I would like to generate a tab-separated file from DrugBank that will include the following tags:
<drugbank-id> <name> <gene-name> <action>
I have tried to use the xmlstarlet tool by following Lyco's instructions from here:
but I don't have any result. xmlstarlet doesn't return anything as result (I believe that the xml structure is a little more complicated than his example and I'm not getting any kind of error). I have also tried to change the namespace that drugBank uses but nothing changed.
I have also tried to use the csv files from DrugBank external links which is fine for the name, the id of the drugs and the protein name but they don't include the "action" information.
So, any help would be greatly appreciated...
Thank you very much in advance, Vasilis.