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The Connection phenotype represents a new information product assembled from the data pairs of the Universal Biology Database. A systems biology assembled from connection phenotypes produces an information system capable of capturing and managing vast amounts of biological complexity.

Introduction...

This work screen uses a series of picture buttons to assemble connection phenotypes. A good way to begin is to read through the worked example – click on the Read button.

When assembling a connection phenotype, we want to match - one for one - the control and experimental data pairs. Often this requires identifying specific control and experimental data pairs within a larger data set. A simple way of doing this is to mark each row individually. This can be done with this screen by clicking on the Mark box or typing in <yes>.

Let's work through some of the steps required to assemble a connection phenotype for diabetes. In the Exposure field, type in <like %diabetes%> and click on the Retrieve button.

The query returns 58 rows of data pairs. To display the results as a scrolling screen, click on the view data button.

Next, click on the sort button.

Clicking on the sort button opens this response screen. Find the citation number (cit_nu) in the list of columns at the left and drag it to the right as shown. Click on the OK button. This will sort the rows by the citation number. We will use these numbers to collect matching data pairs for the controls.

Now the rows are sorted by citation number. Write the unique number of each citation (Cit Nu) on a piece of paper (e.g., 237, 2247, 3056, 3261).

Click on the picture button of the SQL-Control and enter the numbers of the citations into the Cit Nu field: <in (237, 2247, 3056, 3261)>. Click on the Retrieve button.

Following the search on the citation numbers, click on the view data button. Note the equation number (DRE) column highlighted in black. Count the number of times a given DRE appears and enter it into the table illustrated in the next slide.

Enter the DRE counts from the previous screen (SQL-CO) here - under the column marked C. Repeat the procedure for the experimental data (SQL-EX) – see next slide. In turn, these data - when entered into an Excel worksheet - generate the connection phenotype (see the read document for further details).

Return to the SQL-EX screen, sort the rows by the DRE number, count the DREs, and enter them into the same connection phenotype worksheet under the columns marked E.

This connect-the-dots worksheet analyzes the results of an exposure by connecting the data pair of the control to the matching one of the experimental. This detects any changes that may have occurred in the proportions of the parts. The second part of the analysis uses the Stereology Literature Database to look for changes in the amounts of the parts. In this way, we can define the complexity of a biological change mathematically as a function of the proportions and the amounts of the parts.

Let's look at the amounts. Click on the SLD-EX picture button. Enter the citation number (Cit Nu) <2247> into the data entry field and press Enter. Then click on the button marked cc (cell compartment). When yes appears under the column labeled <0.05, the value immediately to the left is significantly different from the control.

The read document describes in detail the procedure for assembling a connection phenotype. This slide shows the transfer of data from the SQL-EX screen to the worksheet and from the worksheet to Excel.

Next, columns are highlighted in Excel and the graph of a connection phenotype is drawn.

Finally, the control (blue=normal) and experimental (red=diabetes) curves are displayed. One can readily identify changes in the parts visually and numerically with the either the 1/2 screen option (shown below) or the connect-the-dots worksheet.

Connection Phenotypes