PubChem News

 

2022

 
February 7, 2022

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).
 
 

2021

 
November 1, 2021

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.
 
 

2020

 
October 19, 2020

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.
 
 

2019

 

August 12, 2019


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.
 
 

2018

 

August 13, 2018


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.
 
 

2017

 

October 26, 2017


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.
 
 

2016

 

November 29, 2016


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.
 
 

2015

 

November 24, 2015


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.
 
 
 

2014

 

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. 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.
 
 

June 26, 2014


Just over 1.4 million structures from Collaborative Drug Discovery (CDD) are now available in PubChem, including almost 94,000 novel structures. These structures have links back to CDD’s public Vault data pages, many of which hold structure-activity data and compound properties, and are accessible through a free login. The announcement from CDD provides additional details.
 
 

January 30, 2014


PubChemRDF is released. It allows PubChem data to be used with semantic web technologies and encodes PubChem information using the Resource Description Framework (RDF). PubChemRDF data can be accessed through a REST interface or bulk downloaded from the PubChem FTP site. One benefit of RDF formatted data is the ability to use schema-less databases (such as a triplestore or a graph database) to import, query, and analyze PubChem data locally. Read the PubChem Blog (http://1.usa.gov/1db9Y4T) to learn more.
 
 
 

2013

 
November 21, 2013
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.
 
 
September 3, 2013
The PubChem Social Media campaign is now launched! Follow us on , and  to keep up with the latest PubChem resources and features. Share PubChem pages with your friends and colleagues. Visit the new PubChem blog to read more about it.
 
 
April 8, 2013
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.
 
 
April 8, 2013
New PubChem Widgets can be used to display a carousel of chemical structures, display the classification of a compound/substance/bioassay of interest, or provide an autocomplete function within your own web page. In addition, features have been added to the table-based widgets (bioactivitypatents, and PubMed), including a share button that allows you to open the widget in a PubChem page or embed the widget in your own page as an iframe, and an option to display graphical filters for subsetting the data (currently available only for the bioactivity widget).
 
 
April 5, 2013
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.
 
 
 

2012

 
 
December 10, 2012
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
The PUG REST 1.0 version is now available! It is a REST-style interface for accessing PubChem data and services through simple HTTP requests, for use in scripts, javascript embedded in web pages, and 3rd party applications, without the overhead of XML, SOAP envelopes, etc., that are required for other versions of PUG. PUG REST can deliver customized output for individual PubChem records, or for small sets of records, in a way that is not possible with other PubChem services. For example, it can retrieve specific data elements, such as molecular weight or a chemical structure image, for a molecule of interest without having to download its full record. PUG REST can also accept a variety of input types, such as chemical name, InChIKey, SMILES, and more, in addition to the traditional SID, CID, and AID numeric identifiers. The PUG REST help document provides technical specifications for the syntax of HTTP requests and the available functions, and a new tutorial provides some examples on how PUG REST can be used. PUG REST 1.0 replaces the April 2012 beta release and represents the stable final form of the tool. While new features may be still added, changes will be backward-compatible.
 
 
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 pubchem-help@ncbi.nlm.nih.gov with questions, problems, or suggestions for new features.
 
 
Feburary 21, 2012
Structures from the Therapeutic Target Database (TTD) are now available in PubChem.

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.
 
 
 

2011

 
 
December 8, 2011
More than 2.5 million structures from the IBM BAO (Business Analytics and Optimization) strategic IP insight platform (SIIP) are now available in PubChem, aggregating data from millions of patents and from the scientific literature through the year 2000. The chemical substances were extracted from the textual content, images, and symbols in patents and literature. The PubChem records link to the IBM web site, where files that list the patent numbers and PubMed IDs for each substance can be downloaded. See more related news...
 
 
October 4, 2011
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.
 
 
August 10, 2011
Structures from AmicBase are now available in PubChem.
 
