Combining Position Weight Matrices and Document-Term Matrix for Efficient Extraction of Associations of Methylated Genes and Diseases from Free Text
KAUST DepartmentBioscience Core Lab
Computational Bioscience Research Center (CBRC)
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Applied Mathematics and Computational Science Program
MetadataShow full item record
AbstractBackground:In a number of diseases, certain genes are reported to be strongly methylated and thus can serve as diagnostic markers in many cases. Scientific literature in digital form is an important source of information about methylated genes implicated in particular diseases. The large volume of the electronic text makes it difficult and impractical to search for this information manually.Methodology:We developed a novel text mining methodology based on a new concept of position weight matrices (PWMs) for text representation and feature generation. We applied PWMs in conjunction with the document-term matrix to extract with high accuracy associations between methylated genes and diseases from free text. The performance results are based on large manually-classified data. Additionally, we developed a web-tool, DEMGD, which automates extraction of these associations from free text. DEMGD presents the extracted associations in summary tables and full reports in addition to evidence tagging of text with respect to genes, diseases and methylation words. The methodology we developed in this study can be applied to similar association extraction problems from free text.Conclusion:The new methodology developed in this study allows for efficient identification of associations between concepts. Our method applied to methylated genes in different diseases is implemented as a Web-tool, DEMGD, which is freely available at http://www.cbrc.kaust.edu.sa/demgd/. The data is available for online browsing and download. © 2013 Bin Raies et al.
CitationBin Raies A, Mansour H, Incitti R, Bajic VB (2013) Combining Position Weight Matrices and Document-Term Matrix for Efficient Extraction of Associations of Methylated Genes and Diseases from Free Text. PLoS ONE 8: e77848. doi:10.1371/journal.pone.0077848.
PublisherPublic Library of Science (PLoS)
PubMed Central IDPMC3797705
- DDMGD: the database of text-mined associations between genes methylated in diseases from different species.
- Authors: Bin Raies A, Mansour H, Incitti R, Bajic VB
- Issue date: 2015 Jan
- DISEASES: text mining and data integration of disease-gene associations.
- Authors: Pletscher-Frankild S, Pallejà A, Tsafou K, Binder JX, Jensen LJ
- Issue date: 2015 Mar
- Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text.
- Authors: Garten Y, Altman RB
- Issue date: 2009 Feb 5
- Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature.
- Authors: Ravikumar KE, Wagholikar KB, Li D, Kocher JP, Liu H
- Issue date: 2015 Jun 6
- Increasing coverage of transcription factor position weight matrices through domain-level homology.
- Authors: Bernard B, Thorsson V, Rovira H, Shmulevich I
- Issue date: 2012