scholarly journals The GNAT library for local and remote gene mention normalization

2011 ◽  
Vol 27 (19) ◽  
pp. 2769-2771 ◽  
Author(s):  
J. Hakenberg ◽  
M. Gerner ◽  
M. Haeussler ◽  
I. Solt ◽  
C. Plake ◽  
...  
Keyword(s):  
Gene Mention

scholarly journals GNormPlus: An Integrative Approach for Tagging Genes, Gene Families, and Protein Domains

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Chih-Hsuan Wei ◽  
Hung-Yu Kao ◽  
Zhiyong Lu
Keyword(s):  
Text Mining ◽  
Protein Domains ◽  
Gene Families ◽  
Integrative Approach ◽  
Name Disambiguation ◽  
Gene Mention ◽  
Web Based ◽  
Gene Normalization ◽  
Document Level ◽  
Gene Normalization Task

The automatic recognition of gene names and their associated database identifiers from biomedical text has been widely studied in recent years, as these tasks play an important role in many downstream text-mining applications. Despite significant previous research, only a small number of tools are publicly available and these tools are typically restricted to detecting only mention level gene names or only document level gene identifiers. In this work, we report GNormPlus: an end-to-end and open source system that handles both gene mention and identifier detection. We created a new corpus of 694 PubMed articles to support our development of GNormPlus, containing manual annotations for not only gene names and their identifiers, but also closely related concepts useful for gene name disambiguation, such as gene families and protein domains. GNormPlus integrates several advanced text-mining techniques, including SimConcept for resolving composite gene names. As a result, GNormPlus compares favorably to other state-of-the-art methods when evaluated on two widely used public benchmarking datasets, achieving 86.7% F1-score on the BioCreative II Gene Normalization task dataset and 50.1% F1-score on the BioCreative III Gene Normalization task dataset. The GNormPlus source code and its annotated corpus are freely available, and the results of applying GNormPlus to the entire PubMed are freely accessible through our web-based tool PubTator.

scholarly journals Integrating high dimensional bi-directional parsing models for gene mention tagging

2008 ◽  
Vol 24 (13) ◽  
pp. i286-i294 ◽  
Author(s):  
C.-N. Hsu ◽  
Y.-M. Chang ◽  
C.-J. Kuo ◽  
Y.-S. Lin ◽  
H.-S. Huang ◽  
...  
Keyword(s):  
High Dimensional ◽  
Gene Mention

scholarly journals Boosting performance of gene mention tagging system by hybrid methods

2012 ◽  
Vol 45 (1) ◽  
pp. 156-164 ◽  
Author(s):  
Lishuang Li ◽  
Wenting Fan ◽  
Degen Huang ◽  
Yanzhong Dang ◽  
Jing Sun
Keyword(s):  
Hybrid Methods ◽  
Gene Mention ◽  
Tagging System

scholarly journals Graph-based Semi-supervised Gene Mention Tagging

2016 ◽  
Author(s):  
Golnar Sheikhshab ◽  
Elizabeth Starks ◽  
Aly Karsan ◽  
Anoop Sarkar ◽  
Inanc Birol
Keyword(s):  
Gene Mention

scholarly journals BioCreAtIvE Task 1A: gene mention finding evaluation

2005 ◽  
Vol 6 (Suppl 1) ◽  
pp. S2 ◽  
Author(s):  
Alexander Yeh ◽  
Alexander Morgan ◽  
Marc Colosimo ◽  
Lynette Hirschman
Keyword(s):  
Gene Mention

scholarly journals Gene mention normalization and interaction extraction with context models and sentence motifs

2008 ◽  
Vol 9 (Suppl 2) ◽  
pp. S14 ◽  
Author(s):  
Jörg Hakenberg ◽  
Conrad Plake ◽  
Loic Royer ◽  
Hendrik Strobelt ◽  
Ulf Leser ◽  
...  
Keyword(s):  
Gene Mention ◽  
Interaction Extraction ◽  
Context Models

Combining multiple disambiguation methods for gene mention normalization

2011 ◽  
Vol 38 (7) ◽  
pp. 7994-7999 ◽  
Author(s):  
Ning Xia ◽  
Hongfei Lin ◽  
Zhihao Yang ◽  
Yanpeng Li
Keyword(s):  
Gene Mention

scholarly journals The value of parsing as feature generation for gene mention recognition

2009 ◽  
Vol 42 (5) ◽  
pp. 895-904 ◽  
Author(s):  
Larry H. Smith ◽  
W. John Wilbur
Keyword(s):  
Feature Generation ◽  
Gene Mention
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