 
June 8, 2011
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  

To find out a CID associated with bioactive data, you may follow the URL at https://www.ncbi.nlm.nih.gov/pccompound?term=pccompound_pcassay_active[filt]. Similarly, to find out a SID associated with bioactive data, you may follow the URL athttps://www.ncbi.nlm.nih.gov/pcsubstance?term=pcsustance_pcassay_active[filt]. You may also go to the advanced search page for PubChem Compound database or Substance database, and followed by making a choice in the "BioAssays" section and clicking the "Go" button.
May 27, 2011
PubChem released the Identifier Exchange Service. For more information, click here.
 
 
May 23, 2011
The BioAssay data specification has been updated. The changes include:
  1. New units in PC-ResultType to facilitate DMPK data submission.
  2. A new element "type" in PC-AnnotatedXRef to record primary citation to advertise primary publications of the depositors and the bioassay results.
  3. A new element "type" in PC-AssayDRAttr to record experimental vs. calculated dose-response data points.

Please review the update at https://ftp.ncbi.nlm.nih.gov/pubchem/data_spec.  

 

 

April 11, 2011
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.
 
 
March 17, 2011
 
 
March 15, 2011
Structures from AKos are now available in PubChem.
 
 
February 22, 2011
RNAi screening data and substances from the Drosophila RNAi Screening Center (DRSC) are now available in PubChem. 

Structures from ABI Chem are now available in PubChem.
 
 
February 7, 2011
Structures from Alsachim are now available in PubChem.
 
 
February 4, 2011
Structures and bioassay data from UCLA Molecular Screening Shared Resource are now available in PubChem.
 
 
January 19, 2011
All ChEMBL assays have been updated and now point to substances deposited by ChEMBL requested by ChEMBL and ChEBI.
 
 
January 13, 2011
The PubChem BioAssay ASN.1/XML data specification has been updated to include new types of target data under PC-AssayTargetInfo and PC-ResultType. For more details, please refer to https://ftp.ncbi.nlm.nih.gov/pubchem/data_spec.
 
 
January 11, 2011
Structures and bioassay data from Abbott are now available in PubChem.
 
 
 

2010

 
December 20, 2010
Structures from AAA Chemistry are now available in PubChem.
 
 
December 16, 2010
Structures from Kingston Chemistry are now available in PubChem.
 
 
November 10, 2010
Structures from Avanti Polar Lipids are now available in PubChem.
 
 
November 1, 2010
Structures from Excenen PharmaTech are now available in PubChem.
 
 
October 29, 2010
Structures from Selleck Chemicals are now available in PubChem.
 
 
October 8, 2010
Structures from Zancheng Functional Chemicals are now available in PubChem.
 
 
September 3, 2010
The PubChem BioAssay FTP updated

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.
  1. 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.
  2. The files were partitioned according to a fixed AID range of 1000.
  3. 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.

 

 

September 3, 2010
 
 
September 3, 2010
The PubChem data specification updated
  1. ASN1/XML data specification for PubChem Substance has been modified to include XRef choices for cross-link to NCBI GEO database.
  2. ASN1/XML data specification for PubChem BioAssay has been modified to include "categorized-comment" field under PC-AssayDescription.

For more details, please refer to https://ftp.ncbi.nlm.nih.gov/pubchem/data_spec

 

 

July 12, 2010
Structures and bioassay data from Finley and King Labs, Harvard Medical School are now available in PubChem.
 
 
June 30, 2010
Structures from Annker Organics are now available in PubChem.
 
 
June 21, 2010
Structures from Tractus are now available in PubChem.
 
 
June 7, 2010
Structures from Ennopharm are now available in PubChem.
 
 
June 4, 2010
Structures from iThemba Pharmaceuticals are now available in PubChem.
 
 
May 29, 2010
Bioassay data from ChEMBL are now available in PubChem.
 
 
May 28, 2010
Structures from Jamson Pharmachem Technology are now available in PubChem.
 
 
May 24, 2010
Structures from Amatye are now available in PubChem.
 
 
May 20, 2010
Structures and bioassay screening data from the GlaxoSmithKline (GSK) are now available in PubChem. More news can be found here.
 
