ChEMBL web services: streamlining access to drug discovery data and utilities

Abstract

ChEMBL is now a well-established resource in the fields of drug discovery and medicinal chemistry research. The ChEMBL database curates and stores standardized bioactivity, molecule, target and drug data extracted from multiple sources, including the primary medicinal chemistry literature. Programmatic access to ChEMBL data has been improved by a recent update to the ChEMBL web services (version 2.0.x, https://www.ebi.ac.uk/chembl/api/data/docs), which exposes significantly more data from the underlying database and introduces new functionality. To complement the data-focused services, a utility service (version 1.0.x, https://www.ebi.ac.uk/chembl/api/utils/docs), which provides RESTful access to commonly used cheminformatics methods, has also been concurrently developed. The ChEMBL web services can be used together or independently to build applications and data processing workflows relevant to drug discovery and chemical biology.

Figure 1.

Interactive online SPORE documentation for the Activity resource.

Figure 2.

ChEMBL web service schema diagram. The oval shapes represent ChEMBL web service resources and the line between two resources indicates that they share a common attribute. The arrow direction shows where the primary information about a resource type can be found. A dashed line indicates the relationship between two resources behaves differently. For example the Image resource provides a graphical based representation of a Molecule.

Figure 3.

ChEMBL web service filtering and sorting examples. A: Example arguments for web service filter query (note the double underscore between <field> and <filter_type>). B: Example web service query returning binding (‘B’) assays. C: Example web service ordering query, which returns molecules ordered by molecular weight in ascending order. The ordering can be changed to descending order by placing a minus sign before the field name, e.g. ‘order_by = -molecule_properties__full_mwt’.

Figure 4.

ChEMBL web service page_meta section from a request to https://www.ebi.ac.uk/chembl/api/data/activity.json.

Figure 5.

Example of using the ChEMBL web service client to return protein targets that interact with drugs classified as being used in the treatment diabetes.

Figure 6.

ChEMBL web service software components. The green circles correspond to python libraries developed by the ChEMBL group and are available on the ChEMBL GitHub site. Django (https://www.djangoproject.com/) and Tastypie (https://django-tastypie.readthedocs.org) are open source python libraries, which are core dependencies of the ChEMBL web services.

Figure 7.

(A) KNIME workflow combining data and utility ChEMBL web service requests. (B) The image of the drug palbociclib is extracted from a patent document and then converted to the corresponding 2D structure via a Beaker call - shown in (C). The structure is then used as a query in a similarity search web service call against the ChEMBL database. Finally, all bioactivities for the drug and its close analogues are retrieved via a third web service call. (D) The resulting bioactivities and filtered and plotted in a heat map across compounds and their corresponding biological targets.