Queue Pubmed Search

KNIME Extensions
1

Hello

I am trying to creat a workflow that will allow me to automatically queue pubmed with a large list (1200+) of drugs for a specified indication, then filter the list to only include pubmed documents that include both the name of the drug and the specification somewhere in the title.  Any advice would be appreciated.

Thanks

2

You could either use the European PubMed Central Advanced Search node, provided by Vernalis in the Trusted Community Extensions, or you would need to use a PubMed web services interface. This might help you get started: https://www.nlm.nih.gov/api/

Note also, the REST nodes that are also available in the Trusted Community extensions.

Best,

Jon

3

The Document Grabber node of the Textprocessing extension is also able to query PubMed and download the results as documents. You can automatically create a query out of the drug names e.g. "drug1 OR drug2 OR drug3 ..." and use this query in the dialog of the Document Grabber node to get all documents.

Then extract the title as string using the Document Data Extractor and filter the data table using the Row Filter in a loop over all drugs and indications. As filter criteria use a regex e.g. ".*drug1.*indication.*.

Cheers, Kilian