how install ChEMBLdb Connector and Domain - Similarity

#1

Hi,
I am trying to use the workflow reported here (https://doi.org/10.1186/s13321-017-0256-5), but I am getting following errors.
It is about the absence of specific nodes “domain similarity and ChEMBLdb” to extract and process the data.
Can you please suggest how to install missing nodes and fix these issues so that I can make full use of your workflow?

FYI- I am new to KNMIME platform, thus please be as elaborate as possible.
On similar topics page, I couldn’t find/understand if a solution is already available.
Please suggest.


Thank you.

Dr. Vaibhav A. Dixit
Asst. Prof. BITS Pilani,


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Log file is located at: C:\Users\user\Google Drive\knime-workdir.metadata\knime\knime.log

ERROR LoadWorkflowRunnable Errors during load: Status: Error: QSAR_modeling_workflow_V1 0 loaded with errors

ERROR LoadWorkflowRunnable Status: Error: QSAR_modeling_workflow_V1 0

ERROR LoadWorkflowRunnable Status: Error: Node “Domain - Similarity” not available from extension “Enalos Nodes for KNIME” (provided by “NovaMechanics Ltd (www.novamechanics.com)”; plugin “com.novamechanics.apd” is not installed)

ERROR LoadWorkflowRunnable Status: Error: Node “Domain - Similarity” not available from extension “Enalos Nodes for KNIME” (provided by “NovaMechanics Ltd (www.novamechanics.com)”; plugin “com.novamechanics.apd” is not installed)

ERROR LoadWorkflowRunnable Status: Error: ChEMBL Database 0:82

ERROR LoadWorkflowRunnable Status: Error: Node “ChEMBLdb Connector” not available from extension “EMBL-EBI Nodes for KNIME” (provided by “EMBL-EBI”; plugin “uk.ac.ebi.chembl.knime” is not installed)

ERROR LoadWorkflowRunnable Status: Error: Node “ChEMBLdb Connector Input” not available from extension “EMBL-EBI Nodes for KNIME” (provided by “EMBL-EBI”; plugin “uk.ac.ebi.chembl.knime” is not installed)

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#2

Hi,

ChEMBL nodes were part of the EMBL-EBI community extension. The nodes point to the old web service API which has now been turned off. With this we had to remove them, as they didn’t work anymore.
If you want to connect with the ChEMBL DB you could also use REST services:

https://www.ebi.ac.uk/training/online/course/embl-ebi-programmatically-take-rest-manual-searches/chembl-programmatically

https://www.ebi.ac.uk/chembl/api/data/docs

Best,
Martyna

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