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

Tips for programmers:


Examples of retrieving a custom report with a list of PDB IDs (or PDBId.ChainId) and report fields:

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: Display a custom report with primary citation and other column fields in XML format:
  • PDB ID: 1stp,2jef,1cdg
  • Fields: Structure Id, Release Date, Structure Author, PubMedId, Doi
  • PrimaryOnly: The primary citation indicator. Specify primaryOnly=1 will eliminate duplicate info from other citations.
http://www.rcsb.org/pdb/rest/customReport.xml?pdbids=1stp,2jef,1cdg&customReportColumns=structureId,releaseDate,structureAuthor,pubmedId,doi&primaryOnly=1
Example 3: Display a custom report with the following PDBIds.ChainId combinations and column fields in CSV format. The Chain Ids are case sensitive.
  • PDBId.ChainId list: 4HHB.A,2CPK.E,3WHM.B,2D5Z.A
  • Fields: Cluster Number for 100% sequence similarity, Cluster Number for 90% sequence similarity, Cluster Number for 70% sequence similarity, UniProt Recommended Name, Gene Names, Taxonomy ID, Taxonomy, Chain Length
http://www.rcsb.org/pdb/rest/customReport.xml?pdbids=4HHB.A.,2CPK.E,3WHM.B,2D5Z.A&customReportColumns=chainLength,clusterNumber100,clusterNumber90,clusterNumber70,uniprotRecommendedName,geneName,taxonomyId,taxonomy&service=wsfile&format=csv
Example 4: 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
Example 5: Download a predefined summary report of all current PDB entries in CSV format. A list of report name can be found in this page.
  • PDB ID: *
  • Report Name: Sequence
http://www.rcsb.org/pdb/rest/customReport.csv?pdbids=*&reportName=Sequence&service=wsfile&format=csv


Please follow the steps below to make sure that the query parameters are supported and up to date.

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 let's POST this query against the Web Service:


Results will go here:
 

Generate field name list in query string

The query URL 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: