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Updated: May 26, 2026

Methyl-binding DNA capture Sequencing for Patient Tissues

Methyl-binding DNA capture Sequencing for Patient Tissues

Published on: October 31, 2016

Event extraction for DNA methylation.

Tomoko Ohta¹, Sampo Pyysalo, Makoto Miwa

¹Department of Computer Science, University of Tokyo, Tokyo, Japan. okap@is.s.u-tokyo.ac.jp.

Journal of Biomedical Semantics

|December 15, 2011

Summary

This summary is machine-generated.

Researchers developed an automated system to extract DNA methylation events from scientific literature. This system achieves 78% precision and 76% recall for identifying methylation events, genes, and sites.

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Area of Science:

Bioinformatics
Molecular Biology
Genomics

Background:

DNA methylation is crucial for epigenetic gene regulation and implicated in cancers.
Automatic information extraction for DNA methylation events remains understudied.
Epigenetic modifications play a vital role in cellular processes and disease development.

Purpose of the Study:

To develop and evaluate an automated system for extracting DNA methylation events from biomedical literature.
To create a manually annotated corpus for DNA methylation events.
To assess the performance of a state-of-the-art event extraction system on DNA methylation data.

Main Methods:

Developed an annotation scheme for DNA methylation events.
Manually annotated a corpus of 200 PubMed abstracts.
Retrained a state-of-the-art event extraction system on the annotated corpus.
Utilized the BioNLP shared task representation for event extraction.

Main Results:

The system achieved 78% precision and 76% recall in extracting DNA methylation events, methylated genes, and methylation sites.
The annotated corpus includes nearly 3000 gene/protein mentions and 1500 DNA methylation/demethylation events.
Demonstrated the feasibility of reliable automatic extraction through corpus annotation and system retraining.

Conclusions:

Reliable extraction of DNA methylation events is achievable via corpus annotation and retraining general event extraction systems.
The developed resources are publicly available for research purposes.
This work facilitates further research into DNA methylation and its role in diseases like cancer.