Combining Position Weight Matrices and Document-Term Matrix for Efficient Extraction of Associations of Methylated Genes and Diseases from Free Text

Abstract

BackgroundIn 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.MethodologyWe 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.ConclusionThe 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.

DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases

“…In addition, TM has been combined with methods from bioinformatics. For example, position weight matrices have been used for text representation and feature generation in a TM system to extract associations between methylated genes and diseases [32,33]. Another study combined TM and bioinformatics approaches for the interpretation of mutations in protein kinases [34].…”

“…DES is a text mining and data mining system that allows the exploration of text through enriched concepts and enriched pairs of concepts in topic-specific literature. We used the DES framework to create several topic-specific KBs [32,33,54,67,[69][70][71][72][73][74][75][76][77][78][79][80][81][82]. The underlying systems, workflow, and concept enrichment process used in the current version of DES have been described in [69].…”

Redox control of vascular biology

“…Data-mining and text-mining techniques have been used to explore the information contained in published biomedical literature. Advancements in these techniques have led to the development of several topic-specific knowledgebases (KB), [141][142][143][144][145][146][147][148][149][150][151][152][153][154][155][156][157][158][159] including the first topic-specific KB for redox control of vascular systems, named DES-RedoxVasc. 160 DES-RedoxVasc was constructed using the search query: (human OR mouse OR rat OR mammal*) AND (radical* OR peroxide* OR "reductive stress" OR ROS OR "reactive oxygen species" OR RNS OR "reactive nitrogen species" OR redox OR "reduction-oxidation reaction" OR oxidative OR nitrosative OR peroxide* OR superoxide* OR detoxifi* OR antioxid* OR "polyunsaturated fatty acids" OR "arachidonic acid" OR "linoleic acid" OR hydroperoxide* OR "hypochlorous acid" OR peroxynitrit* flavoprot* OR xanthine oxidase* OR "cytochromes P450" OR catalase* OR sulfiredoxin* OR peroxiredoxin*) AND ("angina pectoris" OR anemia OR aneurysm* OR angio* OR arter* OR atrial OR atrioventricular OR aort* OR bradycardia OR blood OR brain OR circulati* OR clogging OR cardio* OR coronary OR edema OR heart OR ischemic OR hemo* OR hypertension OR leukemia OR leuko* OR macroangiopathy OR microangiopathy OR neovascularization OR occlusion OR pericardi* OR sepsis OR "sickle cell" OR tachycardia OR tachyarrhythmia OR thromb* OR vaso OR vein* OR ventricular OR vascular* OR vessel*) to retrieve all literature specifically focused on research related to redox effects on the cardiovascular system in mammalian organisms.…”

Literature-Based Enrichment Insights into Redox Control of Vascular Biology

“…Different methods were used for obtaining information from free text [24][25][26][27][28][29][30][31][32][33], many based on heavy utilization of ontologies and ontology structures [28]. Also, there have been systematic efforts to combine text mining with other methods to enhance the capacity to extract useful information (for example, [30][31][32]34]).…”