Workflow examples that illustrate the ChEMBL RESTful web services


Using the ChEMBL web services is a good way to fetch and integrate ChEMBL data without having to install SQL dumps locally or write SQL queries.

I am attaching here a set of workflows that conveniently wrap the functionality of these web services in KNIME.

The workflows can serve as building blocks for more sophisticated and information-rich data analysis. See for example the NN_Activity_Profile workflow attached.

I mainly used the XML reader and the XPath nodes to fetch the URL and tabulate the XML response.

Any comments are welcome.



George Papadatos

ChEMBL group

Wed, 07/04/2012 - 02:36

Is it worth having these uploaded to KNIMES Public Workflow Server.


Thu, 07/05/2012 - 10:37

Hi Simon,

Sure. How does one do this?


Thu, 07/05/2012 - 12:54

Thank you for such nice examples. I have taken the liberty of uploading them to the public example server under the community section (/99_Community/08_ChEMBL_WebServices/).  



Thu, 07/05/2012 - 03:49

Great. Many thanks Aaron.


Fri, 07/06/2012 - 10:32

Thanks for sharing and uploading these workflows. I think these are very useful. How would one get the structures for e.g. target + bioactivities.



Fri, 08/10/2012 - 11:25

In KNIME 2.6 a stricter URL time out limit was introduced.

Please add the following line to your knime.ini file to avoid your ChEMBL web service requests timing out too early.





Fri, 12/14/2012 - 04:20

Dear George,


thank you very much for the updated workflow - I played around with, but I cannot figure out how to dig out the structural data, after I filter out quite a large amount of data..

Cheers & thanks in advance,


Sat, 12/15/2012 - 12:51

Hallo Paul,

In your example, just edit the last joiner node by changing the joining columns:

left table --> ingredient_cmpd_chemblid

right table --> chembl_id

The rest should stay the same and it should work!

Best regards,



Thu, 10/03/2013 - 11:39

Member for

4 years


Hi George,

I was wondering whether the example workflows are still available as I'm having problems accessing them in dropbox.



Wed, 01/29/2014 - 03:40

Member for

3 years 6 months



I just downloaded the zip file above and imported it to KNIME. Fresh installation of KNIME with all updates.

When I run the first node "FETCH" I get the following error:

WARN      GroupBy                            No aggregation column defined
WARN      BrowserInitializer                 Found WebKit version 2.2.3. Only WebKit version 1.x is supported.

ERROR     XML Reader                         Execute failed: Read timed out

Are there other things that must be installed, before I can run it?


I tried to fix it by add


to knime.ini

but it did not solve the problem.