PubChem

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Introduction

PubChem, released by the National Institute of Health (NIH) in 2004, is a free chemical search system created as part of the NIH Molecular Libraries Roadmap Initiative.[1] PubChem is made up of "three linked databases within the NCBI's Entrez information retrieval system":[1]

  • PubChem Substance - "Search deposited chemical substance records using name, synonym or keywords. Links to biological property information and depositor web sites are provided." [2]
  • PubChem Compound - "Search unique chemical structures using names, synonyms or keywords. Links to available biological property information are provided for each compound."[3]
  • PubChem BioAssay - "Search bioassay records using terms from the bioassay description, for example 'cancer cell line.' Links to active compounds and bioassay results are provided."[4]

The three databases are accessible via tabs above the simple search form on the main page of PubChem, and search forms available for all three databases include:

  • Simple search form (one field)
  • Advanced search form - Multiple fields and limiters available.
  • Chemical structure search - Search by name/text, identity/similarity, substructure/superstructure, molecular formula, 3D conformer, or saved search.
  • BioActivity analysis - Search, analyze, and compare data in PubChem collection of BioAssay records. For analysis tools, users can also upload their own data.


Recent Updates

June 2012 - According to the PubChem Announcements:[5]

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 2012 - According to the PubChem Announcements:[5]

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.

March 2012 - Reaxys is now integrated with PubChem. According to the Reaxys website:[6]

[PubChem's] integration with Reaxys means that a single structure search yields results in Reaxys and PubChem in parallel, with the results presented in the familiar Reaxys interface. TOC headers are hyperlinked to PubChem so you can directly access PubChem from Reaxys.

February 2012 - According to the PubChem Announcements:[7]

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 2011 - According to the PubChem Announcements:[7]

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.


Additional Tools

PubChem provides links between the chemical structure records and other Entrez databases:[1]
Links from PubChem's chemical structure records to other Entrez databases provide information on biological properties. These include links to PubMed scientific literature and NCBI's protein 3D structure resource. Links to PubChem's bioassay database present the results of biological screening. Links to depositor web sites provide further information.

Besides the three main databases and links within the chemical structure records, PubChem also provides additional tools, like:[1]

  • PubChem FTP (file transfer protocol) site
  • Download Facility - Structure download and bioassay download
  • Power User Gateway
  • Standardization Service
  • Score Matrix Service
  • Identifier Exchange Service
  • Structure Clustering
  • Deposition Gateway
  • Web-Based 3D Viewer

Sources

  1. 1.0 1.1 1.2 1.3 "About PubChem." NCBI PubChem website, http://pubchem.ncbi.nlm.nih.gov/about.html. Accessed August 30, 2011.
  2. "PubChem: Substance." PubChem website, http://pubchem.ncbi.nlm.nih.gov/#. Accessed August 30, 2011.
  3. "PubChem: Compound." PubChem website, http://pubchem.ncbi.nlm.nih.gov/#. Accessed August 30, 2011.
  4. "PubChem: BioAssay." PubChem website, http://pubchem.ncbi.nlm.nih.gov/#. Accessed August 30, 2011.
  5. 5.0 5.1 "PubChem Announcements." PubChem website, http://pubchem.ncbi.nlm.nih.gov/pcnews.html. Accessed July 1, 2012.
  6. "Latest Release Information." Reasxys website, https://www.reaxys.com/info/latestreleaseinformation. Accessed July 1, 2012.
  7. 7.0 7.1 "PubChem Announcements." PubChem website, http://pubchem.ncbi.nlm.nih.gov/pcnews.html. Accessed March 2, 2012.

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