Human Breathomics Database.

Tien-Chueh Kuo,Kuo-Hsing Chen,Cheng-En Tan,Shu-Wen Lin,Yu-Chieh Yang,Ching-Hua Kuo,San-Yuan Wang,Jessica Lin,Chao-Chi Ho,Olivia A Lin,Bo-Han Su,Yu-Yen Cheng,Ciao-Sin Chen,Yufeng Jane Tseng,Ming-Tsung Hsu

doi:10.1093/database/baz139

Abstract

Breathomics is a special branch of metabolomics that quantifies volatile organic compounds (VOCs) from collected exhaled breath samples. Understanding how breath molecules are related to diseases, mechanisms and pathways identified from experimental analytical measurements is challenging due to the lack of an organized resource describing breath molecules, related references and biomedical information embedded in the literature. To provide breath VOCs, related references and biomedical information, we aim to organize a database composed of manually curated information and automatically extracted biomedical information. First, VOCs-related disease information was manually organized from 207 literature linked to 99 VOCs and known Medical Subject Headings (MeSH) terms. Then an automated text mining algorithm was used to extract biomedical information from this literature. In the end, the manually curated information and auto-extracted biomedical information was combined to form a breath molecule database—the Human Breathomics Database (HBDB). We first manually curated and organized disease information including MeSH term from 207 literatures associated with 99 VOCs. Then, an automatic pipeline of text mining approach was used to collect 2766 literatures and extract biomedical information from breath researches. We combined curated information with automatically extracted biomedical information to assemble a breath molecule database, the HBDB. The HBDB is a database that includes references, VOCs and diseases associated with human breathomics. Most of these VOCs were detected in human breath samples or exhaled breath condensate samples. So far, the database contains a total of 913 VOCs in relation to human exhaled breath researches reported in 2766 publications. The HBDB is the most comprehensive HBDB of VOCs in human exhaled breath to date. It is a useful and organized resource for researchers and clinicians to identify and further investigate potential biomarkers from the breath of patients. Database URL: https://hbdb.cmdm.tw

Highlights

Breathomics is a branch of metabolomics that quantifies volatile organic compounds (VOCs) collected from human exhaled samples or exhaled breath condensate (EBC) samples using gas chromatography–mass spectrometry and gas sensor-driven electronic nose
The electronic nose (eNose) devices are capable of detecting individual or a mixture of molecules, providing results with their probability through the pattern recognition algorithm based on similarity of profiles of exhaled breath [2, 3]
We demonstrate how to use the Human Breathomics Database (HBDB) for finding associated diseases, compounds and references by selecting ‘asthma’ and ‘chronic obstructive pulmonary disease’ as keywords for two cases to display the organized information in HBDB

Summary

Introduction

Breathomics is a branch of metabolomics that quantifies volatile organic compounds (VOCs) collected from human exhaled samples or exhaled breath condensate (EBC) samples using gas chromatography–mass spectrometry and gas sensor-driven electronic nose (eNose). Many of the VOCs in EBC samples are linked to airway disease or lung cancer diagnosis. This is expected, considering that VOCs are transported from organs to the lungs through the circulatory system and exchanged in exhaled breath [6]. 8-isoprostane concentrations in breath condensate may be a potential biomarker for examining asthma severity [8] Other potential biomarkers such as nitrosothiols (RS-NOs), leukotriene B4 and nitrite are linked to chronic obstructive pulmonary disease (COPD) [9,10,11]. PGE2 and 8-isoprostane as the end products of COX-2 metabolism are increased in airway lumen of lung cancer patients and have been linked to tumor development [13]. The rapid and non-invasive method of collecting exhaled breath has been increasingly considered for disease diagnosis [16, 17, 25, 26, 30,31,32]

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