An RxNorm Concept Unique Identifier (RXCUI) was added to the Identifier section of PubChem Compound records, where possible. Approximately, 4,200 RXCUIs were mapped to 4,200 PubChem Compound IDs (CIDs) via a FDA Unique Ingredient Identifier (UNII).
PubChem has been providing many imaging services in the past years. A help page has been created to summarize all PubChem imaging services. To learn more about this, please read the page "Imaging Services".
February 04, 2021
PubChem BioAssay has a new data model, which is publicly available on our web pages and at our FTP site (Bioassay2/). The data with old spec is still available at the FTP site (Bioassay/) but will be archived as /Other/Bioassay1 by June 1, 2021. To learn more about this, please read this PubChem blog.
A significant update has been made to PubChemRDF, machine-readable PubChem data formatted using the Resource Description Framework (RDF) (https://www.w3.org/RDF/). To learn more about this, please read this PubChem blog.
March 19, 2020
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. To learn more about this, please read this post.
March 16, 2020
The World Intellectual Property Organization (WIPO) provided PubChem with more than 16 million chemical structures searchable in its patent database called PATENTSCOPE. To learn more about this, please read this post.
March 16, 2020
PubChem Pathway pages are now available. Pathway information can be very important to provide a context to observed biological activity. To learn more about this, please read this post.
On Aug 25-29, 2019, the American Chemical Society National Meeting will be held in San Diego, CA. The PubChem team will be at the ACS meeting to present new developments and recent changes in PubChem. To learn more about this, please read this post.
March 27, 2019
This year marks 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 introducing the PubChem Periodic Table and corresponding Element pages. To learn more about this, please read this post.
March 26, 2019
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. To learn more about this, please read this post.
March 26, 2019
On March 31-April 4, 2019, the 257th American Chemical Society National Meeting will be held in Orlando, FL. The PubChem team will be at the ACS meeting to present new developments and recent changes in PubChem. To learn more about this, please read this post.
March 18, 2019
We've redesigned PubChem's summary and record pages with a series of updates both behind the scenes and to your own user experience. These changes will make finding the information you’re looking for easier and faster. To learn more about this, please read this post.
March 14, 2019
PubChem is updating the data model for objects returned by the PUG View server. These objects are used by both programmatic users and by PubChem web pages. Programmatic users will need to update the programs that retrieve and interpret data from PUG View. PubChem web users will not be directly affected by the data model changes. To learn more about this, please read this post.
January 15, 2019
PubChem added more than a million links to scientific articles with a focus on chemical synthesis, thanks to contributions from the publisher Thieme Chemistry with support from their technology partner InfoChem. The Thieme Chemistry data collection 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. To learn more about this, please read this post.
On August 19-23, 2018, the 256th American Chemical Society National Meeting will be held in Boston, MA. The PubChem team will be at the ACS meeting to present new developments and recent changes in PubChem. To learn more about this, please read this post.
April 27, 2018
PubChem BioAssay Tools, 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. To learn more about this, please read this post.
March 8, 2018
On March 18-22, 2018, the 255th American Chemical Society National Meeting will be held in New Orleans, LA. The PubChem team will be at the ACS meeting to present new developments and recent changes in PubChem. To learn more about this, please read this post.
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 or free access documents! For more information, please read PubChem Blog.
September 12, 2017
The PubChem Target Summary page is now launched. It provides a convenient way to access information stored in PubChem about a particular biological target. For more information, please read PubChem Blog.
August 31, 2017
Did you know there are a growing number of chemicals in PubChem containing spectral information? There are now more than 300 thousand chemicals with spectra links available, including 13C NMR, 1H NMR, 2D NMR, ATR-IR, FT-IR, MS, Raman, UV-Vis, vapor-phase IR, and more. To learn more about this, please read this post.
August 8, 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. To learn more about this, please read this post.
June 14, 2017
Watch this YouTube video "PubChem: A source of laboratory chemical safety information" to learn how to use PubChem for lab safety. This video shows you how to use the PubChem Laboratory Chemical Safety Summary (LCSS), which provides easily accessible, helpful information for directors and instructors of research and teaching laboratories to assist in the development and implementation of safe laboratory practices.
March 21, 2017
On April 2-6, 2017, the 253rd American Chemical Society National Meeting will be held in San Francisco, CA. The PubChem team will be at the ACS meeting to present new developments and recent changes in PubChem. To learn more about this, please read this post.
PubChem now uses the latest IUPAC recommendations for atomic mass and isotopic composition information. In addition, the allowed isotopes for a given element are restricted to those with a half-life of one millisecond or greater. These changes affect the molecular weight values computed for nearly all compounds in PubChem. To learn more, please read this post.
October 25, 2016
The PubChem Data Sources page is now updated. It helps you to find who provided what information in PubChem. The updated interface has a new look and feel with a unified data source table containing all primary information. This interface provides new and improved capabilities to navigate as a function of data type, category, and country, while also including keyword searching, counts, and geographical visualization. To learn more, please read this post.
September 19, 2016
PubChem Widgets 2.0f is released. PubChem Widgets enable scientific web developers to display PubChem content within webpages they design. All data comes directly from PubChem and, therefore, obviates the need to mirror that content. This makes it easier to harness the vast scientific knowledge within PubChem on your own webpage, such as summaries of patents, bioactivities and PubMed articles linked to a PubChem record. PubChem Widgets 2.0f substantially updates all table-based widgets and classification widgets, while adding new capabilities and features. For more information, please read this post.
August 17, 2016
On August 21-25, 2016, the 252nd American Chemical Society National Meeting will be held in Philadelphia, PA. The PubChem team will be at the ACS meeting to present new developments and recent changes in PubChem. In addition, there will be a Herman Skolnik Award Reception honoring Drs. Stephen Bryant and Evan Bolton for their leadership in the PubChem project. To learn more about this, please read this post.
August 3, 2016
PubChem will adopt a HTTPS-only policy on September 30, 2016. This means PubChem will no longer support HTTP web URLs after that date. The National Center for Biotechnology Information (NCBI) recently announced important changes to NCBI Web Protocols to comply with the US federal government's HTTPS-only policy for all publicly accessible websites. PubChem, as a part of NCBI, will adopt the same HTTPS-only policy. To read more about this, see the PubChem Blog.
March 10, 2016
On March 13-17, 2016, the 251st American Chemical Society National Meeting will be held in San Diego, CA, the theme of which is "Computers in Chemistry". The PubChem team will be at the ACS meeting to present new developments and recent changes in PubChem. To learn more about this, please read the PubChem Blog.
January 19, 2016
A new article about the PubChem Compound and Substance databases can be found in the 2016 Nucleic Acids Research Database issue. It provides an overview of the two databases, including data organization, contents, interfaces, programmatic access and other relevant tools and services. To learn about this and other recent PubChem publications, read the PubChem Blog.
The PubChem BioAssay Record page is now available, which complements a recent revamp of the PubChem Compound Summary page and the Substance Record page. It features mobile-friendly interface, improved data table, extended download functionality and so on. To learn more about the BioAssay Record page, please read the PubChem Blog.
November 16, 2015
PubChem introduces a "legacy" designation. It helps users separate collections that are no longer maintained. To learn more about the legacy designation, read the PubChem Blog.
August 17, 2015
The Laboratory Chemical Safety Summary (LCSS) view is now available in PubChem. An LCSS is a summary of a hazard and safety information for a chemical, including flammability, toxicity, exposure limits and symptoms, first aid, handling, clean up, and so on. To learn more about PubChem LCSS please read the PubChem Blog.
June 23, 2015
The PubChemRDF 1.5β is now available. The new version is faster, supports Linked Data in new formats, features improved search and query functions, and contains new links. To learn more about this, visit the PubChem Blog.
April 9, 2015
The PubChem Substance Record page is now available. It replaces the PubChem Substance Summary page. Similar to the recent update to the PubChem Compound Summary page, this page was given a substantial makeover. Detailed information on the new PubChem Substance Record page is provided in the PubChem Blog.
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. Detailed information on the new PubChem Compound Summary page is provided in the PubChem Blog.
September 16, 2014
PubChem celebrates 10 years of service to the chemical biology community! With humble beginnings, PubChem was first launched in Sep. 16, 2004. Through this time, PubChem’s focus has remained the same: to provide comprehensive information on the biological activities of chemical substances. To read more about this, visit the PubChem Blog.
July 25, 2014
Why contribute your data to PubChem? Maximize the impact of your research. Crosslink your data to key scientific databases. Satisfy data sharing requirements by journals and funding agencies. Flexibility on when your data gets released. Ability to share on-hold data with reviewers and collaborators. To learn more about these, visit the PubChem Blog.
PubChem Upload 1.0f is released! Adding your information to PubChem (https://pubchem.ncbi.nlm.nih.gov/upload/ ) is now easier than ever. The new PubChem Upload system offers streamlined procedures for data submissions and includes an extensive set of wizards, inline help tips, and templates to assist users. Visit the PubChem Blog (http://1.usa.gov/1ayl7ze) to read more about it.
Structures from UniCarbKB are now available in PubChem. UniCarbKB is an initiative to create an online information storage and search platform for glycomics and glycobiology research. UniCarbKB curates information from the scientific literature on glycoprotein derived glycan structures, building on previous curation efforts by GlycoSuiteDB and continuing the principles of EUROCarbDB to provide an open-access platform for glycoinformatics. This is the first phase in the release of structures from UniCarbKB and the entries will be updated as the UniCarbKB structure database develops.
A new PubChem Upload system offers streamlined procedures for data submissions and updates to both the PubChem Substance and BioAssay databases! This system is currently in Beta release, but will eventually replace the original Pubchem Deposition Gateway. The new capabilities offered by PubChem Upload include:
Assay & Substance wizards assist novice users
UI speed greatly improved with newer web technology (minimizing possible time-outs)
Easy new user registration/easy upgrade to production account
Improved help, including hints built into user interface and tutorial
Substance input with CID, SID, SMILES, etc.
Select PubChem substances/assays as templates for new submissions or for record updates
Error display integrated with substance list display
Full editing and integration of assay data & description tables
Expanded import/export handling of spreadsheets for data & description tables
April 5, 2013
Pubchem BioAssay DataDicer: a new, efficient search engine for BioAssay outcomes, is now available at #. The PubChem DataDicer allows both novice and expert scientists to search and subset the greater than 200 million BioAssay outcomes from the PubChem BioAssay database. Users can query by molecular descriptors, genes, pathways, bioassay categories and other data types, in order to retrieve bioactivity outcomes for genes/proteins that were the targets of bioassays, or for small molecules that were screened in the bioassays. The data are linked to multiple NCBI databases, allowing you to traverse to the associated genes, proteins, chemical structures, and more. Data about outcomes, including small molecules, targets, and pathways can be downloaded to your computer as a comma-separated value (CSV) file.
January 23, 2013
Nearly 300,000 structures from ChemAxon's chemicalize.org database are now available in PubChem, including approximately 62,000 novel structures. All structures have links back to chemicalize.org data pages with predicted data including pKa, logP/D, names and identifiers, and more, all of which can be downloaded as structure data files (SDF). The announcement from ChemAxon provides additional details.
More than 8 million structures from the SureChem patent chemistry database are now available in PubChem. SureChem has deposited chemistry for their complete collection of US, EP and WO full text patents from the 1976 to the present, after filtering out common chemicals, reactive groups and fragments. Over 4 million of these structures are new to the PubChem Compound database, significantly expanding public access to novel medicinal chemistry. Users can view the structures within the context of the patent by following the External ID link to SureChemOpen, a free patent chemistry search tool. A press release from SureChem provides additional details.
October 5, 2012
Use the new PubChem Classification Browser to browse PubChem data using a classification of interest, or to search for PubChem records annotated with the desired classification system and term. Illustrated examples of search results for PubChem Compounds classified as methotrexate, and for PubChem BioAssays that tested protein targets involved in DNA repair, are available in the help document.
October 1, 2012
Show data your way with the new PubChem Widgets. Display concise tables of patents, bioactivities, and literature for PubChem data in your web pages with three easy steps. See the help document for details and examples of the data views available.
September 19, 2012
More than 6 million structures from SCRIPDB are now available in PubChem. Extracted from the complex work units of more than 300,000 USPTO patents between the years of 2001-2012, these PubChem Substance records link to both SCRIPDB and the USPTO websites. A full text article describing the SCRIPDB project is available in PubMed Central.
September 17, 2012
PubChem databases and services are now Hypertext Transfer Protocol Secure (HTTPS) compatible, allowing one to use encryption in their interactions with PubChem.
September 13, 2012
September 12, 2012
PubChem reaches milestones on 8th birthday! More than 100 million live records are now available in PubChem Substance, and nearly 200 million outcomes are available in PubChem BioAssay, representing contributions from more than 200 depositors that have joined the PubChem project since its launch on September 16, 2004.
June 5, 2012
The PubChem BioAssay summary pages now display the Gene Ontology (GO) classification of the gene/protein target(s) that were tested by the bioassay. The GO terms are associated with each gene/protein in an automated way as part of the biosystems database data processing procedures, using the method described in the Biosystems help document. All GO terms that apply to the gene(s)/protein(s) tested by the bioassay are shown in the GO hierarchy, including: (1) biological processes, (2) cellular components, and (3) molecular functions. Clicking on any GO term in the hierarchy will retrieve all bioassays that have tested a protein(s) associated with that term. As an example, see the GO terms for the protein target that was tested by the glucocorticoid receptor (GR) redistribution assay (AID 450).
