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ChEMBLdb Connector Input

EMBL-EBI extension for KNIME Workbench version 1.1.0.v201712111223 by EMBL-EBI

Node which tabulates information from the XML web service of ChEMBLdb.

Users can look-up ChEMBL IDs representing compounds, assays or targets and retrieve tabulated information on them, in addition to the relevant bioactivity data If a UNIPROT protein accession number is provided, this takes priority over ChEMBL IDs for doing target searches.

Alternatively an InChiKey can be provided to perform an exact structure search, or canonical SMILES to perform substructure or similarity searches against ChEMBL molecules (retrieves same information as a compound search).

NOTE: The tab clicked on determines the search used (so if the user closes the configuration dialog with the look-up tab in focus, a look-up search will be performed, and vice versa for compound searching).

Author: Edmund Duesbury (EBI Summer 2012).

Acknowledgements:
  • George Papadatos
  • Stephan Beisken

Options

Look-up Tab:
  • Specify a column with ChEMBL IDs from the input table.
  • Choose whether to search for compounds, assays or (protein) targets. Note that the ChEMBL ID must be relevant to the search type (e.g. a ChEMBL ID that corresponds to a compound will throw an error on assay or target searches).
  • If a protein accession number is specified, this can only be used with target searches, and takes priority over a ChEMBL ID.
  • Tick the bioactivities checkbox to retrieve all the bioactivities for a ChEMBL ID.
Compound Search Tab:
  • Specify a column with InChIKeys for an exact structure search.
  • Alternatively, a SMILES (Molecule) column for substructure or similarity searches.
  • The Tanimoto coefficient threshold (%) for similarity searching must be between 70 and 100.

Input Ports

Input table with ChEMBL ID, SMILES (Molecule) or InChIKey columns.

Output Ports

Tabulated information from the ChEMBL database.

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Developers

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