Abner Tagger

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

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.

Tagger 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.

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Workflows

• 05_Named_Entity_Tag_CloudKNIME Hub
• 05_Named_Entity_Tag_CloudKNIME Hub
• 05_Named_Entity_Tag_CloudKNIME Hub
• 05_Named_Entity_Tag_Cloud.knwf 1KNIME Hub
• 10_Disease_GenesKNIME Hub
• ContentMineKNIME Hub
• document_grabber_testKNIME Forum
• Text_mining_in_life_sciences_literatureKNIME Hub
• Text_mining_in_life_sciences_literatureKNIME Hub

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Developers