Tuesday, August 2, 2011

Tabular Report Web Services at the RCSB PDB

I have fallen behind on describing new features of the RCSB PDB web site... Let me catch up! One of the features that I find useful for people who want to script the site is that each of the queries on the site (and there are many) can be represented by simple XML.

How can you find that XML? Once you have run a query, you can access your query history from the left-hand menu. (We might actually move this to the top in the next release to make this more visible, but that's a different story.) Under the Query Details menu you can find the XML.

Here is an example XML for a query. This one below would simply list all current protein structures.

So what can you do with this XML?  You can POST this using the Search Web Services and get back a list of matching PDB IDs for this query. This functionality has been available for a while. As a new feature of the current RCSB PDB website release, Chunxiao extended this service to allow Custom Reports in a few different file formats.

Custom Reports

I have mentioned these reports already in a previous blog entry. On the Web site these reports allow to obtain Image Collages,  pre-defined reports containing various fields, and exports to Excel to mention just a few of the available options.

As part of the new Web service  these reports allow to fetch various fields via XML, comma separated file, or as an Excel file. There are step by step instructions available for how to use this new feature. Happy scripting!