9th National Level Science Symposium. February 24, 2016
Organized by Christ College, Rajkot
dbVBM: DATABASE FOR VITAMINS AND BIOMINERALS
Thakker1,2, Kajal S. Thakkar1,2, John J Georrge1*
1
Department of Bioinformatics, Christ College, Rajkot-360 005, Gujarat
2
. Faculty of Technology and Applied Mathematics, MS University, Baroda, Gujarat
*Corresponding author: johnjgeorrge@gmail.com
ABSTRACT: A vitamin is an organic compound required as a nutrient in tiny amounts by an
organism. When vitamin cannot be synthesized in sufficient quantities by an organism, and
must be obtained from the diet. The dietary focus on biominerals derives forms an interest in
supporting the biochemical reactions of metabolism with the required elemental components.
Appropriate intake levels of certain chemical elements are thus required to maintain optimal
health. dbVBM is a database which provides all necessary information about vitamins and
biominerals. It includes the information like properties, history, function, deficiency, toxicity,
interaction with drug and nutrient.
Availability: http://www.christcollegerajkot.edu.in/dbvbm/index.html
Keywords: Vitamins, Biominerals, deficiency, toxicity
1. INTRODUCTION
The term vitamin is derived from the words vital and amine, because vitamins are required for life and were
originally thought to be amines. Although not all vitamins are amines, they are organic compounds required by
humans in small amounts from the diet. An organic compound is considered as a vitamin if a lack of that compound
in the diet results in overt symptoms of deficiency. Vitamins are classified based on their solubility; they are either
water-soluble or fat soluble (Table 1) (Nancy P.B et al. 4th Ed). There are many databases available for vitamins
(Table 2), which have their own merits and demerits. Most of the available databases are not updated regularly or
URL is not operational or sufficient information about each vitamin is not included.
Minerals formed from the remains, or as a result of the metabolic activity, of long-dead organisms are known
as Biominerals. Biominerals are the chemical elements required by living organisms, other than the four elements
carbon, hydrogen, nitrogen, and oxygen present in common organic molecules. The minerals may be naturally
present in the food (e.g., calcium in dairy milk) or added to the food (e.g., orange juice fortified with calcium, salt
fortified with iodine, iodized salt). Biominerals cannot be made in the body and must be obtained from our diet.
The daily requirements of minerals required by the body can be obtained from a well-balanced diet. Dietary
supplements can provide several different minerals, a combination of vitamins and minerals, or a single mineral,
such as calcium or magnesium (Nancy P.B et al. 4th Ed). The dietary focus on biominerals derives from an interest
in supporting the biochemical reactions of metabolism with the required elemental components (Lippard et al.
1994). Appropriate intake levels of certain chemical elements are thus required to maintain optimal health.
Biominerals provide structure in forming bones and teeth, help to maintain normal heart rhythm, muscle
contractility, neural conductivity, and acid-base balance, and it helps to regulate cellular metabolism by becoming
part of enzymes and hormones that modulate cellular activity. Like vitamins, excess minerals can produce toxic
effects (Brody T. 1999 & McARDLE, W.D. et al. 2000). Approximately 4% of the body's mass consists of
minerals. They are classified as trace minerals or micro minerals (body requires less than 100 mg/day), and major
minerals or macro minerals (body requires more than 100 mg/day) (Table 3).
Macro-minerals are nutrients, which help the body perform numerous functions, such as building strong
bones, transmitting nerve impulses, making hormones and maintaining a regular heartbeat. Trace elements (or
trace minerals) are usually defined as minerals that are required in amounts between 1 to 100 mg/day by adults or
9th National Level Science Symposium. February 24, 2016
Organized by Christ College, Rajkot
make up less than 0.01 percent of total body weight. Ultra-trace minerals generally are defined as minerals that
are required in amounts less than 1 mg/day (McARDLE, W.D. et al. 2000 & Minerals.2012). There are many
minerals / biominerals database are available (Table 4), which have many shortcomings. Most of the available
databases are not included sufficient biological information.
Various databases and tools were developed to store and analyze the data in the bioinformatics and
cheminformatics fields (Sharma et al., 2014; Ukani, Purohit, Georrge, Paul, & Singh, 2011). Also, various novel
approaches adapted in various bio and cheminformatics work (John J Georrge & Umrania, 2011; J. J. Georrge &
Umrania, 2012; John, John, & Kholia, 2012; Rohitkumar & John, 2015; Vaishnav, Gupta, Paul, & John, 2015). In
this information era, every individual need to know the basic information, disease due to deficiency / over dose,
daily recommended allowance, natural source of vitamins and biominerals, etc.. The biomedical researcher may
be interested in the detailed information of each vitamin and biomineral like physical and chemical properties, 2D
and 3D structure, molecular weight, chemical file format, etc. The online database dbVBM is designed as a user
friendly and rectification of all shortcomings of available databases and provides best solution to the ordinary
individuals, to the doctors and researchers. The data available in this database are trust worthy since it is mainly
curated from literature. Hence, all available data having cross reference with literature evidence.
