The Latest Data Updates on PubChem

[tweetmeme source=”Intellogist” only_single=false] The National Institute of Health first released PubChem in 2004, and today PubChem is an important free chemical search platform for patent searchers and other chemical researchers.  According to the “About” section, PubChem allows users to search for “information on the biological activities of small molecules,” and the chemical structures link to other Entrez resources, like PubMed scientific literature. This winter, two new data sources were added to PubChem, and patent searchers looking for prior art in the pharmaceutical and biotechnology fields may find useful data from both resources.

Continue reading for an overview on PubChem and a look at the latest updates to PubChem data coverage!

About PubChem

PubChem is made up of “three linked databases within the NCBI’s Entrez information retrieval system”:

  • PubChem Substance – “Search deposited chemical substance records using name, synonym or keywords. Links to biological property information and depositor web sites are provided.”
  • PubChem Compound – “Search unique chemical structures using names, synonyms or keywords. Links to available biological property information are provided for each compound.”
  • PubChem BioAssay – “Search bioassay records using terms from the bioassay description, for example ‘cancer cell line.’ Links to active compounds and bioassay results are provided.”

The three databases are accessible via tabs above the simple search form on the main page of PubChem, and search forms available for all three databases include:

  • Simple search form (one field)
  • Advanced search form – Multiple fields and limiters available.
  • Chemical structure search – Search by name/text, identity/similarity, substructure/superstructure, molecular formula, 3D conformer, or saved search.
  • BioActivity analysis – Search, analyze, and compare data in PubChem collection of BioAssay records. For analysis tools, users can also upload their own data.

Besides the three main databases and links within the chemical structure records to other Entrez resources, PubChem also provides additional tools, like:

Structures from the Therapeutic Target Database (TTD)

According to the PubChem Announcements, in February 2012:

Structures from the Therapeutic Target Database (TTD) are now available in PubChem.

Therapeutic Target Database (TTD) is a database to provide information about the known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets. Also included in this database are links to relevant databases containing information about target function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and drug structure, therapeutic class, clinical development status.

Select the “structures” link in the above announcement to automatically conduct a search of PubChem for all substance records from the TTD (the exact query is (“Therapeutic Targets Database”[sourcename])).

A chemical structure record from TTD on PubChem.

Structures from the IBM 

According to the PubChem Announcements, in December 2011:

More than 2.5 million structures from the IBM BAO (Business Analytics and Optimization) strategic IP insight platform (SIIP) are now available in PubChem, aggregating data from millions of patents and from the scientific literature through the year 2000. The chemical substances were extracted from the textual content, images, and symbols in patents and literature. The PubChem records link to the IBM web site, where files that list the patent numbers and PubMed IDs for each substance can be downloaded.

Select the “structures” link in the above announcement to automatically conduct a search of PubChem for all substance records from IBM (the exact query is (“IBM”[sourcename])).

A chemical structure record from IBM on PubChem.


The protein and nucleic acid structures from the TTD may provide valuable prior art for patent searchers working on certain pharmaceutical cases.  The chemical structure database from IBM SIIP is an excellent new resource for any patent searcher working on a chemical patent case, since the user can now search and view millions of structures linked to patent documents and scientific literature that may be used as prior art. These new data sources are just a small section of all sources available through PubChem, so chemical patent searchers can find a trove of potential prior art from a wide range of resources simply by searching through this free government platform.

Do you use PubChem during chemical prior art searches?  Tell us about your experiences with the platform in the comments section!

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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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