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ChEMBL

| Website | https://www.ebi.ac.uk/chembl/ | | SPARQL endpoint | https://chemblmirror.rdf.bigcat-bioinformatics.org/sparql/ | | License | CC BY-SA 3.0 |

ChEMBL is a manually curated database of bioactive molecules with drug-like properties [Q27144224,Q27062334]. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs. Built upon the ChEMBL database, an RDF representation of the ChEMBL database is produced by the European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI) and provided for download. The ChEMBL RDF model uses a basic internal ontology, called the ChEMBL Core Ontology (CCO), to identify all of the primary entities (e.g., Documents, Assays, Substances, Targets) in the ChEMBL database.

The Department of Bioinformatics (BiGCaT) at Maastricht University took the initiative to host the RDF and expose it to the scientific community through a SPARQL endpoint where queries can be executed against the RDF to find answers to biological questions. The tool is available through https://chemblmirror.rdf.bigcat-bioinformatics.org/.

Entities

The main classes are:

  • Protein: protein targets
  • Metabolite: ligand, e.g. drug / drug-like compound
  • Assay: measures some property of, for example, the protein-ligand binding
  • Document: source of the data or knowledge

Data model

Graphical representation of RDF schema

Exercises

The simplest SPARQL queries to explore RDF is to retrieve full lists of subjects of a particular type, which is frequently defined with the predicate rdfs:type or "a" which can be used interchangably. The type itself can be part of a hierarchy and then we can specify the type of a particular subclass using the predicate rdfs:subClassOf. See the below example of listing all molecules in the ChEMBL RDF where the molecule type is a subclass of the cco:Substance class.

substances

ChEMBL sources

chemblSources

Counting assays

This query gets the count of the assays used to measure the activity of the molecule with ID (CHEMBL294873):

countingChEMBLAssays

Binding affinities

To get all assay, binding affinity type (Kd, Ki, IC50) and affinity value for all compounds targeting Thrombin protein (CHEMBL204):

bindingAffinities

The above query get assays and molecules information along with binding affinity type and value limited ti the top 100 entry.

Assays and UniProt IDs

To list all assays, target names and UniProt IDs for the drug Paracetamol (CHEBI:46195):

paracetamol

The above query will get assay types, target and UniProt identifier for all the proteins tested fo binding with a single molecule (chembl_molecule:CHEMBL46195):

paracetamol

References