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Updated: May 13, 2026
09:10
A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
Published on: May 22, 2018
Application of text-mining for updating protein post-translational modification annotation in UniProtKB
Anne-Lise Veuthey1, Alan Bridge, Julien Gobeill
1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, 1 Michel Servet, 1211 Geneva 4, Switzerland. anne-lise.veuthey@isb-sib.ch
BMC Bioinformatics
|March 23, 2013
Summary
A new system automates protein post-translational modification (PTM) extraction from scientific literature, aiding UniProtKB curators. This text-mining tool improves PTM annotation efficiency and accuracy.
Area of Science:
- Biochemistry
- Bioinformatics
- Computational Biology
Background:
- Protein post-translational modifications (PTMs) are crucial biological events.
- The increasing volume of PTM research necessitates efficient information extraction tools.
- UniProtKB curators face challenges in manually annotating PTMs from vast literature.
Purpose of the Study:
- To develop an automated system for extracting PTM information from scientific literature.
- To assist UniProtKB curators in managing and annotating PTM data.
- To improve the efficiency and accuracy of PTM database curation.
Main Methods:
- A pattern-matching and rule-based approach was employed for information extraction.
- The system identifies sentences detailing PTM type and modification sites.
- A ranked list of candidate proteins for specific modifications is generated.
Main Results:
- The system achieves high precision (57-94%) and recall (75-95%) for PTM extraction, varying by modification type.
- The tool was successfully used to monitor new PTM publications.
- It aided in identifying supporting evidence for phosphorylation sites from proteomics data.
Conclusions:
- The developed information retrieval and extraction method provides a basis for a PTM curation tool for UniProtKB/Swiss-Prot.
- Simple text-mining tools, when tailored to specific needs, are effective for database curation.
- The system is accessible at http://eagl.unige.ch/PTM/.
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