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 Evaluation criteria

Based on the description on the website of Registry of Standard Biological Parts and advice collected from our instructor, 13 attributes of biobricks are picked out as evaluation criteria in the assessment model.
Considering different aspects users frequently takes into account when choosing a biobrick, we deliberately divided these attributes into 4 properties, which are listed in Table 3.2.1.

　

Property	Description
Status	Will I get this official part? This property measures the availability of the part.
Reliability	Will this part work? This property measures the working quality of the part.
Feedback	What is the review of previous teams or experimenters for this part? This property collects the feedbacks of previous workers on the part.
Publication	How many publications are related to this part? This property contains the related results on Google Scholar.

Table 3.2.1 The four properties in the assessment model

More detailed description of the attributes in the properties are demonstrated in Table 3.2.2.

　

Property	Attribute	Description
Status
	Part Status	The status of a part based on the completeness of its documentation and characterization.
	DNA Status	States the DNA status of your part: Deleted, Planning, Sent, Available, etc. These statuses are generated by the Registry, so the user cannot edit them.
	Whether or not Deleted	Whether the part is deleted or not.
	Confirmed Times	Times of the sequence of the part being confirmed. Part samples are sequenced using the VF2 and VR primer sites on their plasmid backbones. Sequence results are then uploaded and compared to their target sequence (part's documented sequence) through Registry software.
	Length of Documentation	Length of documentation for the part on Registry
Reliability
	Part Results	The experience status for a part, as documented by the part authors. However, the part's experience is not a validation of the part by iGEM HQ.
	Star Rating	Stars given by Registry
	Group Favorite	Whether the part is a favorite of one team/group.
Feedback
	Used Times	The number of times the part has been specified in composite parts in the Registry.
	Average Rating	The average rating given for this part by other users.
	Number of Comments	Times being reviewed by other users.
Publication
	Number of Publication	Number of related literatures and webpages on Google scholar

Table 3.2.2 Detailed attributes in the assessment model

3.2.2 Scores given to the values in each criterion

There are two types of values in all the criteria: categorical variables (such as part status, part results, etc) and continuous variables (such as used times, average stars, etc).
For categorical variables, we give reasonable scores to different values in each criterion based on the researchers’ experience and description of the values.
For continuous variables, we normalize the values in those criteria using the following formula, so that all the continuous variables range from 0 to 1 like categorical variables:

Figure 3.1 The structure of the reconstructed biobrick database