poster

Text mining tools for assisting literature curation

Authors:

Chih-Hsuan Wei,

Hung-Yu Kao,

Zhiyong LuAuthors Info & Claims

BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

Pages 590 - 591

https://doi.org/10.1145/2649387.2660786

Published: 20 September 2014 Publication History

Get Access

Abstract

Today's biomedical research has become heavily dependent on the access to biological knowledge encoded in expert curated biological databases (e.g. Swiss-Prot). As the volume of biological literature grows rapidly, it becomes increasingly difficult for human curators to keep up with the literature because manual curation is an expensive and time-consuming endeavor. Past research has shown that (semi-)automated approach has the potential to greatly improve the manual curation productivity [1-3]. We recently developed PubTator, a web-based application for assisting literature curation through the use of various text mining tools [4-6].

PubTator has several unique features. First, PubTator is a web-based system, thus no installation is required and not restricted to any specific computer platforms. That is, it works on different computing platforms as long as there is a Web browser installed. Second, PubTator features a PubMed-like interface which many human curators find it to be familiar and easy to use with minimal training required. Third, PubTator integrates multiple competition-winning text mining approaches that we recently developed for recognizing important biological entities: Gene/Proteins, Diseases, Mutations, Chemical/Drugs, and Organisms [7-11]. Hence, it can guarantee the state-of-the-art performance on text-mined results. Lastly, PubTator is in sync with PubMed content through nightly updates. Interested users can access our text-mined results via a) PubTator web interface, b) RESTful API or c) ftp download.

We have conducted a formal text-mining aided curation experiment, results of which showed that PubTator was able to greatly improve both the curation efficiency and accuracy [6]. More recently, PubTator has been successfully deployed in practice for the curation of CDC's human genome epidemiology knowledge-base. Hence, we conclude that our text-mining tools and PubTator can provide practical benefits to literature curation in bioinformatics research.

PubTator is freely available at: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/

References

[1]

Van Auken, K., Jaffery, J., Chan, J., Müller, H.-M. and Sternberg, P. W. 2009. Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation. BMC bioinformatics 10, 1(2009), 228. DOI=http://dx.doi.org/10.1186/1471-2105-10-228

Crossref

Google Scholar

[2]

Alex, B., Grover, C., Haddow, B., Kabadjor, M., Klein, E., Matthews, M., Roebuck, S., Tobin, R. and Wang, X. 2008 Assisted Curation: Does Text Mining Really Help? In Proceedings of the Pacific Symposium on Biocomputing (Hawaii, USA, 2008). Citeseer

Google Scholar

[3]

Donaldson, I., Martin, J., De Bruijn, B., Wolting, C., Lay, V., Tuekam, B., Zhang, S., Baskin, B., Bader, G. D. and Michalickova, K. 2003. PreBIND and Textomy--mining the biomedical literature for protein-protein interactions using a support vector machine. BMC bioinformatics 4, 1(2003), 11. DOI=http://dx.doi.org/10.1186/1471-2105-4-11

Crossref

Google Scholar

[4]

Wei, C.-H., Kao, H.-Y. and Lu, Z. 2013. PubTator: a Web-based text mining tool for assisting Biocuration. Nucleic acids research 41, Web Server Issue(2013), W518--W522. DOI=http://dx.doi.org/10.1093/nar/gkt44

Crossref

Google Scholar

[5]

Wei, C.-H., Kao, H.-Y. and Lu, Z. 2012 PubTator: A -like interactive curation system for document triage and literature curation. In Proceedings of the Proceedings of the BioCreative 2012 workshop (Washington DC, USA, 2012). BioCreative

Google Scholar

[6]

Wei, C.-H., Harris, B. R., Li, D., Berardini, T. Z., Huala, E., Kao, H.-Y. and Lu, Z. 2012. Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in abstracts. Database (oxford) 2012 2012), bas041. DOI=http://dx.doi.org/10.1093/database/bas041

Crossref

Google Scholar

[7]

Wei, C.-H., Harris, B. R., Kao, H.-Y. and Lu, Z. 2013. tmVar: A text mining approach for extracting sequence variants in biomedical literature. Bioinformatics 29, 11(2013), 1433--1439. DOI=http://dx.doi.org/10.1093/bioinformatics/btt156

Digital Library

Google Scholar

[8]

Leaman, R., Wei, C.-H. and Lu, Z. 2013 NCBI at the BioCreative IV CHEMDNER Task: Recognizing chemical names in articles with tmChem. In Proceedings of the BioCreative Challenge Evaluation Workshop vol (Bethesda, Maryland, USA, 2013). BioCreative

Google Scholar

[9]

Leaman, R., Doǧan, R. I. and Lu, Z. 2013. DNorm: disease name normalization with pairwise learning to rank. Bioinformatics 29, 22(2013), 2909--2917. DOI=http://dx.doi.org/10.1093/bioinformatics/btt474

