Pubmed

KNIME Extensions
1

I'm trying to parse a Pubmed xml by "Pubmed document parser" and then "Document data extractor". I notice an error in publication date: when I parse the file in attachment I obtain as publication date 2016-04-30 but as you can see in xml there's non way to find such date.

Another question: any idea to parse also authors and their affiliation?

Thank you!

Sergio

2

Hi sergiocima,

I can not reproduce the error. I copied the attached file to an empty directory, used the PubMed Document Parser node and then the Document Data Extractor and extracted title as publication date. It works fine. I am using the latest version 3.1.2. Which version are you using?

Cheers, Kilian
 

 

3

Thank you! Which publication date do you obtain?

Sergio

4

Another thing... If I try to extract "Type" by Document Data Extractor I obtain "Unknow", but as you can see in xml the xml the type is (are...): 

<PublicationType UI="D016428">Journal Article</PublicationType>
<PublicationType UI="D016454">Review</PublicationType>

 

Sergio

5

To specify the document type for PubMed documents you need to set the setting "Document Type" in the dialog of the PubMed Parser node. The setting that is specified in the dialog can be extracted later on using the Document Data Extractor.

Cheers, Kilian

6

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