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

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 View this section in 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.

PubChem BioAssay Tools to be replaced

PubChem BioAssay Tools (https://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi), a legacy collection of bioactivity analysis services, are being retired as part of an on-going technology refresh.  Alternative approaches now exist to perform most of the same tasks, and these newer technologies provide expanded features and capabilities.  The PubChem BioAssay Tools services will be no longer accessible after November 1, 2018.

Why are we phasing out the BioAssay Tools?

The BioAssay tools were developed when PubChem was much smaller.  At PubChem’s current size, the tools do not scale sufficiently to handle most analysis tasks.  Consequently, many users download data for use in their assay analysis workflows instead of using the tools.  Deprecating these BioAssay Tools will free up resources allowing PubChem to develop new and better approaches to accessing bioactivity content.

 

What replaces the BioAssay Tools?

BioAssay Assay Results for CID 2244 There are easier-to-find PubChem services that offer the same or similar functionalities for most BioAssay Tools.  For instance, let’s say you have a compound, like aspirin, for which you would like to analyze all reported bioactivity data.  In the past, you would need to first find the dedicated tool (the BioActivity Summary service) to retrieve the data. Now you will find this information in a BioAssay Results section on the widely accessed Compound Summary page:

https://pubchem.ncbi.nlm.nih.gov/compound/2244#section=BioAssay-Results

Though some tools (like Structure Clustering and Structure-Activity Relationship Analysis) do not currently have direct alternatives in PubChem, most PubChem pages indicate related records such as structurally similar chemicals or assays performed against a given target.  They can be further aggregated using commonly available third-party tools.

Will my old link work to the BioAssay Tools?

URL redirection from BioAssay Tools to their corresponding replacement will be provided for a period beyond November 1, 2018.  Eventually, the redirection links will be removed.

For more detailed information on this topic, please visit this PubChem Help document: https://pubchemdocs.ncbi.nlm.nih.gov/legacy-bioassay-tools

Introducing the PubChem Target Summary

Have you ever wanted a convenient way  to access information stored in PubChem about a particular biological target? We’ve created the PubChem Target Summary page to help you easily explore PubChem content.

 

Why a PubChem Target Summary page?

PubChem Target Page for EGFR

PubChem contains a wealth of information about chemical substances.  Included in this massive corpus is more than 230 million biological activity data results from more than one million biological experiments deposited in the BioAssay database.  Finding all relevant information for a given target can involve a lot of clicking!

This new page provides the means to readily navigate and download PubChem content using a gene-centric data view.  In addition, other pertinent annotation is provided to help give context to the biological target relative to the available PubChem content.  This includes information such as:

  • Protein targets encoded by the gene (i.e., protein gene-products)
  • Known drugs, chemical probes, ligands, and compounds tested against the gene or gene-products
  • Available small molecule and RNAi biological assay experiments for the gene or gene-products
  • Annotated information about the gene and gene-products, such as: biological function, relevance to disease, gene/protein family classifications, gene-gene interactions, and pathways

 

How do I access the new PubChem Target Summary page?

Each PubChem BioAssay Record page with a gene/protein target now has a link to its corresponding PubChem Target Summary page.  This can be located under the “BioAssay Target” section of the Assay Record page.  (See image)

PubChem Target Page for EGFR

In addition, the PubChem Target Summary page for a given gene can be accessed via a web URL that contains the corresponding NCBI Gene ID or Gene Symbol.  For example, the following URLs will give the same PubChem Target Summary page for human epidermal growth factor receptor (EGFR) gene (Gene ID 1956):

https://pubchem.ncbi.nlm.nih.gov/target/gene/1956

https://pubchem.ncbi.nlm.nih.gov/target/gene/EGFR

In this URL scheme, by default, using a gene symbol will yield the corresponding human gene target.  If PubChem does not have content for the human gene, an orthologous gene with available content will be provided.  If there is more than one orthologous gene, the orthologue with the smallest NCBI Taxonomy identifier is used.  One can navigate between PubChem Target Summary pages for orthologous genes using the “Orthologs” link provided in the summary table at the top of each target page.  (See image)

Future directions

The types of targets covered by the PubChem Target Summary page may be expanded to include other known target types, such as cell lines and pathways.  In addition, improvements may be made to expand the annotation content and utility of the PubChem Target Summary page.

