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.

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.

Word tokenizer

Select the tokenizer used for word tokenization. Go to Preferences -> KNIME -> Textprocessing to read the description for each tokenizer.

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