I am very new to Knime and I am trying to mine some data cfrom the Chembl website. So basically I have a an ouput of 1000 plus compounds coming from different assays and I would like to create a loop that goes into the file and collects all the coumpounds that fall under a certain assay e.d assay id "52246" and also complies them into a single file which is then written out as an sdf file and comes back and gets the second assay and does the same proces repeatedly until al the 1000 compounds re in 50 assays of at least 20 compunds/ assay.
Is there any easy way to go about this problem?
I think a ‘group loop start’ node with the chembl assay ID column as the group column will help. Then you will need an edit variable node to generate a path for you output file based on the current loop iteration (the value of the current group column will be in a flow variable). Then you need an sdf writer node, configured to use the filename in a flow variable. Finally you need to close the loop. In this case, a ‘variable loop end’ node is almost certainly what you need. You need to connect its input to the hidden flow variable output port in the sdf writer (right click on the sdf writer and select show flow variable ports)
Hope that helps
Thank you so much and yes that is the way to go about it. Thank you so much
Please find attached the workflow
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