Tuesday, 12 August 2008

PubChemSR makes it to top 10

In the 3 months since publication in Chemistry Central Journal, Junguk Hur and David Wild's paper on PubChemSR has shot up the Chemistry Central rankings and has now entered the top 10 most highly accessed papers of all time (that is, since Jan 2007). I should know, as I've watched it overtake my Pybel paper and squeeze me out of that same top 10, but not for long I hope. :-)

Here's the abstract:
Background
Recent years have seen an explosion in the amount of publicly available chemical and related biological information. A significant step has been the emergence of PubChem, which contains property information for millions of chemical structures, and acts as a repository of compounds and bioassay screening data for the NIH Roadmap. There is a strong need for tools designed for scientists that permit easy download and use of these data. We present one such tool, PubChemSR.

Implementation
PubChemSR (Search and Retrieve) is a freely available desktop application written for Windows using Microsoft .NET that is designed to assist scientists in search, retrieval and organization of chemical and biological data from the PubChem database. It employs SOAP web services made available by NCBI for extraction of information from PubChem.

Results and Discussion
The program supports a wide range of searching techniques, including queries based on assay or compound keywords and chemical substructures. Results can be examined individually or downloaded and exported in batch for use in other programs such as Microsoft Excel. We believe that PubChemSR makes it straightforward for researchers to utilize the chemical, biological and screening data available in PubChem. We present several examples of how it can be used.

3 comments:

Duncan Hull said...

Hi Noel, I can't see the point of a "Web" service if (as they say) "The major limitation of this approach is that the program can only be used in a Windows environment.

One of the web's great features is that it doesn't matter what client you are using. Also, if this is a SOAP-style service, is there a WSDL? Or am I missing something?

baoilleach said...

The web service is by PubChem and I'm sure has SOAP, WSDL, and all of that heavyweight stuff. This paper is about a program that uses the PubChem webservice to provide a nicer interface to PubChem (as I understand it).

Duncan Hull said...

Yes, I see now, I misunderstood. It is a windows-only application, that uses public services on the web (courtesy of NCBI). It would be nice if they could make it more webby, see comments over at friendfeed