Compound data extraction for cell line target from ChEMBL

[Subha_D]

Hi,

How exactly can I download data into KNIME from ChEMBL for a specific cell line? I understand that the previous EMBL nodes have been removed and REST is used. What nodes are needed to import a set of compounds for a cell line?

Thank you

[temesgen-dadi]

Hi @Subha_D,

What kind of data you want to access from ChEMBL? Can you please provide us with an example. It could be a link to a query you created on your browser.

Did you have a look at some of the KNIME verified components in the life sciences category? There are some which are ChEMBL specific. You can access them either from the KNIME Hub or from the example server directly on KNIME Explorer of your Analytics Platform (see screenshot)

You could also get some insights by looking inside this components on how to use reset services from ChEMBL.

Best,
Temesgen

[Subha_D]

Hi @temesgen-dadi ,

Thank you for your reply. I need compound data (SMILES, compound type, GI50 etc) for the a specific cancer cell line. I wanted to extract the bioactivity data for compounds used to target said cell line. I managed to do this using the 03_ChEMBL_Bioactivity_Search workflow however the download file metanode is not showing me the link to download the data I need.

Thank you

[temesgen-dadi]

HI @Subha_D,

That means your original issue is solved. Regarding that example workflow, You are right some nodes are missing that will enable you to download the data as a file. For now, you can simply use one of the writer nodes (Excel writer, CSV Writer …) to do that.

The concept of downloading only makes sense if you are executing the workflow on the KNIME webportal (which is a feature of the commercial KNIME Server product). If that is the case, you can use the modified workflow attached.

Best,
Temesgen
03_ChEMBL_Bioactivity_Search.knwf (585.5 KB)