Database Standardization
Two main focuses of our project was the organization of the available information about Biobricks on iGEM’s website and development of a software application to help synthetic biologists at the experimental set-up level by providing all available construct combinations for any given input and output relations ,which they can utilize for their own project.
Normalization and re-organization of the part information at iGEM’s web site was needed in order to develop our application, which will automatically search the possible construct combinations. For the organization and analysis of the Biobricks, we used part info for Spring 2010 distribution. The information on all three 384 well plates distributed by iGEM scrutinized and checked individually to specify the standards available and needed. iGEM is providing so many parts within a hierarchical way, but there is no order in the information flow and no common standards. Furthermore, the information bulk is being used in an ineffective manner. Some of the parts distributed are known to be nonfunctional. Web pages for parts contain lots of information, but majority of them, are again not ordered. Moreover, some additional information had to be removed or replaced in such a way that the information for parts can be used effectively. And removal of the redundant bulk information related with parts at iGEM’s web site had been recommended for future.
Although, the final standardization, which we have suggested is not for general public use and it was urgently needed in order to satisfy the needs of our algorithm. But, still it will be a valuable resource, since it summarizes the basic information about the parts.
As the first step to build the proposed standardization template, the headings selected related to parts are listed on Table 1. Submission of part IDs for individual parts is an accepted and quite valuable way of tracking information. Although, every part has unique partID, for every part there is a need to assign unique part names as official iGEM names. Part names will have an important role as they will be providing the short description about the part, which synthetic biologists can immediately recognize and utilize during the construction of unique Biobricks. Additionally unique part names will be helpful to identify the devices with more than one Biobrick in their constructs. Assignment of unique and distinct names for parts describing their nature and content will be helpful to researchers for the recognition of and search for the parts.
Headings Selected From Previous Entry Forms for Indication of Standardized Information
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PartID:
PartName:
Bricks:
BrickIDs:
ImageIDs:
RFC10:
RFC21:
RFC23:
RFC25:
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Table 1: The table above basically describes and designates qualities of parts which identifies their compositions and demonstrates the status of previously assigned standards. PartID refers to the unique ID number for parts including atomic parts and assemblies. PartName refers to the given unique names to parts. Bricks, refers to the shortcut names which specifies atomic parts. ImageIDs, refers to individual or combination of numbers that are assigned by us. RFCs refers to the states of parts based on RFC standards.
iGEM both provides individual, atomic parts and pre-combined constructs such as devices and systems. Availability of combined constructs is important to the researchers as combining individual bio-bricks one at a time will be very time consuming. These previously merged constructs, serve as the repository for puzzle and they can be used for different purposes. Up to date the largest and most trustworthy source, for synthetic biology and its components, is iGEM’s parts registry. In 2010, iGEM provided over 1000 parts that have initiated many projects. Having more atomic parts available in the iGEM’s repository, will lead to the design of more complex and robust constructs, and we would have a better chance to design different constructs for unique purposes. Also, for the parts that are already available, extra steps needs to be taken for the quality control and surveillance of these products. The quality control of the information for the parts is essential for the future of iGEM and synthetic biology. Even though we have found pre-determined RFC standards useful and included those to our standardized template, some individual parts still requires re-organization of the information as RFC standards alone for the functionality of parts, does not satisfy the needs for wet lab biologists.
Without a question there is an urgent need to build a distinct and specific database well organized with its own standards for synthetic biology; however, development of such a database is not an easy task.
Contact Information of Part Owners and Qualitative Group Comments about Parts
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Designers: Mail:
GroupFavorite:
StarRating:
Parameters:
Table 2: The above table simply depicts information about possessors of parts and their contact information and the popularity of the parts for groups. Parameters heading, refers distinctive experimental details unique to the usage of parts which should be decided by groups.
Second step for building the standardized template was to get the phylogenic information about the parts development process which includes the name of the group, designer and contact information, along with the comments from the group on the parts they have submitted. Contact information is especially important for iGEM as other groups who need extra information about the available part can reach to the required information. Even though contacting with the designers of the individual parts which are available is highly encouraged by iGEM, unavailability of contact information points at out the fact that iGEM’s parts registry needs strong re-organization in order to serve to the synthetic biology community properly.
Additionally, the “group favorite” and “starRating” fields are also important for individual evaluation of the parts, which doesn’t get the deserved attention from the iGEM groups. “Group Favorite” defines the confidence on the part by the designer group. “StarRating” defines the related part in terms of popularity and usage efficiency among the groups. According to our observations, most groups are not aware of either of the fields or they are used incorrectly or ineffectively. For example for a part with a full reporter which is known to be functional and gives precise and expected results the StarRating should be at least 2 stars, but for most of the parts in 2010 distribution, it is very difficult to observe a part whose “StarRating” is above one. For quick determination of functionality of the parts these two evaluations are important so they have been included in the proposed standardization template. But, as they were not properly used up to now for the re-organization of the parts information during the development of our software application we had to include all parts to our queries regardless of their evaluations based on “Group Favorites” and “ StarRatings”