Spectral Information in PubChem

Did you know that a growing number of chemicals in PubChem contain spectral information?

There are now more than 300 thousand chemicals with spectral information available, including 13C NMR, 1H NMR, 2D NMR, ATR-IR, FT-IR, GC-MS, Raman, UV-Vis, vapor-phase IR, and more.  This content comes primarily from four data sources: the NIST/EPA/NIH Mass Spectral Library, the Hazardous Substances Data Bank (HSDB), the Human Metabolome Database (HMDB), and a new addition, SpectraBase.

The NIST/EPA/NIH Mass Spectral Library includes images of the top-three peaks of GC-MS or MS-MS spectra along with related metadata and annotation for more than two hundred thousand chemicals. The Library’s annotation includes instrument, collision energy, spectrum type, and associated metadata information.

HSDB content is text-based and includes citations and spectra peak information for thousands of chemicals. HMDB annotation includes links to spectra for thousands of chemicals.

PubChem Spectral_data

SpectraBase, provided by Bio-Rad, a commercial publisher of spectral databases and spectroscopy software, includes images of, annotation about, and links to a diverse set of spectral information for tens of thousands of compounds. SpectraBase content includes extensive annotation and a variety of metadata, such as the instrument, measurement technique, sample source, and spectrum source, in addition to the image of the spectra.

For all four sources, additional spectral information is often available directly from the source and easily accessed using the links on the PubChem page.

 

How to find and access spectral data for a compound?

PubChem records with spectral data have a Table of Content (TOC) section labelled “Chemical and Physical Properties” with a “Spectral Properties” subsection. One can use the TOC to jump to a given type of spectral data content.  Clicking the SpectraBase image or the HMDB link directs the user to an external web page for that compound, where one can further interact with the spectral information.

PubChem Classification Browser

The PubChem Classification Browser (https://pubchem.ncbi.nlm.nih.gov/classification/#hid=72) can help you locate all PubChem Compound records containing a particular type of spectral information.  The “Spectral Properties” node can be found under the “Chemical and Physical Properties” section in the PubChem Compound Table of Contents (TOC) classification tree.

PubChem presents at the 254th American Chemical Society National Meeting in Washington D.C. (August 20-24, 2017)

On August 20-24, 2017, the 254th American Chemical Society National Meeting will be held in Washington D.C.  The PubChem team will be at the ACS meeting to present new developments and recent changes in PubChem.  Below is a list of presentations that will be given by the PubChem staff.

 

Day 1 (Sunday, August 20)

 

Day 2 (Monday, August 21)

 

Day 3 (Tuesday, August 22)

  • CINF108: PubChem and open data (S. Kim)
    Junior Ballroom 2 – Washington Marriott at Metro Center, 5:00 pm – 5:25 pm

 

Day 4 (Wednesday, August 23)

 

Day 5 (Thursday, August 24)

 

In addition, one of PubChem’s collaborators will give a presentation on our joint effort to develop a new service that provides information on biologics.

PubChem presents at the American Chemical Society National Meeting in San Francisco (April 2-6, 2017)

On April 2-6, 2017, the 253rd American Chemical Society National Meeting will be held in San Francisco, CA, the theme of which is “Advanced Materials, Technologies, Systems & Processes”.  The PubChem team will be at the ACS meeting to present new developments and recent changes in PubChem.  Below are a list of presentations that will be given by the PubChem staff.

 

Day 1 (Sunday, April 2)

 

Day 2 (Monday, April 3)

 

Day 3 (Tuesday, April 4)

 

Day 4 (Wednesday, April 5)

 

Atomic mass changes in PubChem

PubChem is now using the latest International Union of Pure and Applied Chemistry (IUPAC) recommendations for atomic mass and isotopic composition information.  In addition, PubChem is now restricting the allowed isotopes for a given element to those with a half-life of one millisecond or greater.

