Document Grabber - Read .gz
I’m new to KNIME and currently working on searching the PubMed database. My goal is to generate a file that contains the PubMed ID, all authors, and their corresponding affiliations.
With the EuropePMC node, I can perform the query and extract the XML data using the X-Path node in the required format. However, the EuropePMC database is not as reliable as PubMed. Therefore, I now want to search the PubMed database using the Document Grabber node, which works well for retrieving the data.
The issue arises when extracting the information using the Document Data Extractor node—I am unable to retrieve the affiliations and PubMed IDs. The downloaded
.gzfiles contain XML data, including the ID and affiliations, but I cannot read them directly in KNIME.
Is there a workaround for this, or does anyone have tips on how to implement it? Any help is appreciated!