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named entity recognition

Monday 10 October 2016

recognition of named entities (NER)

The recognition of named entities (NER) is an elementary task in biomedical text mining.

A number of NER solutions have been proposed in recent years, taking advantage of available annotated corpora, terminological resources and machine-learning techniques.

Currently, the best performing solutions combine the outputs from selected annotation solutions measured against a single corpus. However, little effort has been spent on a systematic analysis of methods harmonizing the annotation results and measuring against a combination of Gold Standard Corpora (GSCs).

Authors present Totum, a machine learning solution that harmonizes gene/protein annotations provided by heterogeneous NER solutions. It has been optimized and measured against a combination of manually curated GSCs.

See also

- biomedical names


- Harmonization of gene/protein annotations: towards a gold standard MEDLINE.
Campos D, Matos S, Lewin I, Oliveira JL, Rebholz-Schuhmann D. Bioinformatics. 2012 May 1;28(9):1253-61.
doi : bioinformatics/bts125" target="_blank">10.1093/bioinformatics/bts125
PMID: 22419783