Background: Good automatic information extraction tools offer hope for automatic processing of the exploding biomedical literature, and successful named entity recognition is a key component for such tools. Methods: We present a maximum-entropy based system incorporating a diverse set of features for identifying gene and protein names in biomedical abstracts. Results: This system was entered in the BioCreative comparative evaluation and achieved a precision of 0.83 and recall of 0.84 in the "open" evaluation and a precision of 0.78 and recall of 0.85 in the "closed" evaluation. Conclusion: Central contributions are rich use of features derived from the training data at multiple levels of granularity, a focus on correctly identifying entity boundaries, and the innovative use of several external knowledge sources including full MEDLINE abstracts and web searches.
Exploring the Boundaries: Gene and Protein Identification in Biomedical Text / Finkel J.; Dingare S.; Manning C.D.; Nissim M.; Alex B.; Grover C.. - In: BMC BIOINFORMATICS. - ISSN 1471-2105. - ELETTRONICO. - 6(Suppl 1):(2005).
Exploring the Boundaries: Gene and Protein Identification in Biomedical Text
NISSIM, MALVINA;
2005
Abstract
Background: Good automatic information extraction tools offer hope for automatic processing of the exploding biomedical literature, and successful named entity recognition is a key component for such tools. Methods: We present a maximum-entropy based system incorporating a diverse set of features for identifying gene and protein names in biomedical abstracts. Results: This system was entered in the BioCreative comparative evaluation and achieved a precision of 0.83 and recall of 0.84 in the "open" evaluation and a precision of 0.78 and recall of 0.85 in the "closed" evaluation. Conclusion: Central contributions are rich use of features derived from the training data at multiple levels of granularity, a focus on correctly identifying entity boundaries, and the innovative use of several external knowledge sources including full MEDLINE abstracts and web searches.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
