TMDB: A literature-curated database for small molecular compounds found from tea
© Yue et al.; licensee BioMed Central Ltd. 2014
Received: 5 June 2014
Accepted: 8 September 2014
Published: 16 September 2014
Tea is one of the most consumed beverages worldwide. The healthy effects of tea are attributed to a wealthy of different chemical components from tea. Thousands of studies on the chemical constituents of tea had been reported. However, data from these individual reports have not been collected into a single database. The lack of a curated database of related information limits research in this field, and thus a cohesive database system should necessarily be constructed for data deposit and further application.
The Tea Metabolome database (TMDB), a manually curated and web-accessible database, was developed to provide detailed, searchable descriptions of small molecular compounds found in Camellia spp. esp. in the plant Camellia sinensis and compounds in its manufactured products (different kinds of tea infusion). TMDB is currently the most complete and comprehensive curated collection of tea compounds data in the world. It contains records for more than 1393 constituents found in tea with information gathered from 364 published books, journal articles, and electronic databases. It also contains experimental 1H NMR and 13C NMR data collected from the purified reference compounds or collected from other database resources such as HMDB. TMDB interface allows users to retrieve tea compounds entries by keyword search using compound name, formula, occurrence, and CAS register number. Each entry in the TMDB contains an average of 24 separate data fields including its original plant species, compound structure, formula, molecular weight, name, CAS registry number, compound types, compound uses including healthy benefits, reference literatures, NMR, MS data, and the corresponding ID from databases such as HMDB and Pubmed. Users can also contribute novel regulatory entries by using a web-based submission page. The TMDB database is freely accessible from the URL of http://pcsb.ahau.edu.cn:8080/TCDB/index.jsp. The TMDB is designed to address the broad needs of tea biochemists, natural products chemists, nutritionists, and members of tea related research community.
The TMDB database provides a solid platform for collection, standardization, and searching of compounds information found in tea. As such this database will be a comprehensive repository for tea biochemistry and tea health research community.
Different amounts of chemical constituents from the genus Camellia included in the major compounds databases or dictionaries
Number of compounds from Camellia (sinensis)
The Tea Metabolome Database will collect the small molecular compounds (MW < 2000 Da) found in tea and its related manufactured products.
Description, construction, content
Fundamentally, the TMDB is a multi-purpose biocheminformics database with focus on qualitative, analytic, and molecular scale description of the compounds from tea and their bioactivities. It combines enriched data from textbooks, journal articles, and other existing databases such as HMDB, Pubmed, etc. It also provides a large body of collected experimental data especially the original NMR spectra.
To compile, confirm, and validate the diverse data, the quantity and quality of experimental data, broad knowledge are needed to meet the difficult and time consuming task of constructing the TMDB. Thus, the team of TMDB includes eight tea biochemists and natural products chemists, two NMR specialists, and three bioinformticians with dual training in chemistry and computer science.
The TMDB currently contains more than 1473 compounds entries with more than 30,000 different data entry fields. The metabolic pathways for flavonoids, terpenoids, theanine, and caffeine are also provided. Hundreds of the compounds are linked to experimentally acquired or literature-sourced 1H, 13C NMR, data and the original NMR spectra as well.
Each compound entry contains averagely 24 data fields
3-O-Galloylepigallocatechin. Teatannin II. Epigallocatechin 3-gallate. EGCG
Green tea, Black tea, Oolong tea, Dark tea
Bao Guanhu, Zhu Yunfei
Shows anti-HIV activity. Tumour promotion inhibitor, putative cancer chemopreventive agent, affects tumour cell adhesion and invasion. Implicated in occup. asthma in green tea factories. Inhibits metalloproteinases
J. Chromatogr. A 2005,1083, 223–228; Phytochemistry 2006, 67, 1849–1855; Magn. Reson. Chem. 1996, 34, 887–890. (occur, nmr, ms)
1996. 2005. 2006
1H NMR data
1H NMR spectrum
13C NMR data
13C NMR spectrum
A key feature of TMDB is that it also provides searchable NMR data with the similarity identification which is highly valuable for the identification of metabolites from the crude extract and the tea metabolomics research.
