Team:SJTU-Software/Database/AssessmentModel

3. Assessment Model

An assessment model is optimized to judge the quality of biobricks. With a default score given to each biobrick respectively, biobricks that are related to the input keyword in the “Easy BBK” search engine can be listed in descending order of scores although users can define their own sorting order. If sorted by default scores, users can always get biobricks with high quality. Our assessment model considered 4 general properties, namely status, reliability, feedback and publication, based on 12 attributes of a biobrick. Weights of the attributes in the general properties are already optimized and fixed; weights of the 4 general properties can be adjusted by users although default weights of the properties are optimized already and recommended to users.

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.

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