Integrated Text Mining and Chemoinformatics Analysis Associates Diet to Health Benefit at Molecular Level

Abstract

Awareness that disease susceptibility is not only dependent on genetic make up, but can be affected by lifestyle decisions, has brought more attention to the role of diet. However, food is often treated as a black box, or the focus is limited to few, well-studied compounds, such as polyphenols, lipids and nutrients. In this work, we applied text mining and Naïve Bayes classification to assemble the knowledge space of food-phytochemical and food-disease associations, where we distinguish between disease prevention/amelioration and disease progression. We subsequently searched for frequently occurring phytochemical-disease pairs and we identified 20,654 phytochemicals from 16,102 plants associated to 1,592 human disease phenotypes. We selected colon cancer as a case study and analyzed our results in three directions; i) one stop legacy knowledge-shop for the effect of food on disease, ii) discovery of novel bioactive compounds with drug-like properties, and iii) discovery of novel health benefits from foods. This works represents a systematized approach to the association of food with health effect, and provides the phytochemical layer of information for nutritional systems biology research.

Anti-proliferative effect of main dietary phytosterols and β-cryptoxanthin alone or combined in human colon cancer Caco-2 cells through cytosolic Ca+2 – and oxidative stress-induced apoptosis

“…Colorectal cancer, which is the fourth most common cancer in men and the third most common cancer in women worldwide, has been linked with a diet low in fruits and vegetables, physical inactivity, obesity, and smoking (Center, Jemal, Smith, & Ward, 2009). Considering that prevention rather than treatment is the desired approach, dietary modification through increased phytochemical assumption, could be a good and cost-effective strategy, since more than 500 plants and related bioactive compounds have been associated with health benefits and protection from colon cancer (Jensen, Panagiotou, & Kouskoumvekaki, 2014). Most phytochemicals affect the redox status of either healthy or cancer cells, with remarkably different cell responses at a molecular level (Nair, Li, & Kong, 2007), that possibly may interfere each other.…”

Analysis of free text in electronic health records for identification of cancer patient trajectories

“…We then trained three Naïve Bayes classifiers: one for disease and symptoms, one for drugs and medication and one for the surgical procedures202122 and we compiled language features for each of the three classifiers, to distinguish between real-time events and noise (current – noise), retrospective events and noise (history – noise) and real-time events and retrospective events (current – history).…”

Propelling the paradigm shift from reductionism to systems nutrition

“…With growing possibilities to measure, store, and analyze data and knowledge (e.g., [100]), availability and means to effectively integrate and mine information is rapidly becoming a key determinant of successful translation of nutrition research into human health benefits (e.g., [41, 89]). Application of existing and development of new computational methods (e.g., [68]) are being used for systems analysis of high dimensional, multi-omic data sets (e.g., [47, 49]) and their integration with physiological and clinical endpoints to infer health effects of interventions [48].…”