Pubchem BioAssay DataDicer: a new, efficient search engine for BioAssay outcomes, is now available at
http://dd.ncbi.nlm.nih.gov/datadicer/2/.
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.
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.
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.
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.
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).
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.
December 8, 2011
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).
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.
August 10, 2011
June 8, 2011
May 27, 2011
May 23, 2011
The
BioAssay data specification has been updated. The changes include:
- New units in PC-ResultType to facilitate DMPK data submission.
- A new element "type" in PC-AnnotatedXRef to record
primary citation to advertise primary publications of the depositors and the bioassay results.
- 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.
March 15, 2011
February 22, 2011
February 7, 2011
February 4, 2011
January 19, 2011
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.
December 20, 2010
December 16, 2010
November 10, 2010
November 1, 2010
October 29, 2010
October 8, 2010
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.
- 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.
September 3, 2010
September 3, 2010
The PubChem data specification updated
- ASN1/XML data specification for PubChem Substance has been modified to include XRef choices for cross-link to NCBI GEO database.
- ASN1/XML data specification for PubChem BioAssay has been modified to include "categorized-comment" field under PC-AssayDescription.
For more details, please refer to
ftp://ftp.ncbi.nlm.nih.gov/pubchem/data_spec
July 12, 2010
June 30, 2010
June 21, 2010
June 7, 2010
June 4, 2010
May 29, 2010
May 28, 2010
May 24, 2010
May 20, 2010
April 27, 2010
April 21, 2010
April 13, 2010
March 5, 2010
February 19, 2010
December 15, 2009
November 23, 2009
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 17, 2009
September 2, 2009
August 4, 2009
June 30, 2009
June 12, 2009
June 9, 2009
June 4, 2009
May 21, 2009
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
February 13, 2009
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.
November 28, 2008
November 26, 2008
November 20, 2008
The PubChem
Score Matrix Service, through which one can download similarity scores for selected lists of CIDs, is now released.
November 5, 2008
October 27, 2008
October 20, 2008
September 29, 2008
September 18, 2008
September 11, 2008
September 10, 2008
September 8, 2008
August 15, 2008
July 15, 2008
July 1, 2008
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 5, 2008
February 25, 2008
February 22, 2008
February 1, 2008
January 30, 2008
January 10, 2008
December 20, 2007
December 16, 2007
November 29, 2007
November 20, 2007
November 18, 2007
October 11, 2007
October 3, 2007
Structures from
ORST Small Molecule Screening Center are now available in PubChem.
August 14, 2007
August 6, 2007
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
April 11, 2007
March 6, 2007
November 14, 2006
PubChem
Structure Search v2.0 release.PubChem Structure-Activity Analysis and Structure Clustering tools release.
November 6, 2006
October 16, 2006
October 12, 2006
September 10, 2006
August 9, 2006
August 7, 2006
July 28, 2006
July 24, 2006
July 12, 2006
June 26, 2006
June 16, 2006
June 6, 2006
June 1, 2006
May 1, 2006
March 21, 2006
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
February 1, 2006
January 27, 2006
January 25, 2006
January 18, 2006
December 20, 2005
November 22, 2005
October 31, 2005
October 18, 2005
September 23, 2005
September 6, 2005
September 2, 2005
August 26, 2005
August 18, 2005
August 17, 2005
August 1, 2005
June 9, 2005
May 25, 2005
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.
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.
2012