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An Information Portal to 105097 Biological Macromolecular Structures

Custom Report Web Services

The RCSB PDB website provides pre-defined summary and customizable reports for query results. Web Services can also be used to generate reports. These reports are generated based on

  • PDB IDs: A list of PDB IDs
  • Report name: Summary reports use predefined fields related to the report subject
    or
    Field items: Any combination of fields selected by the user
  • Format (optional): Reports can be generated in XML, CSV, and Excel. Format is an optional parameter; XML is the default.

Retrieve a custom report with a list of PDB IDs and report fields:

Report Service:
Example 1: Display a custom report with the following PDB entries and column fields in XML format:
  • PDB ID: 1stp,2jef,1cdg
  • Fields: Structure Id, Structure Title, Experimental Technique
http://www.rcsb.org/pdb/rest/customReport.xml?pdbids=1stp,2jef,1cdg&customReportColumns=structureId,structureTitle,experimentalTechnique
Example 2: Download a custom report with all current PDB entries and selected column fields in CSV format by appending &format=csv&service=wsfile in the query parameters :
  • PDB ID: *
  • Fields: Structure Id, Structure Title, Experimental Technique
http://www.rcsb.org/pdb/rest/customReport.csv?pdbids=*&customReportColumns=structureId,structureTitle,experimentalTechnique&format=csv&service=wsfile
 

The RCSB PDB is always adding new fields and features to the custom tabular report. Please follow the steps below to make sure that the parameters are supported and up to date.

Step 1: Run a query to get a list of PDB ID (associated with a query id) for your report, or go to Step 2 for a report of all current PDB entries


Sample XML Queries:

The Query is displayed in the Textbox below

Example:
<orgPdbQuery>    
    <queryType>org.pdb.query.simple.UpAccessionIdQuery</queryType>
    <description>Simple query for a list of UniprotKB Accession IDs: P50225</description>   
    <accessionIdList>P50225</accessionIdList>
</orgPdbQuery>
 

Now POST this query against Web Services:


Sort results by:    
Matching PDB IDs will be displayed below; the custom report will reporting on these entries.
 


Step 2: Get a list of field name from custom or summary report list


Generate Report Fields:

Step 3: Specify the format (optional step)


The URL string containing a list of PDB IDs and report fields is displayed in the textbox below

Example:
http://www.rcsb.org/pdb/rest/customReport.csv?pdbids=1stp,2jef,1cdg&customReportColumns=structureId,structureTitle,experimentalTechnique&format=csv
 

Now POST this URL against Web Services for the report dataset



Results will go here:
 



Reports can be exported in in CSV, XML, or Excel format.






Examples: