PubChem is updating its data model used for storing bioassay information.  This update will change the format of data uploaded to or downloaded from PubChem.  As a result, assay data depositors need to format their data based on the new data model to submit them to PubChem.  Also, software programs that download PubChem’s assay data (e.g., in ASN.1, XML, and CSV) for further analysis will need to be updated to load PubChem data correctly.   Major changes to the assay data specifications Some important changes in the new data model are summarized below.  A full data spe ..read more

A significant update has been made to PubChemRDF, machine-readable PubChem data formatted using the Resource Description Framework (RDF) (https://www.w3.org/RDF/).  (If you have never heard about PubChemRDF before, please read this PubChem blog first.) What is PubChemRDF? RDF is a World Wide Web Consortium (W3C) standard model for data interchange on the web.  In RDF, knowledge is expressed as statements, each of which consists of three discrete parts: a subject, an object, and a predicate that specifies the relationship between them.  So, the trio of these parts is called a tri ..read more

PubChem Pathway Pages are now available. Each PubChem Pathway page provides information about chemicals, proteins, genes, and diseases involved in or associated with the biological pathway, which can be very important to provide a context to observed biological activity. In addition, all pathways associated with a given chemical, protein or gene are summarized on the corresponding page. All content comes from existing Pathway resources without any attempt to merge or combine them.  Each page for a given pathway can be accessed via an URL of this form: https://pubchem.ncbi.nlm.nih.gov/pathway ..read more

More than 32,000 compounds in PubChem now have links to hundreds of chemical and physical properties pertinent to chemistry, material science, physics, and other related fields available from SpringerMaterials (see this press release).  These links will help you quickly locate articles for the property in question. Chemicals with SpringerMaterials links will contain a “SpringerMaterials Properties” section in the “Chemical and Physical Properties” table of contents.  This provides a list of chemical properties available at SpringerMaterials for this compound.  For example, the following link s ..read more

The World Intellectual Property Organization (WIPO) is an international organization that aims to promote the protection of intellectual property throughout the world.  WIPO provided PubChem with more than 16 million chemical structures searchable in its patent database called PATENTSCOPE (see this press release).   For each of the chemical structures contributed by WIPO, PubChem provides a direct link to PATENTSCOPE, which allows users to perform searches for patent documents relevant to that chemical structure.  For example, the following URL directs users to the “WIPO PATENTSCOPE” section o ..read more

NLM staff will participate in the next American Chemical Society webinar for the chemical information and cheminformatics community: An Overview of NLM’s Post-TOXNET Resources. TOXNET (the TOXicology Data NETwork) was retired in December 2019 as part of the reorganization associated with the NLM Strategic Plan. Most of TOXNET’s databases have been incorporated into other NLM resources such as PubChem and Bookshelf, or continue to be available elsewhere. This webinar will show you where to go now for TOXNET information. Date and Time: Tuesday, March 17 at 1:00pm EDT. Register  A live Q&A s ..read more

On August 25-29, 2019, the American Chemical Society National Meeting will be held in San Diego, CA, the theme of which is “Chemistry & Water”.  The PubChem team will be at the ACS meeting to present new developments and recent changes in PubChem.  Below is a list of presentations involving PubChem staff.   Day 1 (Sunday, August 25) CINF 1: Enhancing data-driven summarization of relations between chemicals, genes, proteins, and diseases based on text mining of biomedical literature (L. Zaslavsky) Grand Ballroom A – Omni San Diego Hotel, 9:05 AM – 9:25 AM   Day 2 (Monday, August 26) CINF ..read more

The periodic table of chemical elements is one of the most recognized tools in science.  As we mark the 150th anniversary of the periodic table, the scientific community has declared 2019 to be “The International Year of the Periodic Table”.  PubChem is celebrating by launching the PubChem Periodic Table and corresponding Element pages. While PubChem provides each chemical its own page, you can find elements there too.  Such pages are not suited for displaying information specific to elements (such as electronegativity and electron configuration).  The PubChem Periodic Table and Element pages ..read more

We’ve redesigned PubChem’s homepage to give you easier access to the information you need, where you need it. The mobile-friendly, responsive design works on the device you want to use. And the streamlined, intuitive interface puts the data you need at your fingertips. Here are some of the changes you can expect to see at the new PubChem homepage: The menus at the top of the page and the sidebar have been replaced with a minimal set of important links. These links include “About,” “Blog,” “Submit,” and “Contact.” The “About” link will bring you to the PubChem Docs site, where you can find an ..read more

On March 31-April 4, 2019, the 257th American Chemical Society National Meeting will be held in Orlando, FL, the theme of which is “Chemistry for New Frontiers”.  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, March 31) CINF 11: FAIR chemical data for health and safety: Connecting the dots with cheminformatics and librarianship (E. Bolton & L McEwen) West Hall B4 – Theater 11, Orange County Convention Center, 9:40 AM – 10:10 AM CINF 13: PubChem ..read more