Last week PubChem announced their User Gateway SOAP Web Services layer (PUG SOAP). Quoted from the website

“PubChem’s PUG (Power User Gateway), documented elsewhere, is an XML-based interface suitable for low-level programmatic access to PubChem services, wherein data is exchanged through a relatively complex XML schema that is powerful but requires some expertise to use. PUG SOAP contains much of the same functionality, but broken down into simpler functions defined in a WSDL (, using the SOAP protocol ( for information exchange. ”

We have integrated the PubChem Structure Search capabilities on ChemSpider under the Search Tab or they are available directly via this URL:

This will bring you to a page showing an input image that will open up an applet where the user can either convert a chemical name, convert a SMILES or InCHI, upload a molfile or sketch a molecule.

Following input of the molecule the user can select from any of the variants of searching shown below.

Callout boxes will be added shortly to explain the various options as we are presently testing the system. We are having some teething problems at present and are investigating whether it is our implementation or not. For example, a full structure search on Chlorobenzene gives:

0 hits found in 0.33 seconds.
Search terms: SingleComponent AND NonIsotopic
NCBI C++ Exception: Error: SERIAL(CSerialException::eFail) “/net/napc02/vol/pubchem/Libraries-64/c++/src/serial/objistrxml.cpp”, line 2271: — line 1: error decoding base64Binary data Error: SERIAL(CSerialException::eFail) “/net/napc02/vol/pubchem/Libraries-64/c++/src/serial/member.cpp”, line 725: — error while reading structure ( at .BodyBody[]InputStructureBase64.structure)

PUG is only under beta-testing at present so we do expect some teething problems with the integration for the immediate future. From the website “Please note that PUG SOAP is in BETA TESTING mode right now, and as such it is subject to change without notice. While we have attempted to make what’s there fully functional, it’s possible that some things may not work. We welcome feedback and suggestions; please direct these to NCBI’s help desk at”

PUG offers a great opportunity to the community for deeper integration with PubChem and integration and reuse of their data. Excellent.

Stumble it!

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