Workflow examples that illustrate the ChEMBL RESTful web services

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madgpap
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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.

 

Regards,

George Papadatos

ChEMBL group

madgpap
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Joined: 10/11/2009

See also: http://chembl.blogspot.co.uk/2012/07/access-to-chembl-web-services-via.html

richards99
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Is it worth having these uploaded to KNIMES Public Workflow Server.


Simon.

madgpap
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Hi Simon,

Sure. How does one do this?

George

Aaron Hart
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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/).  

Regards,

Aaron

madgpap
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Joined: 10/11/2009

Great. Many thanks Aaron.

George

nbrooijmans
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Joined: 01/02/2012

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

Best,

Natasja

madgpap
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Joined: 10/11/2009

Hi Natasja,

Here you go:

https://dl.dropbox.com/u/22273283/Compound%2BAssay%2BTarget_Bioactivitie...

Please note that if you have more than 1000 bioactivities for a target or assay, it is not a good idea to fetch the compound information. In such case, try first to filter out bioactivities (e.g. keep only IC50 values) and then retrieve the compound information.

 

George

ChEMBL group

pc
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Joined: 04/20/2011

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,

Paul

AttachmentSize
get_herg_chembl_cpd-based.zip 401.88 KB
madgpap
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Joined: 10/11/2009

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,

George

 

madgpap
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Joined: 10/11/2009

Hello again,

I changed your workflow again to make it more general and more efficient.

Please use this version and let me know if it works as expected.

 

George

AttachmentSize
get_herg_chembl_cpd-based_GP.zip 136.6 KB
pc
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Joined: 04/20/2011

Dear George,

thanks a lot for the updated workflow, it works perfect!

Cheers & Thanks,

Paul

madgpap
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Joined: 10/11/2009

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.

-Dknime.url.timeout=6000

 

Regards,

George

bazimboye
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Joined: 08/09/2013

Hi George,

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

Thanks!

Barry

serendip42
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Joined: 01/28/2014

Hi,

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

-D.knime.url.timeout=100000

to knime.ini

but it did not solve the problem.

best