Crossref

Google Scholar

[10]

Wei, C.-H., Kao, H.-Y. and Lu, Z. 2012. SR4GN: a species recognition software tool for gene normalization. Plos one 7, 6(2012), e38460. DOI=http://dx.doi.org/10.1371/journal.pone.0038460

Crossref

Google Scholar

[11]

Wei, C.-H. and Kao, H.-Y. 2011. Cross-species gene normalization by species inference. BMC bioinformatics 12, Suppl 8(2011), S5. DOI=http://dx.doi.org/10.1186/1471-2105-12-S8-S5

Crossref

Google Scholar

Cited By

View all

Frihat SFuhr N(2025)Integration of biomedical concepts for enhanced medical literature retrievalInternational Journal of Data Science and Analytics10.1007/s41060-025-00724-zOnline publication date: 3-Feb-2025
https://doi.org/10.1007/s41060-025-00724-z
Westergaard DStærfeldt HTønsberg CJensen LBrunak S(2018)A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstractsPLOS Computational Biology10.1371/journal.pcbi.100596214:2(e1005962)Online publication date: 15-Feb-2018
https://doi.org/10.1371/journal.pcbi.1005962

Index Terms

Text mining tools for assisting literature curation
1. Information systems
  1. World Wide Web
    1. Web applications
    2. Web services

Recommendations

A Text-Mining System for Concept Annotation in Biomedical Full Text Articles
BCB '19: Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics

PubTator Central (https://www.ncbi.nlm.nih.gov/research/pubtator/) [1] is a web service for exploring and retrieving bioconcept annotations in full text biomedical articles. PubTator Central (PTC) provides automated annotations from state-of-the-art ...
SimConcept: a hybrid approach for simplifying composite named entities in biomedicine
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

Many text-mining studies have focused on the issue of named entity recognition and normalization, especially in the field of biomedical natural language processing. However, entity recognition is a complicated and difficult task in biomedical text. One ...
Text Mining of Protein Phosphorylation Information Using a Generalizable Rule-Based Approach
BCB'13: Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics

Literature-based annotation of protein phosphorylation is the focus of many biological databases, as phosphorylation is a global regulator of cellular activity. To speed up manual curation of phosphorylation information, text mining technology has been ...

Comments

Information & Contributors

Information

Published In

BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

September 2014

851 pages

ISBN:9781450328944

DOI:10.1145/2649387

General Chairs:
Pierre Baldi
University of California, Irvine
,
Wei Wang
University of California, Los Angeles

Permission to make digital or hard copies of part or all of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for third-party components of this work must be honored. For all other uses, contact the Owner/Author.

Publisher

Association for Computing Machinery

New York, NY, United States

Publication History

Published: 20 September 2014

Check for updates

Author Tags

Qualifiers

Poster

Conference

BCB '14

Sponsor:

SIGBio

BCB '14: ACM-BCB '14

September 20 - 23, 2014

California, Newport Beach

Acceptance Rates

Overall Acceptance Rate 254 of 885 submissions, 29%

Contributors

Other Metrics

View Article Metrics

Bibliometrics & Citations

Bibliometrics

Article Metrics

2
Total Citations
View Citations
162
Total Downloads

Downloads (Last 12 months)2
Downloads (Last 6 weeks)1

Reflects downloads up to 28 Feb 2025

Other Metrics

View Author Metrics

Citations

Cited By

View all

Frihat SFuhr N(2025)Integration of biomedical concepts for enhanced medical literature retrievalInternational Journal of Data Science and Analytics10.1007/s41060-025-00724-zOnline publication date: 3-Feb-2025
https://doi.org/10.1007/s41060-025-00724-z
Westergaard DStærfeldt HTønsberg CJensen LBrunak S(2018)A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstractsPLOS Computational Biology10.1371/journal.pcbi.100596214:2(e1005962)Online publication date: 15-Feb-2018
https://doi.org/10.1371/journal.pcbi.1005962

View Options

Login options

Check if you have access through your login credentials or your institution to get full access on this article.

Full Access

Get this Publication

View options

PDF

View or Download as a PDF file.

PDF

eReader

View online with eReader.

eReader

Abstract

References

Cited By

Index Terms

Recommendations

A Text-Mining System for Concept Annotation in Biomedical Full Text Articles

SimConcept: a hybrid approach for simplifying composite named entities in biomedicine

Text Mining of Protein Phosphorylation Information Using a Generalizable Rule-Based Approach

Comments

Information

Published In

Sponsors

Publisher

Publication History

Check for updates

Author Tags

Qualifiers

Conference

Acceptance Rates

Contributors

Other Metrics

Bibliometrics

Article Metrics

Other Metrics

Citations

Cited By

Login options

Full Access

View options

PDF

eReader

Share

Share this Publication link

Share on social media

Affiliations