Site utilization examples

The Charts website provides several layers of data visualization. The first bar chart that you will encounter when navigating through the data shows the number of annotations divided into annotation types. These sets generally correspond to different data providers in the case of protein level annotations. There are some cases where the data from a single provider naturally falls into well-separated sets. One exmple of this is for the Gene Ontology (GO). Data from GO is separated into Biological process, Cellular component, and Molecular function. The residue level annotation types are sequence annotation features as defined by UniProt. Only those annotation types that are naturally occuring are used. Annotations that are the result of experimental modifications or conditions are excluded at this time. These top level bar charts are further refined into a second tier of charts that visualize data from a single annotation type. These charts then give access to lists of structures with a given annotation.

Figure 1 shows the top protein level bar chart for PSI:Biology structures in a dashboard-like layout. There are 4 main areas of the dashboard: (1) the bar chart, (2) a table showing the data for the bar chart, (3) a category picker for choosing one or more annotation type of interest for the visualization, and (4) a range slider to constrain the values displayed in the visualization.

At the top of the dashboard is the bar chart panel (grey outline in Figure 1). This panel can be resized vertically by clicking and dragging on the lower right corner of the panel if the user would like to view more of the chart. Hovering over any of the bars will expose a balloon indicating the label and value of the bar. Clicking on the bar takes the user to the next level of detail for that label as demonstrated in the site utilization examples below.

Below the bar chart panel are 3 panels, the 2 controls panels on the left and the data table on the right (blue outline in Figure 1). The data table shows the information from the bar chart in tabular form. Clicking on any of the column headers in the table will sort the table according to that column. Clicking on an entry in the first column of a data table links the user to information about the entry.

The controls panel has two different methods of controlling the visualization. First, there is a category picker (red outline in Figure 1) that allows the user to choose particular annotations to visualize in the chart and data table. The user can begin typing in the box (auto-completion is enabled) or click for a drop-down list of available choices. Multiple aannotations can be chosen and will be listed as labels below the category picker as they are chosen. The user can remove any choice by clicking on the "x" in its label. Below the category picker is a horizontal slider (green outline in Figure 1) that can control the limits of the x axis. There is a thumb at the minimum and maximum value of the chart that can be adjusted. As with the category picker, all adjustments are reflected in both the bar chart and the data table.

Some charts have a large number of entries that would require a long time to load. The initial chart show limits the number of annotations shown to the highest 150 annotations. If there are more than 150 annotations for the chart, a link to the full list is given above the upper right corner of the chart. This full chart also contains a link in the same location for returning to the abbreviated chart.

Figure 1

Example of navigating protein level bar charts to mitochondrion related structures

In this example, we show the case where a user is interested in finding PSI:Biology structures associated with mitochondia at the entire protein level. The first step is to either click the link for protein level annotations under the PSI:Biology structures header on the home page (highlighted in Figure 2) or from the Coose bar chart menu item at the top of the page to navigate to the top protein level bar chart for PSI:Biology (Figure 3). There is a GO term mitochondion that is assigned to structures under the GO Cellular component ontology. By clicking on the bar chart bar for GO Cellular Component (as indicated by the cursor arrow in Figure 3), the user navigates to the second tier bar chart for all GO Cellular component annotations (Figure 4). You will notice that a baloon will pop up indicating the name and value from the data table for the bar hovered over. The user can then click on the bar for mitochondrion to retrieve a ranked list of structures in the KB-Rank tool that have that annotation (indicated by the arrow in Figure 4). The user can also retrieve an unordered list of structures by clicking the number link in the table column Number of structural chains at the mitochondrion row (yellow arrow in Figure 4). This unordered list contains links to the SBKB page for each structure.

Figure 2

Figure 3

Figure 4

Example of navigating residue level bar charts to mitochondrion related structures

In this example, we show the case where a user is interested in finding PSI:Biology structures associated with mitochondia at the residue level. The first step is to either click the link for residue level annotations under the PSI:Biology structures header on the home page (highlighted in Figure 5) or from the Choose bar chart menu item at the top of the page to navigate to the top residue level bar chart for PSI:Biology (Figure 6). Transit peptides are resposible for the transport of a protein to mitochondria so the user would be interested in looking at the Transit peptide bar chart. Figure 6 shows the bar chart after the Transit peptide annotation type has been chosen in the category picker in the lower left of the screen. By clicking on the bar chart bar for Transit peptide (as indicated by the cursor arrow in Figure 6), the user navigates to the second tier bar chart for all GO Cellular component annotations (Figure 7). Again, you will notice that a baloon will pop up indicating the name and value from the data table for the bar hovered over. The user can then click on the bar for Mitochondrion to retrieve a ranked list of structures in the KB-Rank tool that have that annotation (indicated by the arrow in Figure 7). The user can also retrieve an unordered list of structures by clicking the number link in the table column Number of structural chains at the Mitochondrion row (yellow arrow in Figure 7). This list also indicates which residue numbers, as prescribed by UniProt, have the annotation. This unordered list contains links to the SBKB page for each structure.

Figure 5

Figure 6

Figure 7


All charts on this site utilize Google Charts.