The goal of this proposal is to provide a venue for the evaluation of biomedical text mining tools via the shared task paradigm, particularly tools with relevance to problems in biocuration. Biocurators will help define use cases and desired functionalities;stakeholders will come to agreement on task definitions, data sets, and evaluation metrics;text mining teams will then work on these consensus tasks and come together to share their results and gain further feedback from biocurators.

Public Health Relevance

This project consists of the evaluation of biomedical text mining tools, particularly ones applied to projects in biocuration. The results of biocuration are extensively used in modern medical practice, particularly personalized medicine, so the work of the grant has the potential to have a substantial impact on the cutting edge of human healthcare.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Conference (R13)
Project #
1R13GM109648-01A1
Application #
8786017
Study Section
Special Emphasis Panel (ZGM1)
Program Officer
Ravichandran, Veerasamy
Project Start
2014-09-01
Project End
2017-08-31
Budget Start
2014-09-01
Budget End
2015-08-31
Support Year
1
Fiscal Year
2014
Total Cost
Indirect Cost
Name
University of Colorado Denver
Department
Pharmacology
Type
Schools of Medicine
DUNS #
City
Aurora
State
CO
Country
United States
Zip Code
80045
Peng, Yifan; Arighi, Cecilia; Wu, Cathy H et al. (2016) BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph. Database (Oxford) 2016:
Ding, Ruoyao; Arighi, Cecilia N; Lee, Jung-Youn et al. (2015) pGenN, a gene normalization tool for plant genes and proteins in scientific literature. PLoS One 10:e0135305
Van Auken, Kimberly; Schaeffer, Mary L; McQuilton, Peter et al. (2014) BC4GO: a full-text corpus for the BioCreative IV GO task. Database (Oxford) 2014:
Mao, Yuqing; Van Auken, Kimberly; Li, Donghui et al. (2014) Overview of the gene ontology task at BioCreative IV. Database (Oxford) 2014:
Arighi, Cecilia N; Wu, Cathy H; Cohen, Kevin B et al. (2014) BioCreative-IV virtual issue. Database (Oxford) 2014: