Creating a Biomarker Database for Future Teams
After our team set up the goal to detect endometriosis non-invasively, our wet lab team began to identify potential biomarkers for endometriosis. To do so, we spent more than two months reading primary research articles and consulting professionals in the field; we also went through the Wiki pages of previous iGEM teams who also chose endometriosis as their project. Although we successfully identified biomarkers for our project, we found this searching process time consuming, energy draining, and sometimes frustrating, as we cannot find enough information regarding the biomarker’s concentration, specificity, or standardized detection method. Meanwhile, we noticed that, from 2016 to 2020, on average 26 iGEM teams per year selected the diagnostic track, and most of them could not avoid the process of identifying biomarkers. In addition, although many teams tried to diagnose the same disease, they did not benefit from previous teams’ findings, as the processes of identifying biomarkers were not always well documented on their Wiki. Considering these situations, we have created a biomarker database where iGEM teams can store their information about biomarkers as a resource for future iGEM teams who work on the same topic.
In summary, we created an online database integrated in a website that has four pages: Home page, Browse page, Contribution page, and About page. Home page will tell the user that biomarker database is created for iGEM teams; Browse page will display all 11 variables and allow users to search for their biomarker information by keywords; Contribution page will allow users to add new biomarker information to the database; and About page will have an introduction of this database as well as our contact information.
Below are the introductions to each website page.
Figure 1: Home Page
Figure 1 shows the Home page. On the left, it shows the name of the website, biomarker database, and a sentence stating that the database is contributed by iGEM teams. On the right, there is an image describing a classic procedure of detecting biomarkers from a blood sample. On the top, there is a tap bar that directs users to the four web pages: Home page, Browse page, Contribute page, and About page.
Figure 2: Browse Page
Figure 2 shows the Browse page. The main data table is displayed at the center of this web page. The data table contains a Search function at the top right corner. This function will be introduced later in the Software Flow section. On the top left, it allows users to see how many entries, or number of biomarkers, are displayed on the data table. On the bottom left corner, it shows the number of biomarkers displayed and the total number of biomarkers in the database. The “Next” button on the bottom right allows users to change pages to view more biomarker information. In addition, below the data table is the Download function that allows users to download full information of the displayed biomarkers. This function will also be described in the Software Flow section.
Figure 3: Contribution Page
Figure 3 shows the Contribution page. It has a questionnaire containing 12 questions. By filling out the questionnaire and clicking the Submit button, users are able to add new biomarker information into the database.
Figure 4: About Page
Figure 4 shows the About page. This page contains an introduction of the database. This introduction states the designer, purpose, and function of the database. It also contains our contact information.
Robinson, M.-P., Ke, N., Lobstein, J., Peterson, C., Szkodny, A., Mansell, T. J., Tuckey, C., Riggs, P. D., Colussi, P. A., Noren, C. J., Taron, C. H., DeLisa, M. P., & Berkmen, M. (2015). Efficient expression of full-length antibodies in the cytoplasm of engineered bacteria. Nature Communications, 6(1), 8072. https://doi.org/10.1038/ncomms9072