")
#> $mechanisms
#> action_type binding_site_comment direct_interaction disease_efficacy
#> 1 CHELATING AGENT NA 1 1
#> 2 CHELATING AGENT NA 1 1
#> max_phase mec_id
#> 1 4 2200
#> 2 4 2224
#> mechanism_comment
#> 1 Trivalent metal cations chelating agent; inhibition of the metal-dependent enzymes that are responsible for the degradation of peroxides within the fungal cell
#> 2 Trivalent metal cations chelating agent; inhibition of the metal-dependent enzymes that are responsible for the degradation of peroxides within the fungal cell
#> mechanism_of_action
#> 1 Iron chelating agent
#> 2 Aluminium chelating agent
#> mechanism_refs
#> 1 20964457, 23416050, Ciclopirox#cite_note-pmid12760852-4, PubMed, PubMed, Wikipedia, http://europepmc.org/abstract/MED/20964457, http://europepmc.org/abstract/MED/23416050, http://en.wikipedia.org/wiki/Ciclopirox#cite_note-pmid12760852-4
#> 2 20964457, 23416050, Ciclopirox#cite_note-pmid12760852-4, PubMed, PubMed, Wikipedia, http://europepmc.org/abstract/MED/20964457, http://europepmc.org/abstract/MED/23416050, http://en.wikipedia.org/wiki/Ciclopirox#cite_note-pmid12760852-4
#> molecular_mechanism molecule_chembl_id parent_molecule_chembl_id record_id
#> 1 1 CHEMBL1413 CHEMBL1413 1343970
#> 2 1 CHEMBL1413 CHEMBL1413 1343970
#> selectivity_comment site_id target_chembl_id variant_sequence
#> 1 NA NA CHEMBL2363058 NA
#> 2 NA NA CHEMBL2366381 NA
#>
#> $page_meta
#> $page_meta$limit
#> [1] 20
#>
#> $page_meta$`next`
#> NULL
#>
#> $page_meta$offset
#> [1] 0
#>
#> $page_meta$previous
#> NULL
#>
#> $page_meta$total_count
#> [1] 2The getChemblResources() function returns a list of
possible resources that can be queried:
getChemblResources()
#> [1] "activity" "assay"
#> [3] "atc_class" "binding_site"
#> [5] "biotherapeutic" "cell_line"
#> [7] "chembl_id_lookup" "compound_record"
#> [9] "compound_structural_alert" "document"
#> [11] "document_similarity" "document_term"
#> [13] "drug" "drug_indication"
#> [15] "drug_warning" "go_slim"
#> [17] "image" "mechanism"
#> [19] "metabolism" "molecule"
#> [21] "molecule_form" "organism"
#> [23] "protein_classification" "similarity"
#> [25] "source" "status"
#> [27] "substructure" "target"
#> [29] "target_component" "target_relation"
#> [31] "tissue" "xref_source"The getChemblResourceFields(resource) function returns a
list of possible fields that can be queried for a given resource:
getChemblResourceFields("mechanism")
#> [1] "action_type" "binding_site_comment"
#> [3] "direct_interaction" "disease_efficacy"
#> [5] "max_phase" "mec_id"
#> [7] "mechanism_comment" "mechanism_of_action"
#> [9] "mechanism_refs" "molecular_mechanism"
#> [11] "molecule_chembl_id" "parent_molecule_chembl_id"
#> [13] "record_id" "selectivity_comment"
#> [15] "site_id" "target_chembl_id"
#> [17] "variant_sequence"The getChemblFilterTypes() function returns a list of
possible filter types.
getChemblFilterTypes()
#> [1] "exact" "iexact" "contains" "icontains" "startswith"
#> [6] "istartswith" "endswith" "iendswith" "regex" "iregex"
#> [11] "gt" "gte" "lt" "lte" "range"
#> [16] "in" "isnull" "search" "only"