Team:SJTU-Software/Database

3. Database

Here, we have reconstructed the database of the current existing biobricks. All the necessary information available on the Registry are collected and used to construct our own database. In this part, the source of data, the way of data collection, database structure and some facts of the biobricks in the database are introduced.

3.1.1 Data collection

Data are collected from 5 different websites on the Registry and Google Scholar.
The data needed in the reconstructed biobrick database is available from 5 sources, with four of them from the websites of Registry of Standard Biological Parts and 1 of them from Google Scholar. Addresses of those sources for BBa_B0034 are listed in Table 2.1.1, and the part name could be replaced by any biobrick.

　

Name of Websites	Address
XML format	http://parts.igem.org/cgi/xml/part.cgi?part=BBa_B0034
Hard information	http://parts.igem.org/cgi/partsdb/part_info.cgi?part_name=BBa_B0034
Get part	http://parts.igem.org/partsdb/get_part.cgi?part=BBa_B0034
Experience	http://parts.igem.org/Part:BBa_B0034:Experience
Google scholar	http://scholar.google.com.cn/scholar?q=BBa_B0034

Table 2.1.1 Sources of the data in the biobrick database, using BBa_B0034 as an example

PERL scripts are composed to connect to those links and to pick out the information we need. In order to connect to those links, we need to understand the way how biobricks on the website are named. There exist two main ways to name the biobricks, which are illustrated in Table 2.1.2 and Table 2.1.3. “BBa” is used for most biobricks, names of which consist of 3 parts. The first part is “BBa_”; the second part is a capitalized letter; the third part is several digits, the number of which depends on the previous capitalized letter (possible combinations are listed in Table 2.1.2). “pSB” is specially used for plasmids, names of which consist of 4 parts. The first part is “pSB”; the second part is one digit ranging from 1 to 9; the third part is a single pattern or a combination of two patterns listed; the fourth part can be any number from 1 to 29.

　

The First Part of the Name	The Second Part of the Name	The Third Part of the Name (Number of Digits)	Examples
BBa_
	A	6	BBa_A340620
	B	4	BBa_B0034
	C	4/5/6	BBa_C0053; BBa_C10001
	E	4	BBa_E5504
	F	4	BBa_F2622
	G	4/5	BBa_G0011; BBa_G00500
	I	4/5/6	BBa_I10018
	J	4/5/6	BBa_J52100; BBa_J540013
	K	6/7	BBa_K374013; BBa_K1218016
	M	4/5	BBa_M1904; BBa_M31000
	P	4	BBa_P2007
	Q	5/6	BBa_Q200514
	R	4	BBa_R4037
	S	5	BBa_S01297
	T	4	BBa_T1009
	V	4	BBa_V1022
	Y	5	BBa_Y00100
Z	4/5	BBa_Z0506; BBa_Z52935

Z 4/5 BBa_Z0506; BBa_Z52935 Table 2.1.2 Rules in naming biobricks starting with “BBa_”

3.1. 2 Database Structure

The structure of the database is presented in Figure 3.1. The primary key in table “Main” is “part name”, with all the other tables linked to it by identical “part name”. There is no primary key in the tables except “Main” because biobricks could belong to more than one category or have more than one twins. Thus, the part name in the rest tables could be repeated for several times, depending on different biobricks.

Figure 3.1 The structure of the reconstructed biobrick database