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PubMed Document Parser

KNIME Textprocessing Plug-in version 4.0.2.v201909251213 by KNIME AG, Zurich, Switzerland

This node allows you to parse the PubMed documents of search results (for more details see (http://www.ncbi.nlm.nih.gov/entrez/query/DTD/pubmed_060101.dtd). The specified directory will be searched for xml, gz or zip files, if recursive search is activated the subdirectories are going to be searched too. All the contained xml, gz or zip files are parsed. The document data is stored in the outgoing data table.


Document directory
Set the directory containing the files to parse.
Search recursively
If checked, the specified directory is searched for files recursively.
Ignore hidden files
If checked, hidden files will not be considered for parsing.
Document category
Specifies the category of the documents.
Document source
Specifies the source of the documents. If no source is specified the PubMed default source "PubMed" is used by default.
Document type
Specifies the type of the documents.
Word tokenizer
Select the tokenizer used for word tokenization. Go to Preferences -> KNIME -> Textprocessing to read the description for each tokenizer.

Output Ports

An output table containing the parsed document data.

Best Friends (Incoming)

Best Friends (Outgoing)


To use this node in KNIME, install KNIME Textprocessing from the following update site:

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