Human Breathomics Database

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.

Figure 1

User interface and visualization of disease mapping. (a) Browse and search interface of the HBDB. (b) Disease mapping to human physiology and statistics of references associated with diseases. (c) The collected compounds, references and diseases are listed in three tabs for browsing.

Figure 2

Results of searching for ‘asthma’ in the HBDB. (a) Associated references for asthma. (b) Associated compounds for asthma in descending order of related number of references. (c) Associated diseases for asthma.

Figure 3

Information on 8-epi-PGF2α with associated curated diseases. Diseases associated with 8-epi-PGF2α are mapped to a human physiological map in red and listed in a table with MeSH definition.

Figure 4

Information on asthma with associated references and compounds. (a) Disease description. (b) Downloadable list of associated references for asthma. (c) Downloadable list of associated compounds for asthma.

Figure 5

Information on COPD with associated references and compounds. (a) Disease description. (b) Downloadable list of associated references for COPD. (c) Downloadable list of associated compounds for COPD.