 
April 27, 2010
 
 
April 21, 2010
Structures from the Golm Metabolome Database (GMD), Max Planck Institute of Molecular Plant Physiology are now available in PubChem. Structures from the Nitric Oxide Research, National Cancer Institute (NCI) are now available in PubChem.Structures from the Creasyn Finechem are now available in PubChem.
 
 
April 13, 2010
Structures from the ICCB-Longwood/NSRB Screening Facility, Harvard Medical School are now available in PubChem. Structures from the Nature Communications are now available in PubChem.
 
 
March 5, 2010
Structures from TCI (Tokyo Chemical Industry) are now available in PubChem.
 
 
February 19, 2010
Structures from the molport are now available in PubChem.
 
 
 

2009

 
 
December 15, 2009
Structures from MIC Scientific are now available in PubChem.
 
 
November 23, 2009
Structures from ChEBI are now updated with ChEBI release 62.
 
 
October 30, 2009
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.
 
 
September 30, 2009
 
 
September 17, 2009
 
 
September 2, 2009
Structures from Biological Magnetic Resonance Data Bank (BMRB) are now available in PubChem.
 
 
August 4, 2009
Structures from Tyger Scientific are now available in PubChem. 

Structures from PennChem-GAM are now available in PubChem.
 
 
June 30, 2009
Structures from IS Chemical Technology are now available in PubChem.
 
 
June 12, 2009
Protein-ligand binding affinity data from the PDBbind database have now been deposited into PubChem BioAssay database by the Shanghai Institute of Organic Chemistry

The ALA (American Library Association) selected PubChem as one of the Best Free Reference Web Sites 2009.
 
 
June 9, 2009
Structures from ZINC are updated in PubChem.
 
 
June 4, 2009
Structures from Vitas-M Laboratory are now available in PubChem.
 
 
May 21, 2009
Structures from Shanghai Sinofluoro Scientific Company are now available in PubChem. 

Structures from Alinda Chemical are now available in PubChem.
 
 
April 24, 2009
 
 
April 2, 2009
Structures from novo|seek are now available in PubChem. Novo|seek is a search engine for biomedical literature in Medline and US Grants.
 
 
March 30, 2009
 
 
February 25, 2009
Structures from Nature Chemistry are now available in PubChem.
 
 
February 13, 2009
Structures from Thermo Scientific Dharmacon RNAi Technologies are now available in PubChem.
 
 
February 3, 2009
PubChem3D is released consisting of a single theoretical 3D conformer per compound record and includes a new similarity relationship (Similar Conformers). 

XLogP is now updated to version 3.0 of the algorithm.  InChI and InChIKey are now updated to use the version 1.0.2 standard.
 
 
 

2008

 
 
November 28, 2008
Structures from Vanderbilt University Medical Center are now available in PubChem.
 
 
November 26, 2008
BioAssay data, Kinase Inhibitor Selectivity Profiling Assay, from Ambit Biosciences are now available in PubChem.
 
 
November 20, 2008
The PubChem Score Matrix Service, through which one can download similarity scores for selected lists of CIDs, is now released.
 
 
November 7, 2008
 
 
November 5, 2008
Structures from EMD Biosciences are now available in PubChem.
 
 
October 27, 2008
Structures from ChemSynthesis are now available in PubChem.
 
 
October 20, 2008
Structures from PENN-ABS are now available in PubChem. 

Structures from IUPHAR-DB are now available in PubChem. 

Structures from True PharmaChem are now available in PubChem.
 
 
September 29, 2008
Structures from Comparative Toxicogenomics Database are now available in PubChem. 

Structures from HDH Pharma are now available in PubChem. 

Structures from Johns Hopkins Ion Channel Center are now available in PubChem. 

Structures from Biosynth are now available in PubChem.
 
 
September 18, 2008
PubChem PUG SOAP is officially released. 

 RSS feed is available for PubChem announcements (Atom version).
 
 
September 11, 2008
Structures from MP Organic & Rare Chemicals are now available in PubChem.
 
