Chemical Structure Searching Now Available on Wikipedia

This is a guest post contributed by Shankar Manyem, a Patent Analyst in Landon IP’s Patent Search Group’s Chemistry Team.


Wikipedia is a very useful resource for searching information on chemicals, with the platform hosting more than 15,000 of them. However, until now, it was only possible to search Wikipedia using text terms such as chemical names (and fragment names), trade names, CAS Registry numbers, and to a limited extent, SMILES text.  Now, a structure search engine, Wikipedia Chemical Structure Explorer, is available that allows structure searching of Wikipedia chemical entries. The Wikipedia Chemical Structure Explorer was produced by joint collaboration by researchers from Novartis, École polytechnique fédérale de Lausanne (EPFL), and Actelion Pharmaceuticals.

The website allows for searching chemicals through either exact, similarity, or sub-structure options. Upon accessing the website, four modules are presented:

  1. Module which allows for a structure to be drawn through the JSME Molecular Editor.
  2. Basic information module that provides options to view the result in Wikipedia and to search other similar molecules.
  3. List module that provides a list of results based on the structure search.
  4. Synopsis module that provides the Wikipedia entry for the top hit structure.

Currently, there are about 13263 structure searchable entries, which are typically updated nightly (e.g., on 4/10/15, there were only 13250 structure searchable entries).

Wikipedia Chemical Structure Search User Interface.

Wikipedia Chemical Structure Search User Interface.


Wikipedia Chemical Structure Explorer Advantages:

  • The results are presented on the fly as the structure is drawn, providing for structure query modification depending on the number of results.
  • It is possible to combine structure searching with keyword search, although the keyword has to be part of the title of the article in Wikipedia – this allows for identifying, e.g., all amines that contain a benzene ring by drawing a benzene ring and using “amin” as text filter.
  • The results are limited to common chemicals, e.g., active pharmaceutical ingredients, pesticides, etc., for which a reference would typically be provided in the Wikipedia page.


Wikipedia Chemical Structure Explorer Limitations:

  • The data set is, of course, limited to chemicals in Wikipedia, i.e., popular chemicals – even here, not all chemicals in Wikipedia are structure searchable since many entries just have text entries and are missing structural entries in a form recognizable by the search script.
  • Keywords other than those in the title of the article are not searchable and cannot be used as text limitations, e.g., property data such as molecular weight or formula cannot be used to limit a search.
  • The results are limited to and are linked to the English pages of Wikipedia – the chemicals in the French or German versions will possibly be included in future versions.


Further description of the Wikipedia chemical structure explorer can be found in an article published in Journal of Cheminformatics.

Patent Searches from Landon IP

This post was contributed by Abhishek Tiwari. The Intellogist blog and Intellogist are provided for free by Landon IP, which is a CPA Global company. Landon IP is a major provider of professional services meeting the needs of the IP community, including patent searches; analytics and technology consulting; patent, legal, and technical translations; and information research and retrieval.


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!
Continue reading

More Free Chemical Search Tools: Materials Project and ChemExper

[tweetmeme source=”Intellogist” only_single=false] Here at the Intellogist blog, we’ve discussed free online tools for chemical searches ranging from government resources, like the ever-trusty PubChem and the Chemical Data Access Tool from the EPA, to international tools like the Chinese chemical search tool ChemYQ. Here are two more free chemical search tools to add to the list:

  • Materials Project – A collaboration between Massachusetts Institute of Technology (MIT) and Lawrence Berkeley National Laboratory (LBNL) that provides users with access to a number of tools for searching and analyzing materials based on their various properties.
  • ChemExper (which I originally heard about through the CHMINF listserv) – A free chemical directory created by ChemExper Inc. that allows users to locate chemical products and suppliers.

The Materials Project site provides a number of research support tools that will be useful for patent searchers conducting chemical prior art searches who need to quickly locate detailed information on a particular material. ChemExper will help prior art searchers and chemists quickly locate suppliers for a particular material, and ChemExper also provides a chemical structure drawing tool that greatly enhances the search capabilities of the site.  After the jump, learn about the chemical search tools available on Materials Project and ChemExper!

Continue reading

The Evolution of Free Chemical Patent Searching: The New SureChemOpen

[tweetmeme source=”Intellogist” only_single=false] Since SureChem was purchased by Macmillan Publishers Ltd. in 2009, it has undergone a variety of changes that are chronicled in the Major Recent Updates section of the SureChem System Report on Intellogist. In April 2012, the SureChem website announced SureChemOpen, a free chemistry search product that was being launched prior to the release of two subscription search products (SureChemPro and SureChemDirect).  The SureChem website offers a comparison of all three products, and these features are listed for SureChemOpen:

  • $0 per month
  • Free patent chemistry search
  • Search and view patent chemistry and full text
  • Search SureChem patents alongside Royal Society of Chemistry journals and ChemSpider
  • No data export

Read on to learn more about the new SureChemOpen product, including the coverage, chemical patent search and viewing options, and how you can register to use the portal for free!

Continue reading

The Newest Chemical Patent Search Features on SciFinder

[tweetmeme source=”Intellogist” only_single=false] The STN Intellogist Report was recently updated, and we listed some of the major improvements to the product: new full-text patent databases, improvements to current full-text patent databases, improved bio-sequence and chemical structure search options, and new Assistants and Wizards on STN Express and STN on the Web. STN is a fantastic platform for expert searchers who’ve mastered the syntax of the command line interface, but novice searchers may prefer the simpler interface of the SciFinder platform, another search system produced by the Chemical Abstracting Service.  SciFinder offers access to many of the same CAS databases offered on STN, but through a much more user-friendly interface.  For a detailed comparison of STN and SciFinder, check out this blog post.

Like STN, SciFinder has seen a variety of updates to both content and search features in the last few months.  After the jump, we’ll look at the newest coverage and interface updates on SciFinder!

Continue reading

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!

Continue reading

Free Chemical and Sequence Searching in Chinese Patent documents: ChemYQ and NASDAP

[tweetmeme source=”Intellogist” only_single=false] If Chinese non-patent literature searches are difficult for English-language prior art searchers, you can imagine how challenging chemical and genetic sequence searching within Chinese patent documents can be.  Many tools for chemical and genetic sequence searches in patent documents are available, both for free and by subscription, and many tools also exist for searching within Chinese-language patent documents.  Few tools, however, combine the Chinese patent coverage and chemical/genetic sequence search options; we’ve looked at only one subscription-based genetic sequence search tool, GenomeQuest, which recently added Chinese patent sequence data to their collection.  Today we’ll look at two free tools that can be used by English-language searchers to locate chemical names and genetic sequences within Chinese patent documents: ChemYQ and NASDAP.

After the jump, learn more about the Chinese chemical search engine ChemYQ and the Chinese genetic sequence search site NASDAP!

Continue reading