Paper Info
Title
tmChem: a high performance approach for chemical named entity recognition and normalization.
Abstract
Chemical compounds and drugs are an important class of entities in biomedical research with great potential in a wide range of applications, including clinical medicine. Locating chemical named entities in the literature is a useful step in chemical text mining pipelines for identifying the chemical mentions, their properties, and their relationships as discussed in the literature. We introduce the tmChem system, a chemical named entity recognizer created by combining two independent machine learning models in an ensemble. We use the corpus released as part of the recent CHEMDNER task to develop and evaluate tmChem, achieving a micro-averaged f-measure of 0.8739 on the CEM subtask (mention-level evaluation) and 0.8745 f-measure on the CDI subtask (abstract-level evaluation). We also report a high-recall combination (0.9212 for CEM and 0.9224 for CDI). tmChem achieved the highest f-measure reported in the CHEMDNER task for the CEM subtask, and the high recall variant achieved the highest recall on both the CEM and CDI tasks. We report that tmChem is a state-of-the-art tool for chemical named entity recognition and that performance for chemical named entity recognition has now tied (or exceeded) the performance previously reported for genes and diseases. Future research should focus on tighter integration between the named entity recognition and normalization steps for improved performance. The source code and a trained model for both models of tmChem is available at: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/tmChem. The results of running tmChem (Model 2) on PubMed are available in PubTator: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator.
Year
DOI
Venue
2015
10.1186/1758-2946-7-S1-S3
J. Cheminformatics
Keywords
Field
DocType
Marginal Probability, Conditional Random Field, Allopregnanolone, Entity Recognition, Binary Feature
Conditional random field,Data mining,Text mining,Normalization (statistics),Information retrieval,Computer science,Bioinformatics,Named-entity recognition,Marginal distribution
Journal
Volume
Issue
ISSN
7
Suppl 1 Text mining for chemistry and the CHEMDNER track
1758-2946
Citations 
PageRank 
References 
61
1.66
25
Authors
3
Name
Order
Citations
PageRank
Robert Leaman191439.98
Chih-Hsuan Wei254627.43
Zhiyong Lu32735171.27