Tool Overview

SynBio Search is an online tool that generates data sheets for over 2700 biological parts by aggregating data from various publicly available resources. It integrates and links information from various data sources, including the Registry of Standard Biological Parts, the iGEM Archive, Google Scholar, and PubMed. SynBio Search builds on the collected sources by providing a structured view that relates heterogeneous information, links back to original data sources, and allows users to customize and organize the display. It enables researchers to discover the most comprehensive view of freely available data about biological parts from a single online search. SynBio Search allows users to search by keyword (e.g. tuberculosis) or by part name.

Implementation

As a web application, SynBio Search was implemented using multiple platforms. Information is gathered by crawling through multiple databases using CGI scripts written in Ruby. The search results are then outputted into JSON files; once the files are parsed using JavaScript and jQuery, the information is displayed in a clear and logical format on a web page for the user to access.

Purpose

While there are already several search engines for synthetic biology, none are exactly what users neither want nor need. For example, many iGEM participants and biology scientists and engineers use the Registry of Standard Biological Parts to document their experience on new or previously made biological parts. However, the Registry is poorly organized, information is hard to locate, and certain data are missing. Thus, the purpose of our project is to create a resource that is not only qualitatively and quantitatively comprehensive, but also more accessible to users. It collects results from multiple data sources, allowing users to view more complete information in an organized and efficient manner.

The home page of SynBio Search where users can query by keyword or by part name.

The results page when the keyword "diabetes" is searched.

The data sheet produced for the part BBa I14018: The part's summary is displayed at the top.

The data sheet for part BBa I14018: Users can customize their data sheet to only display the references.

Results

SynBio Search study results...

An example of a collection showing parts, vectors, and features

A DNA sequence opened in sequence viewer with features highlighted.

Demo Video

Future Work

• Include more information in the data sheet for each part, such as chassis, regulation, strength, and twins.
• Attain search results for Google Scholar in a similar format as those for the Parts Registry.
• Evaluate the effectiveness of the SynBio Search relative to other synthetic biology search engines.