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Abner tagger

StreamableDeprecatedKNIME Textprocessing Plug-in version 4.2.1.v202008251908 by KNIME AG, Zurich, Switzerland

This node recognizes biomedical named entities, such as genes, proteins or cells and assigns tags to the corresponding terms like "PROTEIN", "RNA", "DNA", "CELL LINE" or "CELL TYPE". Furthermore it can be specified that found named entities are marked as unmodifiable, meaning that they are not going to be modified by any node afterwards. As underlying named entity recognition software ABNER (A Biomedical named entity recognizer) was used. For more details see: http://pages.cs.wisc.edu/~bsettles/abner/.

Options

Set named entities unmodifiable
Sets recognized named entity terms unmodifiable.
ABNER model
Specifies the ABNER model to use. The Biocreative model recognizes proteins only, the NLPBA model recognizes cells, dna and rna lines as well.
Word tokenizer
Select the tokenizer used for word tokenization. Go to Preferences -> KNIME -> Textprocessing to read the description for each tokenizer.

Input Ports

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The input table containing the documents to tag.

Output Ports

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An output table containing the tagged documents.

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

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

KNIME 4.2

A zipped version of the software site can be downloaded here.

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Developers

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