The Tabular Report system provides a broad view of PDB data and a friendly interface for users to browsing, filtering, and searching the data. Users can view data in various predefined standard reports or by creating customized reports with selected data items.
- Standard Reports vs. Custom Reports
- Rich User Interface
- Inline Filter vs. Filter Results
- One-to-Many Relationships in Report Tables
- Exporting to other formats
Standard Reports vs. Custom Reports
The tabular report system includes a list of pre-generated summary reports and links to custom reports. These reports are accessible from the Generate Reports pull down menu on the query result page. The pre-generated summary reports usually focus on certain aspect of the structures, such as Sequence Report, Ligands Report, etc. With these standard reports, users can quickly view the data with one mouse click.
The tabular report system contains the curated structural data and data from external resources, such as GO, SIFTS, and BindingDB, etc. Data items have been categoried as structure based and entity based.
Some users may want to have a report containing data items from multiple standard reports or specially want to include Domain details, they can select "Tabular Report" from the drop down menu to link to Custom Tabular Report, and then select the interested items and generate a custom report.
Rich User Interface
A rich user interface supporting large data set has been implemented. User can easily browsing, sorting, filtering, searching, and exporting data.
Pagination and Bidirectional Sorting
Instead of including all structures in a report on a single page, reports are now available on multiple, customizable pages. By default, the first 20 records sorted by PDB ID will be rendered. The user can page through the report using the navigation bar. There is an option to list 5, 10, 20, 50, 100, 1000 records per page.
Table sorts can be done on the entire report by clicking the column headers. Two yellow triangles are displayed in the current sorted column. The screen shot below is a Structure Summary report sorted by Resolution column.
The Customize Columns button at the bottom of the table enables users to select and reorder columns for display. Clicking Customize Columns will open a dialogue window as shown below.
The "Show/Hide Columns" interface allows users to specify which columns to display in the report. The columns listed on the left hand panel will be displayed in the report, while the ones listed on the right hand panel will be hidden. Clicking and will move a column between these two panels and make it to be displayed or hidden. Users can also reorder columns by dragging the columns with sign up and down.
In the example above, the following changes to columns have been made: The "NDB ID" has been moved to the right hand panel to hide it. The "Structure Author" column has been moved up next to "Structure Title" instead of being displayed as the last column.
- Hyperlink columns: Within the reports themselves, PDB IDs link to that entry's Structure Summary page, PubMed IDs link to the abstract, and Ligand IDs link to a Ligands Summary page. Other hyperlinkable columns are GO IDs (displayed based on three ontologies, molecular function, biological process, and cellular component) in Biological Details reports.
- Column resizable: All column widths are resizable by dragging the line between two columns.
- Report resizable: The report table is resizeable by dragging the triangle at the right bottom corner.
- Sorting entity based data: Sequence Report, Biological Details Report, and reports contain entity based data will always be sorted by the combination of the structure ID and chain IDs. Any entry with multiple chains will always be displayed with chain IDs sorted ascending, as PDB entry 1CF0 shown in the screen shot of Biological Details Report below.
Inline Filter vs. Filter Results
The Inline Filter feature provides an easy way for user to search the result set in the tabular report. User can input the criteria data in any text box, the records matching the data will be retrieved automatically. With the inline filter feature, user can quickly filter the result set without leaving the page.
The picture below illustrates a Structure Summary Report generated after the Text search "actin". And also two filter conditions have been applied on "Exp. Method" and "Classification" columns.
Compare to Inline Filter, the Filter Results feature provides more comprehensive options to refine a result set. Instead of going back to the Advanced Search interface to refine queries and to re-generate the report, they can explore the data in the report directly.
The picture below illustrates a report after the user conducted filter refinement. First, a Structure Summary Report was generated based on Text search "actin". Then the user was interested to see the "X-Ray structures with Resolution greater than 2.0".
Generally speaking, the inline filter conducts a "contains" search. Multiple inline filters can be combined. But for more complicated criteria, such as "greater than", "does not contain", etc. use the Filter Results form at the bottom of the table.
One-to-Many Relationships in Report Tables
Reports that have to display a lot of information for a single structure are formatted in a compact way. For example, a single structure may be associated with multiple GO IDs. The picture below is a screen shot of the Biological Details Report with three PDB entries.
In the Biological Details report, GO Term IDs are displayed based on three gene ontologies , molecular function, biological process, and cellular component.
Another example about one-to-many relationship is CATH, SCOP and PFAM in Domain details. They have been organized based on the combination of PDB ID and Chain ID. Residue ranges have been added to each CATH, SCOP, and PFAM domain. The Excel and CSV export will keep the one-to-many presentation.
Exporting to other formats
The report exporting feature has been greatly enhanced. Tables can be exported in three formats:
- Excel 97-2003 format: Multiple work sheets will be generated for very large data sets to accommodate the row limitation (65,536) in older versions of Excel.
- Excel 2007 or newer versions: This version supports up to 1,048,576 rows per work sheet.
- CSV: Comma Separated Value format (no limitations, recommended for extra large data sets)
The Excel spreadsheets have been reformatted with customized column width, text wrapping, alignment, and hyperlinks on selected columns. Formatting issues with PDB IDs that resemble floating point numbers such as 1E10 have been resolved.
Only the filtered result set will be exported to Excel or CSV, if user conducted a search using Inline Filter or Filter Results. And the presentation of one-to-many relationships is maintained in the exported Excel report.
Please contact us if, after reading the Tabular Report System explanations, additional help on generating report is needed.