User submit to TMDB
For user submissions, primary required fields are: 1) plant species, 2) compound name, 3) compound formula, 4) compound molecular weight, 5) compound structure, 6) NMR data, 7) MS data, 8) tea taxonomy, 9) reference. The curator(s) at our site conducts manual verification of the original publication(s) for data validation purposes to maintain the quality and integrity of the database. Submissions that pass this review process are then approved for entry into the TMDB database. Notably, all new submission will be made available in coming TMDB versions on a monthly release schedule.
The TMDB is essentially a web-friendly front-end to a sophisticated MSSQL server relational database (2008 R2). Both are maintained on a Windows server 2003 equipped with a 2 GHz CPU processor and 2 GB of RAM. JSP scripts are run every night to read selected portions of the MSSQL database and to write out the data into raw text and XML formats. The raw text is dynamically rendered into HTML (with images and hyperlinks) using a series of custom JSP scripts. It is a Java application that uses Apache Tomcat server 7.0 technologies such as Java server Pages (JSP) and Java servlets to manage web-based data input and data queries.
The tea metabolome database is defined as the first comprehensive collection of small molecular compounds found from tea. Constitution of the tea metabolome database depends on that a compound is found from tea or tea products including the original tea plant, the processed or manufactured tea. The molecular weight of a compound is below 2000 Da which excludes big molecules such as protein and polysaccharides. Currently, TMDB does not collect metals either. Tea compounds are first identified by literature surveys such as text books, Dictionary of Natural Products (DNP), HMDB, and most from original journal articles. Some of the data especially the NMR data and spectra are collected from experimental sources in our team (NMR experiments were carried out using a Bruker Avance 400 MHz NMR spectrometer, DMSO-d6, δ as ppm). If a compound is found to originate from tea and to be within the molecular weight limit, information about it is prepared by one member of our curation team and separately checked by other member of the team. Additional consistency checks of the information (molecular weight matches chemical formula, CAS number is correct, etc.) will be performed by senior natural products chemists. Every effort is being made to ensure the database is as complete, correct, and current as possible.
Compounds reported in different tea infusion and materials
Number of compounds reported
The Tea metabolome database project, reported herein, provides the initial groundwork for an ongoing program for cataloging and utilizing compounds information in tea. Notably, the current version is not as comprehensive as we envision future versions to be. Ongoing collection and curation of new publications related to the concentration and MS in formation of metabolites from tea and tea products is essential to this program’s success. New versions of the databases are currently scheduled to be released on a yearly basis, incorporating all new submissions to the database over the last month of the preceding year. This practice is expected to increase comprehensiveness and accessibility of the database, promoting broader interest from researchers worldwide.
We constructed the first comprehensive database for small molecular compounds from tea. The web-based program was created by manually reviewing widely scattered scientific literatures. This database, however, also provides a convenient submission interface for contribution of novel candidates by independent researchers. TMDB provides comprehensive, keyword-searchable tea compounds. Thus, TMDB will aid in rapid and complete exploration of the discovery of new compounds in tea and tea products, qualitative and quantitative analysis of tea products, standardization of the processing and manufacturing of tea and even chemical taxonomy of tea, serving as a valuable resource for future investigators in experimental chemistry and biochemistry concerned with commercial tea processing and characteristics.
Availability and requirements
Project name: TMDB: A literature-curated database for small molecular compounds found from tea.
Project home pages: http://pcsb.ahau.edu.cn:8080/TCDB/index.jsp.
Operating system(s): Platform independent.
License: Not required.
Any restrictions to use by non-academics: None.
YY and GC designed the software and website. ZZ, TX, XW initiated these studies. XL, TL, WW, and GL collected the materials, TY, XT, and GB designed the structure and filled in all data. GB designed and analyzed data and, with contributions from all authors, wrote the paper. All authors read and approved the final manuscript.
The research was supported by grants from the National “Twelfth Five-Year” basic research program of China (973, 2012CB722903), the National Natural Science Foundation of China (Grant Nos. 81170654/H0507), the National “Twelfth Five-Year” Technology Support Program of China (2011BAD01B01), and Anhui Agricultural University Talents Foundation (YJ2011-06), Major program of Acquisition of Academy Lead talent and team in Anhui Province Special Projects on Science and Technology of Anhui province (13Z03012) and Program for Changjiang Scholars and Innovative Research Team in University IRT110. Funding to pay the Open Access publication charges for this article was provided by the above grants.
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