Oscar Tagger

Assigns chemical named entity tags to terms which are recognized by the OSCAR chemical named entity recognizer framework version 4.1.2 (see https://bitbucket.org/wwmm/oscar4/overview for details). As tags the default named entity types of the OSCAR framework are used (see http://apidoc.ch.cam.ac.uk/oscar4-4.0.1/). The OSCAR tag filter is afterwards able to filter the assigned tags.

Options

General options

Document column

The column containing the documents to tag.

Replace column

If checked, the documents of the selected document column will be replaced by the new tagged documents. Otherwise the tagged documents will be appended as new column.

Append column

The name of the new appended column, containing the tagged documents.

Word tokenizer

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

Number of maximal parallel tagging processes

Defines the maximal number of parallel threads that are used for tagging. Please note, that for each thread a tagging model will be loaded into memory. If this value is set to a number greater than 1, make sure that enough heap space is available, in order to be able to load the models. If you are not sure how much heap is available for KNIME, leave the number to 1.

Tagger options

Set named entities unmodifiable

Sets recognized named entity terms unmodifiable.

Input Ports

The input table containing the documents to tag.

Output Ports

An output table containing the tagged documents.

Best Friends (Incoming)

• PubMed Document Parser (11 %) 
• OpenNLP NE Tagger (11 %) Streamable
• Strings To Document (11 %) Streamable
• String To Term (11 %) 
• Column Combiner (5 %) Streamable
• Row Filter (5 %) Streamable
• Row Filter (5 %) Streamable
• Case Converter (5 %) Streamable
• N Chars Filter (5 %) Streamable
• Stop Word Filter (5 %) StreamableDeprecated
• Tag Stripper (5 %) Streamable
• Abner Tagger (5 %) Streamable
• Abner Tagger (5 %) Streamable
• POS Tagger (5 %) Streamable
• Document Data Extractor (5 %) 
• Show all 15 recommendations

Best Friends (Outgoing)

• Column Filter (11 %) Streamable
• Punctuation Erasure (11 %) Streamable
• Stop Word Filter (11 %) Streamable
• Tag Filter (11 %) Streamable
• POS Tagger (11 %) Streamable
• Stanford Tagger (11 %) Streamable
• Bag Of Words Creator (11 %) 
• Document Viewer (11 %) 
• Bag Of Words Creator (11 %) 
• Show all 9 recommendations

Workflows

• ContentMine

Installation

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

Developers

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.