 
September 10, 2008
Structures from NextBio are now available in PubChem.
 
 
September 8, 2008
Structures from Isoprenoids are now available in PubChem.
 
 
August 15, 2008
Structures from Ambit Biosciences are now available in PubChem. 

Structures from Paul Baures are now available in PubChem.
 
 
July 15, 2008
Structures from LeadScope are now updated in PubChem.
 
 
July 1, 2008
Structures from the Hangzhou Trylead Chemical Technology are now available in PubChem.
 
 
May 19, 2008
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).
 
 
May 9, 2008
PubChem Compound/Substance Summary v3.0 release.
 
 
May 5, 2008
PubChem Structure Search v3.0 release.
 
 
February 25, 2008
 
 
February 22, 2008
Structures from Aronis are now available in PubChem.
 
 
February 1, 2008
The PubChem Standardization service release.
 
 
January 30, 2008
New formats: images, SMILES, and InChI are added to the PubChem download service

Structures from the Columbia University Molecular Screening Center are now available in PubChem.
 
 
January 10, 2008
PubChem BioAssay service v4.1 release. PubChem contains more than 800 bioassays. 

Structures from Exclusive Chemistry are now available in PubChem.
 
 
 

2007

 
 
December 20, 2007
PubChem contains more than 38 million substances, 18 million compounds, and 710 bioassays. 

Structures from NIH Clinical Collection are now available in PubChem. 

Structures from Shanghai Institute of Organic Chemistry are now available in PubChem.
 
 
December 16, 2007
PubChem contains more than 38 million substances, 18 million compounds, and 680 bioassays. 

Structures from ChemSpider are now updated in PubChem.
 
 
November 29, 2007
Structures from DrugBank are now available in PubChem.
 
 
November 20, 2007
Structures from Calbiochem are now available in PubChem. 

Structures from R&D Chemicals are now available in PubChem.
 
 
November 18, 2007
PubChem contains more than 21 million substances, 11 million compounds, and 660 bioassays.
 
 
October 11, 2007
Structures from InFarmatik are now available in PubChem.
 
 
October 3, 2007
Structures from ORST Small Molecule Screening Center are now available in PubChem.
 
 
August 14, 2007
PubChem BioAssay service v4.0 release.
 
 
August 6, 2007
Structures from Ambinter are now available in PubChem.
 
 
July 18, 2007
Structures from Sigma-Aldrich, representing the specialty chemicals from its primary catalog, are now updated in PubChem.
 
 
June 6, 2007
PubChem Power User Gateway (PUG) is released. PUG is an XML-based programmatic interface to PubChem that can perform structure searching and structure download. A SOAP-compliant wrapper is available.
 
 
May 9, 2007
PubChem contains more than 17 million substances and 500 bioassays. 

Structures from ChemSpider are now available in PubChem.
 
 
April 11, 2007
Structures from Sigma-Aldrich are now available in PubChem.
 
 
March 6, 2007
PubChem contains more than 400 bioassays.

The PubChem BioAssay services now provide target links and bioassay neighboring information identified by activity overlap and target sequence similarity.
 
 
 

2006

 
 
November 14, 2006
PubChem Structure Search v2.0 release.PubChem Structure-Activity Analysis and Structure Clustering tools release.
 
 
November 8, 2006
Structures from Specs are now available in PubChem.
 
 
November 6, 2006
Structures from Thomson Pharma are now available in PubChem.
 
 
October 16, 2006
Structures and BioAssay data from Diabetic Complications Screening are now available in PubChem.
 
 
October 12, 2006
PubChem BioAssay service v3.0 release.
 
 
September 10, 2006
 
 
August 9, 2006
Structures from UM-BBD are now available in PubChem. 

Structures from Total TOSLab Building-Blocks are now available in PubChem.
 
 
August 7, 2006
Structures from ZINC are now updated in PubChem.
 
 
July 28, 2006
Structures from Prous Science are now available in PubChem.
 
