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.

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.

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.

PubChem databases and services are now Hypertext Transfer Protocol Secure (HTTPS) compatible, allowing one to use encryption in their interactions with PubChem.

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.

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.

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).

PubChem PUG REST - a RESTful web interface to PubChem data and services. Documentation and examples are available at http://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.

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.

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...

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).

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.

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.

Structures from AmicBase are now available in PubChem.

PubChem is now providing an enhanced bioactivity analysis tool for retrieving bioassay data for a chemical. The tool can be accessed at http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?cid=myCID for a given CID or http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgisid=mySID for a given SID.
E.g. For CID 2244, the link is: http://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 http://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 at http://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.

PubChem released the Identifier Exchange Service. For more information, click here.

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 ftp://ftp.ncbi.nlm.nih.gov/pubchem/data_spec.  

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.

Structures from Immunology Lab, Department of Biotechnology, Calicut University are now available in PubChem.

Structures from AKos are now available in PubChem.

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.

Structures from Alsachim are now available in PubChem.

Structures and bioassay data from UCLA Molecular Screening Shared Resource are now available in PubChem.

All ChEMBL assays have been updated and now point to substances deposited by ChEMBL requested by ChEMBL and ChEBI.

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 ftp://ftp.ncbi.nlm.nih.gov/pubchem/data_spec.

Structures and bioassay data from Abbott are now available in PubChem.