Latest PubChem News: Reaxys Integration, RESTful Interface, and Improved BioAssay Summaries

[tweetmeme source=”Intellogist” only_single=false] Last time we looked at the free chemical search platform PubChem, structures from the Therapeutic Target Database (TTD) and structures from IBM BAO (Business Analytics and Optimization) strategic IP insight platform (SIIP) became accessible through the portal.  Further updates related to system access and information display have taken place since March 2012, including an integration of PubChem onto the Reaxys platform,  a beta release of a RESTful web interface to PubChem data and services, and new information and display features on the PubChem BioAssay summary pages.  PubChem is a useful free resource for patent searchers conducting chemical prior art searches, both as a source of reference information and as a search resource (since the IBM structures on the platform are linked to patents and scientific literature).  Professional patent searchers will use a combination of subscription search systems, such as STN, and free resources like PubChem to conduct a comprehensive chemical prior art search.  It therefore helps to stay up-to-date on the latest news about central free resources like PubChem.

After the jump, learn about major updates to the access and viewing options for PubChem!

March 2012- PubChem is now accessible through Reaxys, a (subscription-based) chemical search, analysis and workflow tool. According to the Reaxys website:

[PubChem’s] integration with Reaxys means that a single structure search yields results in Reaxys and PubChem in parallel, with the results presented in the familiar Reaxys interface. TOC headers are hyperlinked to PubChem so you can directly access PubChem from Reaxys.

April 2012- According to PubChem Announcements:

PubChem PUG REST is a RESTful web interface to PubChem data and services. Documentation and examples are available here. This service is considered to be in a beta state right now, meaning it is under active development and some changes may occur but the interface should be mostly stable. The purpose of this beta release is to make some basic functionality available now, and to invite feedback from the PubChem user community. Please try it out and tell us what you think; contact with questions, problems, or suggestions for new features.

The documentation for PUG REST, available on the PubChem website (see the above link), describes how to construct search queries through HTTP requests and how to access other search and display features by altering the URL.

June 2012-  According to the PubChem Announcements:

The PubChem BioAssay summary pages now display the Gene Ontology (GO) classification of the gene/protein target(s) that were tested by the bioassay. The GO terms are associated with each gene/protein in an automated way as part of the biosystems database data processing procedures, using the method described in the Biosystems help document. All GO terms that apply to the gene(s)/protein(s) tested by the bioassay are shown in the GO hierarchy, including: (1) biological processes, (2) cellular components, and (3) molecular functions. Clicking on any GO term in the hierarchy will retrieve all bioassays that have tested a protein(s) associated with that term. As an example, see the GO terms for the protein target that was tested by the glucocorticoid receptor (GR) redistribution assay (AID 450).

The Gene Ontology classifications displayed on a PubChem BioAssay summary page.

In addition, the PubChem BioAssay data summary for a compound now displays a graphical summary of the bioassays that have tested the compound, categorizing the bioassays by: (1) bioactivity outcomes (active, inactive, inconclusive, unspecified); (2) top targets; (3) bioactivity types (IC50, EC50, Potency, Ki, etc.); (4) bioassay types (screening, confirmatory, summary, other). The bar graphs are clickable and serve as filters to display data from the selected category, refreshing both the bar graphs and the tabular summary of bioassays to reflect the data subset you have selected. As an example, see the bioassay data summary for aspirin (CID 2244).

A graphical summary of the bioassays that have tested the compound on a BioAssay summary page.


Although these updates may only be of minor use to professional patent searchers, the new interface options do offer time-saving shortcuts for users who have a Reaxys subscription or users who are comfortable searching through a RESTful web interface.  Anyone who uses Reaxys can conduct a chemical search simultaneously in the Reaxys database and through PubChem, thereby saving the searcher the time of conducting two separate searches.  The new RESTful interface for PubChem allows users to craft queries directly within the URL path, thereby acting as a sort of command line interface that saves the user the time of manipulating fielded search forms to craft the correct query. The addition of Gene Ontology classifications to PubChem BioAssay summary pages may help the user broaden or narrow their query with additional relevant terms if they utilize the BioAssay summary pages as a source of reference material.  The addition of graphical summaries to the BioAssay summary pages will guide the user to more rapidly comprehend the information summarized on the page.  Patent searchers can leverage these small improvements to important search resources to help them increase the efficiency and accuracy of their prior art searches.

Do you know of any other recent improvements to PubChem or another NCBI Entrez resource that you think should be highlighted in a blog post?  Let us know in the comments!

Technical Translations from Landon IP

This post was contributed by Joelle Mornini. The Intellogist blog is provided for free by Intellogist’s parent company Landon IP, a major provider of patent searches, trademark searches, technical translations, and information retrieval services.

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