 
July 24, 2006
BioAssay data from NCGC (NIH Chemical Genomics Center) are now updated in PubChem.

BioAssay data from University of Pittsburgh Molecular Library Screening Center are now updated in PubChem. 

BioAssay data from Scripps Florida are now updated in PubChem.
 
 
July 12, 2006
BioAssay data from Columbia University Molecular Screening Center are now available in PubChem. 

BioAssay data from Vanderbilt Screening Center for GPCRs, Ion Channels and Transporters are now available in PubChem.
 
 
June 26, 2006
Structures and data from Structural Genomics Consortium [SGCStoCompounds] are now available in PubChem. 

BioAssay data from Emory University Molecular Libraries Screening Center are now available in PubChem.
 
 
June 16, 2006
Structures from LeadScope are now available in PubChem.
 
 
June 6, 2006
Structures from ChemBank are now updated in PubChem.
 
 
June 1, 2006
Structures and data from PDSP are now available in PubChem. 

Structures and data from PANACHE are now available in PubChem.
 
 
May 1, 2006
Structures and data from Structural Genomics Consortium (Oxford) [SGCOxCompounds] are now available in PubChem. 

BioAssay data from San Diego Center for Chemical Genomics are now available in PubChem.
 
 
March 21, 2006
Structures from DiscoveryGate are now available in PubChem.
 
 
March 8, 2006
BioAssay data from SRMLSC (Southern Research Institute Molecular Libraries Screening Center) are now available in PubChem.
 
 
February 27, 2006
 
 
February 10, 2006
 
 
February 8, 2006
Structures and BioAssay data from MTDP (Molecular Targets Development Program) are now available in PubChem.
 
 
February 1, 2006
Structures and BioAssay data from BindingDB are now available in PubChem.
 
 
January 27, 2006
Structures from NMRShiftDB are updated in PubChem.
 
 
January 25, 2006
Structures from CambridgeSoft CorporationKUMGM, and SMID are now available in PubChem. Click herehere, and here to see data from three data sources, respectively.

Structures and BioAssay data from NMMLSC (New Mexico Molecular Libraries Screening Center) are now available in PubChem.
 
 
January 18, 2006
BioAssay data from Scripps Florida are now available in PubChem.
 
 
 

2005

 
 
December 20, 2005
Structures from xPharm are now available in PubChem.
 
 
November 22, 2005
 
 
October 31, 2005
PubChem Deposition Gateway is now available.
 
 
October 18, 2005
Structures from NIAID are now updated. 

Structures and Bioassay Data from ChemBlock are now available in PubChem.
 
 
September 23, 2005
Structures from ChemDB are now available in PubChem.
 
 
September 6, 2005
 
 
September 2, 2005
 
 
August 26, 2005
Structures from ZINC are now available in PubChem.

Structures from ASINEX are now available in PubChem.

BioAssay data from NCGC (NIH Chemical Genomics Center) is now available in PubChem.
 
 
August 18, 2005
 
 
August 17, 2005
Structures from ChemIDplus and NIAID are now updated. Click here and here to see data from two datasources, respectively.

Structures from ChemBridge are now available in PubChem.
 
 
August 1, 2005
The PubChem Download Facility is available. For more information, click here.

Structures from ChemExper Chemical Directory are now available in PubChem.
 
 
June 9, 2005
Structures from MLSMR are now available in PubChem.

Structures from BIND are now available in PubChem.
 
 
May 25, 2005
Structures from Nature Chemical Biology are now available in PubChem.

Structures from NMRShiftDB are now available in PubChem.
 
 
April 6, 2005
PubChem/Compound now provides improved linkage to Medical Subject Annotations and PubMed biomedical literature citations. 

PubChem/Compound now contains unique structures only, and compound identifiers have changed. Please update links to PubChem/Compound based on "cid" identifiers. For additional information, click here.
 
 
 

2004

 
 
September 16, 2004
PubChem release. PubChem contains the chemical structures of small organic molecules and information on their biological activities. For more information, go to PubChem homepage.

 

 

 

 

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