In addition, the PubChem BioAssay data summary for a compound now displays a graphical summary of the bioassays that have tested the compound, categorizing the bioassays by: (1) bioactivity outcomes (active, inactive, inconclusive, unspecified); (2) top targets; (3) bioactivity types (IC50, EC50, Potency, Ki, etc.); (4) bioassay types (screening, confirmatory, summary, other). The bar graphs are clickable and serve as filters to display data from the selected category, refreshing both the bar graphs and the tabular summary of bioassays to reflect the data subset you have selected. As an example, see the bioassay data summary for aspirin (CID 2244).
April 24, 2012
PubChem PUG REST - a RESTful web interface to PubChem data and services. Documentation and examples are available at https://pubchem.ncbi.nlm.nih.gov/pug_rest/ . This service is considered to be in a beta state right now, meaning it is under active development and some changes may occur but the interface should be mostly stable. The purpose of this beta release is to make some basic functionality available now, and to invite feedback from the PubChem user community. Please try it out and tell us what you think; contact firstname.lastname@example.org with questions, problems, or suggestions for new features.
Therapeutic Target Database (TTD) is a database to provide information about the known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets. Also included in this database are links to relevant databases containing information about target function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and drug structure, therapeutic class, clinical development status. All information provided are fully referenced.
PubChem updated the compound and substance summary pages to load faster, to include dramatically expanded biomedical annotation, and to give an updated look and feel. For example, the PubChem Compound summary page for aspirin (CID 2244).
October 3, 2011
A new layer called PubChem3D is added to PubChem to assist with interrelating diverse chemical structures with similar biological efficacies against targets. As a part of this, PubChem computes a 3-D conformer model description for records in the PubChem Compound database when possible (92% of all records when considering the parent compound of salts). A pre-computed search per compound record gives immediate access to a set of 3-D similar compounds (called "Similar Conformers") in PubChem and their respective superpositions. Systematic augmentation of PubChem resources to include a 3-D layer provides users with new capabilities to search, subset, visualize, analyze, and download data. For additional information, please visit the PubChem3D thematic series with the (BMC) Journal of Cheminformatics: http://www.jcheminf.com/series/pubchem3d.
August 12, 2011
PubChem's information content continues to increase. As of August, 2011, deposited substance records have reached 85 million, representing to over 30 million chemically unique compounds. Deposited bioassay records have reached 500 thousand, representing over 130 million experimental bioactivity results. New substance and bioassay records continue to be deposited, and the PubChem team expects that the steady growth in content and usage seen over the past 7 years will continue.
PubChem is now providing an enhanced bioactivity analysis tool for retrieving bioassay data for a chemical. The tool can be accessed at https://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?cid=myCID for a given CID or https://pubchem.ncbi.nlm.nih.gov/assay/assay.cgisid=mySID for a given SID.
E.g. For CID 2244, the link is: https://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?cid=2244
PubChem released two new data analysis tools for the bioassay services - Target and Compound/Substance views for the BioActivity Analysis service. These new tools together with the original bioassay view component will allow users to explore bioactivity data from molecular target, chemical structure, and biological experiment perspectives. For more information, see the related section in the help page.
To expedite the download speed for growing number of assays in the PubChem Bioassays FTP site, we have introduced several changes that may impact all of the BioAssay FTP users.
Data and description files are now partitioned and compressed as "zip" format. Each compressed zip file contains a directory with a list of BioAssay files according to the range of AID(BioAssay ID), the directory named as the AID range, and each individual data filename prefixed by the AID. For example, the file "0000001_0001000.zip" contains the compressed zip archive directory which contains individual Bioassay files. Each Bioassay file contains an AID record within the range of 1 through 1,000.
The files were partitioned according to a fixed AID range of 1000.
The zip file format has been natively supported on Windows, Mac OS X, Linux, Unix and other systems. There are also a number of ZIP tools and libraries available and free for your programming environments.
PubChem Entrez displays now include a "Selected Records" panel to help users discover informative annotations and subsets among search results. For example, following a keyword search of PubChem Compound for "aspirin", the "Selected Compounds" panel includes a line saying "Protein 3D Structures, Compound Count: 4." This indicates that 4 of the 85 compound records retrieved by the "aspirin" search were derived from Protein 3D structures. Clicking on "4" shows which 4 out of the 85 compounds were observed binding to proteins. Clicking on "Protein 3D Structures" shows the 20 experimental protein 3D structures observed to bind these compounds. Structures from the Ganolix are now available in PubChem.
An open BETA test of PubChem's new PUG SOAP web services is now available. Included are sample interfaces for GUI workflow applications (Taverna, Pipeline Pilot) and SOAP-aware programming and scripting languages (Java, C#, VB, Python, Perl).