One tagger, many uses - Illustrating the power of ontologies in dictionary-based named entity recognition

Lars Juhl Jensen

doi:10.1101/067132

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bioRxiv · 10.1101/067132

One tagger, many uses - Illustrating the power of ontologies in dictionary-based named entity recognition

Lars Juhl Jensen

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Abstract

Automatic annotation of text is an important complement to manual annotation, because the latter is highly labour intensive. We have developed a fast dictionary-based named entity recognition (NER) system and addressed a wide variety of biomedical problems by applied it to text from many different sources. We have used this tagger both in real-time tools to support curation efforts and in pipelines for populating databases through bulk processing of entire Medline, the open-access subset of PubMed Central, NIH grant abstracts, FDA drug labels, electronic health records, and the Encyclopedia of Life. Despite the simplicity of the approach, it typically achieves 80-90% precision and 70-80% recall. Many of the underlying dictionaries were built from open biomedical ontologies, which further facilitate integration of the text-mining results with evidence from other sources.

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Lars Juhl Jensen. 2016-08-02. One tagger, many uses - Illustrating the power of ontologies in dictionary-based named entity recognition. https://doi.org/10.1101/067132

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