Pubmed output processing

KNIME Extensions
1

HI 

I am trying to extract information from Pubmed using 'Pubmed Document Parser' node (version 2.10.3). The output contain only the 'Title' of the article from Pubmed but missing other information like author, Abstract etc. I am not sure whether I am missing some settings in the configuration (Document source =Pubmed & Document category =Pubmed). The source file is an xml file downloaded from Pubmed search. Any suggestion is highly appreciated.

 

Thanks

Baskaran 

2

Hi Baskaran,

each result document is stored in KNIME internally as a document cell. If you open the output table view of the Document Grabber node, to inspect the result set, only the titles of the document cells are shown. However, the cell contains more information then just the title, which is just not shown in this view. To see the full document you can use the Document Viewer node. Alternatively you can extract the additional information of documents (e.g. author, text, ...) with the Document Data Extractor node.

Cheers,
Kilian

 

3

Hi Kilian,

What about the full text of the publications?
With the Document Grabber node, Document Data Extractor nod, and then the Document Viewer node, I can see some meta-information as well as the abstract of the papers. Unfortunately, I am not able to see the full text of the publications.
Is there a way to extract the entire text?

Thank you in advance.
Cheers,
Reno

4

Hi Reno,

unfortunately, there is no Full Text available via the PubMed Web Service we are using for the extraction. It is a pity I know but we are taking the maximum of what is possible.
If you have a link you could try to use the Webpage retriever but this would mean a lot of effort to get then the correct text out of the html tags.

Best,
Martyna

5

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