Questions about "from SMILE (or inChiKeys) to PubChem IDs".

#1

Hello everyone,

I had a long list of compounds' SMILE, InChiKeys and SpiderChem IDs, and I try to fetch these compounds' PubChem ID. CIR node failed and I find "PubChem ID exchanger" works perfectly (https://pubchem.ncbi.nlm.nih.gov/idexchange/idexchange.cgi). However, when I try to incorporate this transformation into the workflow by using the Generic Web Service Client node, the query fails. I think the problem is the "InputListKey" field that I may have to add some string to the SMILE or InChiKeys columns. Does anyone know how to correct this? or other methods to convert SMILE/InChiKeys in Knime?

 

Thanks a lot!!!!

 

Warren

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#2

Hi Warren,

With which error message does the CIR node fail? The CIR node is provided as part of community contributions and was developed by by the CADD Group at the NCI/NIH. I could try to help you here but it would be best to ask the developers directly for the support on this. Could you maybe attach a template workflow to reproduce the issue?

Regarding converters:
The Molecule Type Cast node allows to convert a chosen string column to an appropriate chemistry type format (mol2, sdf, smiles…). The node is available through KNIME Base Chemistry Types & Nodes extensions.

There are a few other converters available from Community Contributions, such as RDKit to Molecule or RDKit to InChI nodes.

Hope it helps.
Best,
Daria

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#3

Hi Warren,

I developed the CIR node for KNIME. It uses the service provided by NCI, take into account that Chemical Identifier Resolver from NCI does not support ChemSpider ID anymore.

The last version of CIR knime node is available at: https://www.alvascience.com/knime-cir/

Best regards,
Andrea Mauri

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