Call ChEMBL Data Web Service Directly

Molecule Tutorials - Herong's Tutorial Examples

∟ChEMBL Database - European Molecular Biology Laboratory

∟Call ChEMBL Data Web Service Directly

Provides a tutorial example on how to call ChEMBL data Web services directly with the 'curl' command.

If you want to call ChEMBL Web Services directly with HTTPS GET/POST protocols, you can follow this tutorial.

1. Make sure you have "curl" installed on your computer.

2. Get a list of all records of a given resource with a GET request.

(syntax)
curl https://www.ebi.ac.uk/chembl/api/data/{resource}

(example)
herong$ curl https://www.ebi.ac.uk/chembl/api/data/molecule

<response>
  <molecules>
    <molecule>
      <molecule_chembl_id>CHEMBL6329</molecule_chembl_id>
      <molecule_properties>
        <alogp>2.11</alogp>
        <aromatic_rings>3</aromatic_rings>
        <full_molformula>C17H12ClN3O3</full_molformula>
        <full_mwt>341.75</full_mwt>
      </molecule_properties>
      <molecule_structures>
        <canonical_smiles>Cc1cc(-n2ncc(=O)[nH]...</canonical_smiles>
        <molfile>
            ...

3. Get a single resource with the resource id.

(syntax)
curl https://www.ebi.ac.uk/chembl/api/data/{resource}/{id}

(example)
herong$ curl https://www.ebi.ac.uk/chembl/api/data/molecule/CHEMBL6329

<molecule>
  <molecule_chembl_id>CHEMBL6329</molecule_chembl_id>
  <molecule_properties>
    <alogp>2.11</alogp>
    <aromatic_rings>3</aromatic_rings>
    <full_molformula>C17H12ClN3O3</full_molformula>
    <full_mwt>341.75</full_mwt>
  </molecule_properties>
  <molecule_structures>
    <canonical_smiles>Cc1cc(-n2ncc(=O)[nH]...</canonical_smiles>
    <molfile>
      ...

4. Filter resource records with a keyword.

(syntax)
curl https://www.ebi.ac.uk/chembl/api/data/{resource}/search?q={keyword}

(example)
herong$ curl https://www.ebi.ac.uk/chembl/api/data/molecule/search?q=aspirin

<response>
    <molecules>
        <molecule>
            <cross_references>
                <molecule>
                    <xref_id>aspirin</xref_id>
                    <xref_name>aspirin</xref_name>
                    <xref_src>DailyMed</xref_src>
                </molecule>
                ...

5. Filter with resource records with other filters:

https://www.ebi.ac.uk/chembl/api/data/target?pref_name__iregex=(cdk1|cdk2)
https://www.ebi.ac.uk/chembl/api/data/target?target_type__exact=SINGLE+PROTEIN

6. Get result in JSON format.

(syntax)
curl https://www.ebi.ac.uk/chembl/api/data/{resource}?format=json

(example)
herong$ curl https://www.ebi.ac.uk/chembl/api/data/molecule?format=json