DATA QUERY, REPORTING AND ACCESS

RCSB PDB BETA SITE FEATURES

I
n July 2004, the RCSB PDB released a reengineered beta site (pdbbeta.rcsb.org) for public testing. Some of the features of this site are described below.

Comments and suggestions about the beta site are welcomed at betafeedback@rcsb.org.

  • Query-by-Example in Structure Explorer Pages

    • The Structure Explorer page for any PDB entry can perform several "query-by-example" searches. Using the information available in a particular entry, structures containing the same data can be quickly found by clicking on that data item.

    For example, all other entries by a specific primary citation author can be found by clicking on the author's name. A search of the database for all structures in which the selected author appears in the citation will be presented in a Query Results Browser.

    Authors, Primary Citation Authors, Chemical Components, and GO, CATH, and SCOP classifications can all be used in "query-by-example" searches.


    Query-by-Example: Selecting the author name "Wüthrich, K."


    Returns all PDB entries with that author in the primary citation.


  • Detailed Help System

    • The beta site uses Macromedia® RoboHelp® software to offer detailed guidance for navigating the site and understanding the information available from the RCSB PDB. The integrated system organizes all the help pages on the site and offers a table of contents, index, and glossary on every page. These tools help users to access the rich content offered by the help pages.

    The help system launches into a separate browser window to allow users to access the help information and the beta site at the same time. Once users are in the RoboHelp system, they can access help on specific topics by browsing through the table of contents in the left hand menu. These topics include Getting Started, Deposit Data, Validate Data, Download Files, FTP Server, Search/Browse the Database, Query Results Browser, and Viewing Molecules.

    The Help link located at the top of the home page launches the system. Links to specific help features and topics (such as "How to Validate Data", "How to Search", and "Molecular Viewer Help") are located in the left hand navigation bars, menus and pages throughout the website. An introduction to using RoboHelp on the beta site is available.

    The Glossary offered by the help system provides definitions for terms related to structural biology, and is an excellent source of information.


    The beta site help system

  • New Customizable Tabular and Structure Reports

    • Customizable reports are now available as a new feature on the beta site. Users can select specific data items to display for individual structures or for a group of structures. These reports can be saved in a CSV format that can be opened in spreadsheet application programs.

    Individual customizable reports can consolidate information from the four major areas of the "Summarize" pulldown menu found on the 'Structure Explorer' page (Biology and Chemistry, Materials and Methods, Sequence Details and Structural Features). The report also can display information specific for the type of the experimental method (X-Ray and NMR). In addition, the report can also provide ligand details, SCOP and CATH classifications, and the primary citation. An option to generate a custom structure report can be found in the pulldown menu on the 'Structure Explorer' page for a single structure. These reports include images of the asymmetric and biological units. A PDF can be viewed and saved by clicking on the 'Print Page' link in the navigation bar at the top of the page.

    Reports for a set of structures can include information from a variety of areas, including Sequence, Ligands, Biological Details, and Experimental Details. After selecting the set of structures, these reports can be generated by using the "Customize Report" option from the "Report" pulldown menu on the 'Query Results Browser' page. The report generated can be sorted in ascending/descending order of any column by clicking on the column headers.

TIME-STAMPED COPIES OF PDB ARCHIVE AVAILABLE VIA FTP

S
tarting with January 2005, time-stamped yearly snapshots of the PDB Archive will be available from ftp://snapshots.rcsb.org/. It is hoped that these snapshots will provide readily identifiable data sets for research on the PDB archive.

Currently, the directory 20050106 is available. This directory contains the exact and complete contents of the FTP archive as it appeared on January 6, 2005. This includes the 29040 experimentally-determined coordinate files that were current (i.e., not obsolete) in PDB and mmCIF formats. Data in XML (PDBML) format are not included in this first snapshot, but will be made available on DVD in the near future. Subsequent snapshots on this FTP server will include data in PDB, mmCIF, and PDBML formats.

This snapshot follows the historical directory structure -- coordinate files are contained in subdirectories named after the two middle characters of the PDB ID, for example, 100d is found in the directory '00'.

The date and time stamp of each file indicates the last time the file was modified. Entries in the PDB archive have been processed by the three members of the wwPDB (RCSB, MSD-EBI, and PDBj).

WEBSITE STATISTICS

T
he PDB is available from several Web and FTP sites located around the world. Users are also invited to preview new features at the RCSB PDB beta test site, accessible at pdbbeta.rcsb.org.

The access statistics are given below for the primary RCSB PDB website at www.pdb.org.