Team:SJTU-Software/Database

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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 WebsitesAddress  
XML formathttp://parts.igem.org/cgi/xml/part.cgi?part=BBa_B0034  
Hard informationhttp://parts.igem.org/cgi/partsdb/part_info.cgi?part_name=BBa_B0034
Get parthttp://parts.igem.org/partsdb/get_part.cgi?part=BBa_B0034
Experiencehttp://parts.igem.org/Part:BBa_B0034:Experience
Google scholarhttp://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 NameThe Second Part of the NameThe Third Part of the Name (Number of Digits)Examples
BBa_  
A6BBa_A340620
B4BBa_B0034
C4/5/6BBa_C0053; BBa_C10001
E4BBa_E5504
F4BBa_F2622
G4/5BBa_G0011; BBa_G00500
I4/5/6BBa_I10018
J4/5/6BBa_J52100; BBa_J540013
K6/7BBa_K374013; BBa_K1218016
M4/5BBa_M1904; BBa_M31000
P4BBa_P2007
Q5/6BBa_Q200514
R4BBa_R4037
S5BBa_S01297
T4BBa_T1009
V4BBa_V1022
Y5BBa_Y00100
Z4/5BBa_Z0506; BBa_Z52935  

Table 2.1.2 Rules in naming biobricks starting with “BBa_”

 
The First Part of the NameThe Second Part of the NameThe Third Part of the Name The Fourth Part of the NameExamples  
pSB1~9A/C/E/G/K/N/Na/R/S/St/T/Tm/Z1~29pSB1K16
pSB1~9Combination of 2 letters above1~29pSB1K16  

Table 2.1.3 Rules in naming biobricks starting with “pSB”

By substituting the names listed in Table 2.1.2 and Table 2.1.3 for the part name (BBa_B0034) in the addresses listed in Table 2.1.1, we can get access to the links about the information on biobricks. Data that are collected by PERL scripts from each website are listed in Table 2.1.4. More detailed description of those data are available in Table 2.1.5. PERL scripts used to collect those data are available on GitHub.

 
Name of WebsitesAddress  
XML formatpart id; part name; part short name; part short description; part type; part status; sample status; part results; part nickname; part rating; part url; part entered; part author; Sequences; Samples; References; groups; deep subparts; specified subparts; specified subscars; features; parameters; categories; twins
Hard informationDNA status; Group Favorite; Whether or not deleted; Used Times; Length of Documentation
Get partConfirmed Times; Not Confirmed Details
ExperienceAverage Rating; Number of Comments
Google scholarNumber of Publication; URL of the most related publication  

Table 2.1.4 Data collected from the 5 sources

 
PropertyDescription  
part idOfficial name of the part
part nameBBa_B0034
part short namePart name without “BBa_”
part short descriptionThe short description is usually a biological or technical descriptor of the part. It will show up on the part page
part typeThis will state the part type/function, and will show up at the top of the part page, to the left of the DNA Status
part status The status of the part based on the completeness of its documentation and characterization.system not currently in place
sample statusThe status of the part's physical DNA (sample) in the Repository
part resultsThe experience status for a part, as documented by the part authors
part nicknameNickname of the part
part ratingWhether there is a registry star for the part
part urlURL of main page for the part
part enteredEntered date of the part
part authorAuthor of the part
SequencesNucleotide sequence of the part
SamplesIt’s not enabled now
ReferencesIt’s not enabled now
GroupsIt’s not enabled now
deep subpartsAll subparts that compose the subparts in the part
specified subpartsAll subparts that compose the part
specified subscarsAll scars between subparts
FeaturesFeatures of the part
ParametersThe parameters are submitter-decided, allowing for a degree of technical specification for the part.
CategoriesCategories allow for a part to become content in automatically generated part tables, which is important in defining the organization of your part within the Registry, and specifically for the Catalog of Parts and Device
TwinsTwo or more parts are twins if they have the same sequence
DNA statusStates the DNA status of your part: Deleted, Planning, Sent, Available, etc. These statuses are generated by the Registry, so the user cannot edit them.
Group Favorite One can choose if the part is a favorite of your team/group.
Whether or not deletedWhether the part is deleted
Used TimesThe number of times the part has been specified in composite parts in the Registry
Confirmed TimesThe number of times the part sequence has been confirmed by users
Not Confirmed DetailsDetails of not confirmed facts
Average ratingThe mean value of rating for the part given by users
Number of CommentsThe number of comments from users
Number of PublicationThe number of related results of the part on Google Scholar
URL of the most related publicationThe most related result of the part on Google Scholar  

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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



3.1.3 Quick Facts about the Biobricks

Here are figures counting the number of the values of some important attributes judging the quality of the biobricks.



iGemdry2014@163.com

SJTU-Software,Shanghai,China

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