Compound Summary Page Redesigned
Posted on October 20, 2014
A revamped PubChem Compound Summary page is now available. Technology has advanced considerably since the last major update in 2011, so this page was given a substantial makeover.
PubChem is organized as three interconnected databases: Substance, Compound, and BioAssay. PubChem Compound contains the unique chemical structure content of PubChem Substance, after normalization processing. Each individual PubChem Compound record (accession CID) has a web page called a “Compound Summary” that recaps all information known about a particular chemical. For example, take a look at the Compound Summary page for aspirin: https://pubchem.ncbi.nlm.nih.gov/compound/aspirin.
Quite a lot. Improvements were made in four primary areas:
- Emphasis on speed
Considerable attention was focused on making the page load faster. This was achieved by both reducing the amount of data required to display the page and by improving the PubChem computational infrastructure which reduced the time to respond to requests.
- Universally device-friendly
The new interface uses a responsive design approach and is optimized for both touch- and mouse-based interfaces. In addition, the new page automatically adjusts to the available screen size, making it friendly for desktops, tablets, and phones.
- Tool tips
Each section and subsection now has its own built in help making it easier to immediately learn what each section or subsection is about by clicking on the “?”.
- Provenance information
Annotation sources are now prominently highlighted. The organization providing the data is indicated to the right of the assertion. Additionally, when provided by the data source, a bibliographic citation is displayed under the assertion. Lastly, an overall list of annotation sources for the entire Compound Summary page is available in a new “Information Sources” section at the bottom of the web page, helping to summarize additional reference sources.
- Icon bar
An icon bar at the top summarizes key types of available information and provides the means to quickly jump to that section.
- Table of Contents
The table of contents was reorganized, optimized, and expanded. On larger screens, the table of contents is now ‘sticky’, staying with you as you move around the web page, making for easier navigation. On smaller screens, the table of contents is available when clicking the three horizontal bars.
- Bookmark a given section
As you navigate to a given section or subsection, the URL changes making it easier to bookmark or share a direct link to a specific part of the page.
- MeSH synonyms
Medical Subject Heading (MeSH) is used to manually cross-index the biomedical literature. Chemical names found in MeSH for the chemical record are now displayed in their own section.
Unique Ingredient Identifiers (UNIIs) and pharmacological classifications were added from the U.S. Food and Drug Administration (FDA).
Anatomical Therapeutic Codes (ATC) and International Nonproprietary Names (INNs) were added from the World Health Organization (WHO).
- Chemical, Safety, and Toxicology
Expanded physical properties, safety, and toxicology information from various organizations (including NIH, NIOSH, OSHA, EPA, and ICSC) was added.
- Other Identifiers
A new section includes key identifiers for a given chemical. These include FDA Unique Ingredient Identifiers (UNIIs), European Community (EC) numbers, International Chemical Safety Card (ICSC) number, and more.
- Downloadable record data
The available annotation information can now be downloaded in multiple formats, including JSON and XML.
- Improved printing
Special attention to format and layout was made when printing. For example, like book chapters, each section now starts on its own page. In addition, a “print” button was added.
- Chemical Vendors
The chemical vendor section was revamped and added into the table of contents.
- Added ‘widgets’
Interactive interfaces are now provided for PDB and pathway data. In addition, the 2D and 3D chemical structure now have their own respective sections and interfaces.
- URL interface
The URL for the Compound Summary page has changed. While old-style URLs will automatically be redirected, the new URL interface can be used to text search PubChem. For example, these will all work to find the chemical structure of ‘Aspirin’:
This update to the Compound Summary page reflects a new approach to PubChem web pages. An update to the Substance Summary page using this new framework is anticipated in early 2015. The old version of the Compound Summary page will continue to remain accessible but will be retired within a year. To access the old version of the page, the parameter “&r=summary” will need to be added to the URL. For example, to access the old version of the Compound Summary page for Aspirin: https://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=2244&r=summary