Fundamental changes within atomic mass information

Hydrogen and DeuteriumNormally atomic mass updates are not blog worthy; however, there are some fundamental changes in the way masses are conceptualized that affect the atomic weight values computed for nearly all compounds in PubChem.

Molecular weight is one of the most frequently requested pieces of information about a chemical.  To compute a molecular weight of a molecule, one consults a periodic chart and sums the average atomic weights of the elements comprising the chemical, while considering any specified isotopic enrichment information.  Although the molecular weight computation seems straightforward, as greater degrees of precision in atomic masses are known, the chemical science community is recognizing complex issues with average atomic weight and isotopic data.

The abundance ratio between different isotopes of a given element is used to determine its average atomic weight.  As the sensitivity of measuring equipment has increased, scientists now notice a distinct difference in these abundance ratios depending on the material source of that element.  To reflect this variation, and as explained in this IUPAC technical report, many elements are now given an atomic weight interval, consisting of a range of known discrete values reflecting the varying isotopic abundance ratios found in different elemental material sources. For example, the atomic weight interval of carbon is 12.0096 to 12.0116.

Another complicating factor is that the abundance ratio of naturally occurring isotopes is not available for all elements.  Some elements like radon do not have any stable isotope and no characteristic isotopic composition in earthly materials.  It means that no average atomic weight can be determined!  There are also a growing number of elements that do not exist in nature, being “synthesized” in the lab.  These artificially created elements are metastable, rapidly decaying into other elements.  Importantly, because different isotopes of a given element decay at different rates, the isotopic abundance ratio between isotopes is time-dependent.

All of these considerations contribute to the uncertainty in atomic weight and isotopic information, which in turn impacts the molecular weight of a compound.

What changes did PubChem make?

All molecular weights in the PubChem Compound database were updated as such:

  • Adoption of “conventional atomic weights”Periodic Table
    To provide a single, representative average atomic-weight value for an element ignoring any material source uncertainties, the latest IUPAC recommendations include a concept of “conventional atomic weight value” whereby most or all atomic-weight variation in normal materials is covered (with an interval of ± 1 in the last digit).  PubChem has adopted this approach for the twelve elements (hydrogen, lithium, boron, carbon, nitrogen, oxygen, magnesium, silicon, sulfur, chlorine, bromine, and thallium) with standard atomic weights given as intervals.
  • Standard atomic weights updated
    Standard atomic weights in PubChem use the latest values provided by IUPAC (except when a conventional atomic weight value is used).  For the thirty-four elements without any abundance information (e.g., technetium), the atomic weight of the most stable, non-theoretical isotope was used, as found in the NuBase2012 evaluation (http://amdc.in2p3.fr/nubase/nubtab12.asc) of nuclear and decay properties.
  • Trimmed precision of molecular weights
    To take into account the uncertainties in elemental abundances and masses, the precision of all molecular weight values were reduced from six to three digits beyond the decimal point.
  • Updated allowed isotopes for elements
    The internal PubChem knowledgebase used to generate the PubChem Compound database from the PubChem Substance database was updated.  (Read this blog if you are not familiar with how these two databases differ from each other.)  As a part of this, only isotopes for elements with an experimentally measured half-life of one millisecond or greater were allowed when using the NuBase2012 evaluation of nuclear and decay properties (http://amdc.in2p3.fr/nubase/nubtab12.asc).  This (slightly) modifies the scope of what can be found in the PubChem Compound database.

 Where can you learn more about this topic?

To learn more about this topic, please read the following:

  • Atomic weights of the elements 2013 (IUPAC Technical Report)
    Meija et al., Pure Appl. Chem. 2016; 88(3): 265-291.
    doi: 10.1515/pac-2015-0305
  • Isotopic compositions of the elements 2013 (IUPAC Technical Report)
    Meija et al., Pure Appl. Chem. 2016; 88(3): 293-306.
    doi: 10.1515/pac-2015-0503