Tagging small molecules

Hi all,

I would like to tag small molecule (lipids, metabolites) with PHARMA tag. Which enrichment node should I use?

Thanks a lot for the help.

Hey Canan,

if you have dictionaries for lipids, metabolites etc. you could use the Dictionary Tagger node. It simply tags the terms you defined in the dictionary. You can set the corresponding tag in the node dialog. If you have more than one dictionary, you could use the Dictionary Tagger (Multi Column) node. It is basically the same node, but you can use multiple dictionaries for different tags.

However I don’t think there is a node that is specialized on tagging small molecules right now.
There is the ABNER Tagger which tags biomedical entities. The tag set covers proteins, dna, rna, gene, cell_line and cell_type. I don’t think small molecules were used to train the model, but you could give it a try. Another option would be the Oscar Tagger, but it’s specialized on chemical compounds.

I hope this helps.


Hi Julian,

Both suggestions worked pretty well. Thank you very much.