PubChem presents at the American Chemical Society National Meeting in Boston (August 19-23, 2018)

On August 19-23, 2018, the 256th American Chemical Society National Meeting will be held in Boston, MA, the theme of which is “Nanoscience, Nanotechnology & Beyond”.  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 19)

 

Day 2 (Monday, August 20)

 

Day 3 (Tuesday, August 21)

 

Day 4 (Wednesday, August 22)

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

PubChem presents at the American Chemical Society National Meeting in New Orleans (March 18-22, 2018)

On March 18-22, 2018, the 255th American Chemical Society National Meeting will be held in New Orleans, LA, the theme of which is “Nexus of Food, Energy & Water”.  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, March 18)

 

Day 2 (Monday, March 19)

 

Day 3 (Tuesday, March 20)

 

Day 5 (Thursday, March 22)

Publisher Springer Nature contributes millions of chemical-article links

PubChem added more than 26 million links to scientific articles, thanks to contributions from the publisher Springer Nature.  Of these, 1.6 million links point to open access or free-to-read documents! (Read Springer Nature’s press release and presentation about it.)

Springer Nature includes the SpringerLink, SpringerOpen, and BioMed Central research platforms as well as the nature.com website.  Combined, they include more than 10 million scientific documents spanning the primary literature, book chapters, and reference works.  InfoChem, a subsidiary of Springer Nature, identified the chemicals mentioned in these scientific articles using a proprietary approach.

 

What was contributed?

The Springer Nature data collection in PubChem covers over 600 thousand chemical substance records, and contains nearly 4 million scientific article descriptions (of which almost 300 thousand are open- or free-access) and 26.8 million links between chemicals and articles.  The document descriptions include information such as a document object identifier (DOI), publication title, name of the journal or book, document type, subject matter classification, language, open/free access availability, and publication year.

 

Why is this important?

This contribution, which doubles the number of chemical structures in PubChem with links to the scientific literature, improves the accessibility and discoverability of information about chemicals. Nearly all link content provided by Springer Nature is novel to PubChem, with only 10% of the provided chemical structures having a previous link to the scientific literature.

Integration of the Springer Nature links and data within PubChem has opened new possibilities for organizations and researchers. As a result of the contribution, PubChem added the capability to handle DOI-based annotation content. Additional appropriate DOI-based linked content (articles, data sets, and more) can now be added to PubChem.

 

What is Springer Nature?

PubChem Source page for Springer Nature

Springer Nature is a scientific publishing company and a leading global research, educational and professional publisher formed through the merger of Nature Publishing Group, Palgrave Macmillan, Macmillan Education, and Springer Science+Business media.

The SpringerLink research platform provides access to more than 6 million journal articles, 3.7 million book chapters, and more than 480,000 reference works primarily in the areas of science, technology, and medicine.

 

Where can I access the contributed content?

Springer Nature References for CID 19

Each chemical record with a Literature “Springer Nature References” section includes a table containing document links from Springer Nature.  As an example, below are the links to the Springer Nature References section for aspirin (Compound ID 2244 and Substance ID 341138876).  (Read this blog if you are not familiar with how Compounds and Substances in PubChem are different from each other.)

https://pubchem.ncbi.nlm.nih.gov/compound/2244#section=Springer-Nature-References

https://pubchem.ncbi.nlm.nih.gov/substance/341138876 #section=Springer-Nature-References

Click an article title to access the document on a Springer Nature website.  To download all the contributed document data for a chemical record in CSV format, click the “Download” button at the top right of the table (see image). There is a full table data view accessible (by clicking the  icon), where you can see additional data columns such as the DOI.  By default, the articles are ordered by degree of “relevance” to the chemical as provided by Springer Nature, but the sorting field is easily changed through a pulldown menu, and sort direction also may be changed.

 

How to find chemical records with the Springer Nature references?

There are multiple ways to get a complete list of PubChem Substance or Compound records with “Springer Nature References”.  One can:

The PubChem Classification Browser provides the means to navigate PubChem contents using various hierarchical classification trees.  The PubChem Compound TOC (Table of Contents) classification tree allows you to find all chemicals with a given annotation section.  In this case, one can click ‘Literature’ to view the subset fields under literature and find the ‘Springer Nature References’ section.  Clicking on the number will then show compound records with that section.

The entire list of chemical substances provided by Springer Nature is available using the PubChem Data Sources page. (Read this blog to learn more about the PubChem Data Sources page.)  Searching for “Springer Nature” from the list of data sources shown on the page will help lead you to the Springer Nature data source page that has a link to the PubChem records provided by Springer Nature.  Alternatively, you can search the PubChem Compound or PubChem Substance database using the query: “Springer Nature”[sourcename].

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.