2. MATERIAL AND METHODS
dbVBM contains range of information about physical and chemical properties, descriptors, recommended daily
allowance, upper taken level, food source, images of scientists, food sources and pathology condition, and many
more. Significantly, 2D structure of molecules can be visualized. Also 2D and 3D structure of molecules can be
downloaded in specific chemical file formats. The database includes 23 vitamins (Table 1) and 24 biominerals
(Table 3) with easy search options.
The overall construction strategy of this database is shown in Fig. 1. It was constructed in MySQL
(http://www.mysql.com/) for easy access and portability. MySQL is an open source relational database
management system (RDBMS) (Schumacher et al. 2011). MySQL front-end tools, MySQL Workbench
(http://dev.mysql.com/downloads/workbench/) was used to create and manage MySQL databases, build database
structures, back up data, inspect status, and work with data records. The MySQL Workbench is a free integrated
environment developed by MySQL AB that enables users to graphically administer MySQL databases and visually
design database structures. MySQL Workbench. 12 tables for vitamin and 13 tables for biominerals were created
in MySQL, which includes cross reference databases, physical and general properties, structural properties,
isotopic properties, descriptors, basic information, recommended daily allowance, upper taken level, food source,
history image, and food source image.
The web interface was designed by PHP (http://www.php.net/). It is an open source general-purpose serverside scripting language originally designed for web development to produce dynamic web pages. It is one of the
first developed server-side scripting languages to be embedded into an HTML source document rather than calling
an external file to process data (PHP Manual. 2012). The command ‘mysql_connect’ was used to open a
connection to a MySQL Server.
2.1. Data Input
The preliminary data was collected from numerous books, research articles and web resources. Detailed
information of each vitamin and biomineral was collected from different reliable chemical databases. Few of them
are PubChem (http://pubchem.ncbi.nlm.nih.gov) (Bolton E et al. 2008), ChEBI (www.ebi.ac.uk/chebi/)
(Degtyarenko K et al. 2009), ChemSpider (http://www.chemspider.com) (Antony J.W. 2008) and DrugBank
(www.drugbank.ca) (Knox C et al. 2011). All data for 23 vitamins and 24 biominerals was collected based on
MySQL table information. Apart from that, 3D structure of all molecules was retrieved in sdf (Structure Data
9th National Level Science Symposium. February 24, 2016
Organized by Christ College, Rajkot
Format) and pdb (Protein Data Bank) format.
2.2. Retrieval of Data
dbVBM provides easy search options from home page itself. Three levels of retrieval systems were
employed in this database. First, user need to select any one sub-database from available two options: vitamins
and biominerals. Secondly, subtypes of vitamin (water or fat soluble) or biomineral (macro or trace) need to be
selected. Thirdly, user can select any option from generic descriptor name, properties and information of vitamins
or biominerals. The database is designed such a ways that, user can easily switch over from one sub-database to
another
3.
RESULTS AND DISCUSSION
Constructed database comprised nearly all available vitamins and minerals with its detailed information. In this
database major features incorporated were general, physical, chemical, atomic and isotopic properties, history,
descriptors, function, occurrence, deficiency, overdose, recommended daily allowance, disease prevention and
treatment, upper intake level, drug interactions, food sources, stability, toxicity and many more. Results will
display the images of scientists, food sources and pathology condition where ever necessary. The download option
is available to download 2D and 3D structure of molecules with SDF and PDB file format.
This database also included few more sections from web portal are introduction, about dbVBM, references,
and suggestions. Introduction includes basic information on vitamins and biominerals, which aims to help
beginners and non-biologists. About dbVBM web page comprises basic information on the database and the
included data. Literature evidence for each vitamins and biominerals can be obtained from reference section,
which helps users for further detailed literature study. Users may send their views and suggestions through web
portal by simply filling the form which will be delivered to the database administrator.
The screenshot of constructed database is shown in Fig.2, which gives brief information about the database
with two sub-databases search option. Fig.3 elucidates the method of searching against the sub-database vitamin
and it displays the results at different level. Searching against the sub-database biominerals is described in Fig.4
with its result. Major advantages of dbVBM over other databases are user friendly, all available 23 vitamins and
24 biominerals were included. All information from fundamental to advance level about each molecule included.
It provided cross reference to other chemical databases ChEBI, ChemSpider, PubChem and DrugBank. Structure
download in chemical file format is another available special option. Functionality to add and edit data to the
database through user friendly web based portal facilities available to the researchers to update and maintain
database.
4. CONCLUSION
dbVBM database included all aspects of vitamins and biominerals required for the common man to scientific self.
It provides easy access of wide range of information and assist in data warehousing and data mining.
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9th National Level Science Symposium. February 24, 2016
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