More than a million chemical-article links from Thieme Chemistry added into PubChem


Posted on January 15, 2019


More than a million links to scientific articles with a focus on chemical synthesis have been added to PubChem, thanks to contributions from the publisher Thieme Chemistry with support from their technology partner InfoChem. (Read Thieme’s press release about it.)


The Thieme Chemistry information in PubChem covers nearly 700,000 chemical substance records, nearly 700,000 scientific article descriptions, and over 1.2 million links between chemicals and articles.  The document descriptions include information such as a digital object identifier (DOI), publication title, name of the journal or book, publication type, language, and publication year.


The Thieme Chemistry contribution dramatically increases the number of chemical structures in PubChem with links to the scientific literature from nearly 1.0 million to 1.6 million.  Of the approximately 700,000 Thieme Chemistry chemical structures contributed to PubChem, 42% are new to PubChem, and 89% previously lacked literature links.


Finding chemicals with Thieme references

You can easily retrieve a complete list of PubChem Substance or Compound records that have Thieme references through the  PubChem Classification Browser, the PubChem Data Sources page, or by searching in the Substance or Compound databases.  (Not sure about how Compounds and Substances in PubChem are different from each other? Read this blog post.)


Within the PubChem Classification Browser, the PubChem Compound TOC (Table of Contents) classification tree allows you to find all chemicals with a given annotation section.  You can click “Literature” to view the subset fields under literature and find the “Thieme References” section.  Clicking on the number will then show compound records with that section.


The entire list of chemical substances provided by Thieme Chemistry is also available through the PubChem Data Sources page. (Read this blog post to learn more about the PubChem Data Sources page.)  Searching for “Thieme Chemistry” from the list of data sources shown on the page will lead you to the Thieme Chemistry data source page that has a link to the PubChem records provided by Thieme Chemistry.


You can also search the PubChem Compound or PubChem Substance databases directly using the query “Thieme Chemistry”[sourcename].


Thieme references in chemical records

Each chemical record with a Literature / Thieme References section includes a table containing document links from Thieme Chemistry.  The figure below shows the Thieme References section of the Compound record for ciprofloxacin (CID 2764).


The Literature / Thieme References section of the ciprofloxacin Compound record
Figure 1. The Literature / Thieme References section of the ciprofloxacin Compound record (CID 2764). Clicking the title (red circle) loads the article at the Thieme Chemistry site.


The article title links to the article on the Thieme-Chemistry site. You can download all references for a chemical record in CSV format through the “Download” button at the top right of the table. You can also expand to the full table by clicking the full screen icon, where you can see additional data columns.  By default, the articles are ordered by Publication Date as provided by Thieme Chemistry, but you can easily change the sorting order through the pulldown menu.


PubChem, along with contributors such as Thieme Chemistry, is helping to fuel a modern, data-driven research ecosystem.  Literature links from Thieme Chemistry dramatically expand the findability, accessibility, interoperability, and reusability (FAIR) of synthesis-related chemical information.  In addition, this contributed content helps to further enhance global open science by allowing researchers to locate key information about chemicals.

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