Abstract

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.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Conference (R13)
Project #
5R13GM109648-03
Application #
9135507
Study Section
Special Emphasis Panel (ZGM1-TRN-3 (CO))
Program Officer
Ravichandran, Veerasamy
Project Start
2014-09-01
Project End
2017-08-31
Budget Start
2016-09-01
Budget End
2017-08-31
Support Year
3
Fiscal Year
2016
Total Cost
$12,000
Indirect Cost

  Institution

Name
University of Colorado Denver
Department
Pharmacology
Type
Schools of Medicine
DUNS #
041096314
City
Aurora
State
CO
Country
United States
Zip Code
80045

  Publications

Huang, Hongzhan; Arighi, Cecilia N; Ross, Karen E et al. (2018) iPTMnet: an integrated resource for protein post-translational modification network discovery. Nucleic Acids Res 46:D542-D550
Huang, Liang-Chin; Ross, Karen E; Baffi, Timothy R et al. (2018) Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources. Sci Rep 8:6518
International Society for Biocuration (2018) Biocuration: Distilling data into knowledge. PLoS Biol 16:e2002846
Ding, Ruoyao; Boutet, Emmanuel; Lieberherr, Damien et al. (2017) eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality. Database (Oxford) 2017:
Poux, Sylvain; Arighi, Cecilia N; Magrane, Michele et al. (2017) On expert curation and scalability: UniProtKB/Swiss-Prot as a case study. Bioinformatics 33:3454-3460
The Gene Ontology Consortium (2017) Expansion of the Gene Ontology knowledgebase and resources. Nucleic Acids Res 45:D331-D338
Natale, Darren A; Arighi, Cecilia N; Blake, Judith A et al. (2017) Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. Nucleic Acids Res 45:D339-D346
The UniProt Consortium (2017) UniProt: the universal protein knowledgebase. Nucleic Acids Res 45:D158-D169
Ross, Karen E; Huang, Hongzhan; Ren, Jia et al. (2017) iPTMnet: Integrative Bioinformatics for Studying PTM Networks. Methods Mol Biol 1558:333-353
Singhal, Ayush; Leaman, Robert; Catlett, Natalie et al. (2016) Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges. Database (Oxford) 2016:

Showing the most recent 10 out of 19 publications