The following node is available in the Open Source KNIME predictive analytics and data mining platform version 2.7.1. Discover over 1000 other nodes, as well as enterprise functionality at http://knime.com.

PubMed Document Parser

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.

Dialog Options

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.

Ports

Output Ports
0 An output table containing the parsed document data.
This node is contained in KNIME Textprocessing Plug-in provided by KNIME GmbH, Konstanz, Germany.