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 du...
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| Published in | Database : the journal of biological databases and curation Vol. 2020 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Oxford University Press
2020
|
| Subjects | |
| Online Access | Get full text |
| ISSN | 1758-0463 1758-0463 |
| DOI | 10.1093/database/baz139 |
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| Abstract | 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 |
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| AbstractList | 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.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. 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 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 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 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. 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 |
| Author | Chen, Ciao-Sin Lin, Olivia A Chen, Kuo-Hsing Su, Bo-Han Lin, Shu-Wen Kuo, Ching-Hua Wang, San-Yuan Kuo, Tien-Chueh Lin, Jessica Hsu, Ming-Tsung Cheng, Yu-Yen Yang, Yu-Chieh Tseng, Yufeng Jane Ho, Chao-Chi Tan, Cheng-En |
| AuthorAffiliation | 3 Drug Research Center, College of Pharmacy, College of Medicine, National Taiwan University , No. 33, Linsen S. Road, Taipei 10055, Taiwan 6 Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica , No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan 8 Department of Obstetrics and Gynecology, National Taiwan University Hospital—Yunlin Branch , No. 579, Sec. 2, Yunlin Road, Douliu, Yunlin County 640, Taiwan 1 Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University , No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan 10 Graduate Institute of Clinical Pharmacy, College of Medicine, National Taiwan University , No. 33, Linsen S. Road, Taipei 10055, Taiwan 2 The Metabolomics Core Laboratory, Centers of Genomic Medicine and Precision Medicine, National Taiwan University , No. 2, Syu-Jhou Road, Taipei 10055, Taiwan 4 Department of Computer Science and Information Engineering, National Taiwan University , No. 1, Sec. 4, Roosevel |
| AuthorAffiliation_xml | – name: 5 Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical University , No. 250, Wu-Hsing St., Taipei 11031, Taiwan – name: 11 Department of Internal Medicine, National Taiwan University Hospital , No. 7, Chung-Shan South Road, Taipei 10002, Taiwan – name: 2 The Metabolomics Core Laboratory, Centers of Genomic Medicine and Precision Medicine, National Taiwan University , No. 2, Syu-Jhou Road, Taipei 10055, Taiwan – name: 8 Department of Obstetrics and Gynecology, National Taiwan University Hospital—Yunlin Branch , No. 579, Sec. 2, Yunlin Road, Douliu, Yunlin County 640, Taiwan – name: 3 Drug Research Center, College of Pharmacy, College of Medicine, National Taiwan University , No. 33, Linsen S. Road, Taipei 10055, Taiwan – name: 1 Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University , No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan – name: 6 Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica , No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan – name: 7 Department of Pharmacy, School of Pharmacy, College of Medicine, National Taiwan University , No. 33, Linsen S. Road, Taipei 10055, Taiwan – name: 4 Department of Computer Science and Information Engineering, National Taiwan University , No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan – name: 9 Department of Oncology, National Taiwan University Hospital, National Taiwan University Cancer Center , No. 1, Sec. 4, Roosevelt Road, Taipei 10048, Taiwan – name: 10 Graduate Institute of Clinical Pharmacy, College of Medicine, National Taiwan University , No. 33, Linsen S. Road, Taipei 10055, Taiwan |
| Author_xml | – sequence: 1 givenname: Tien-Chueh surname: Kuo fullname: Kuo, Tien-Chueh email: cot@cmdm.csie.ntu.edu.tw organization: Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan – sequence: 2 givenname: Cheng-En surname: Tan fullname: Tan, Cheng-En email: b96b02054@csie.ntu.edu.tw organization: The Metabolomics Core Laboratory, Centers of Genomic Medicine and Precision Medicine, National Taiwan University, No. 2, Syu-Jhou Road, Taipei 10055, Taiwan – sequence: 3 givenname: San-Yuan surname: Wang fullname: Wang, San-Yuan email: syw@tmu.edu.tw organization: The Metabolomics Core Laboratory, Centers of Genomic Medicine and Precision Medicine, National Taiwan University, No. 2, Syu-Jhou Road, Taipei 10055, Taiwan – sequence: 4 givenname: Olivia A surname: Lin fullname: Lin, Olivia A email: olivia22lin@gmail.com organization: Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan – sequence: 5 givenname: Bo-Han surname: Su fullname: Su, Bo-Han email: suborhang@gmail.com organization: Department of Computer Science and Information Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan – sequence: 6 givenname: Ming-Tsung surname: Hsu fullname: Hsu, Ming-Tsung email: trams10@gmail.com organization: Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan – sequence: 7 givenname: Jessica surname: Lin fullname: Lin, Jessica email: jessica1338@gmail.com organization: Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan – sequence: 8 givenname: Yu-Yen surname: Cheng fullname: Cheng, Yu-Yen email: yuyen255@gmail.com organization: Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan – sequence: 9 givenname: Ciao-Sin surname: Chen fullname: Chen, Ciao-Sin email: chelseachen112@gmail.com organization: Department of Pharmacy, School of Pharmacy, College of Medicine, National Taiwan University, No. 33, Linsen S. Road, Taipei 10055, Taiwan – sequence: 10 givenname: Yu-Chieh surname: Yang fullname: Yang, Yu-Chieh email: jackyang0216@gmail.com organization: Department of Obstetrics and Gynecology, National Taiwan University Hospital—Yunlin Branch, No. 579, Sec. 2, Yunlin Road, Douliu, Yunlin County 640, Taiwan – sequence: 11 givenname: Kuo-Hsing surname: Chen fullname: Chen, Kuo-Hsing email: jeff40537@gmail.com organization: Department of Oncology, National Taiwan University Hospital, National Taiwan University Cancer Center, No. 1, Sec. 4, Roosevelt Road, Taipei 10048, Taiwan – sequence: 12 givenname: Shu-Wen surname: Lin fullname: Lin, Shu-Wen email: shuwenlin@ntu.edu.tw organization: Graduate Institute of Clinical Pharmacy, College of Medicine, National Taiwan University, No. 33, Linsen S. Road, Taipei 10055, Taiwan – sequence: 13 givenname: Chao-Chi surname: Ho fullname: Ho, Chao-Chi email: ccho1203@ntu.edu.tw organization: Department of Internal Medicine, National Taiwan University Hospital, No. 7, Chung-Shan South Road, Taipei 10002, Taiwan – sequence: 14 givenname: Ching-Hua surname: Kuo fullname: Kuo, Ching-Hua email: kuoch@ntu.edu.tw organization: The Metabolomics Core Laboratory, Centers of Genomic Medicine and Precision Medicine, National Taiwan University, No. 2, Syu-Jhou Road, Taipei 10055, Taiwan – sequence: 15 givenname: Yufeng Jane surname: Tseng fullname: Tseng, Yufeng Jane email: yjtseng@csie.ntu.edu.tw organization: Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 10617, Taiwan |
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Breathomics is a special branch of metabolomics that quantifies volatile organic compounds (VOCs) from collected exhaled breath samples. Understanding... Breathomics is a special branch of metabolomics that quantifies volatile organic compounds (VOCs) from collected exhaled breath samples. Understanding how... |
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| SubjectTerms | Breath tests Data mining Database Tool Information processing Medical Subject Headings-MeSH Metabolomics VOCs Volatile organic compounds |
| Title | Human Breathomics Database |
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