Introducing the PubChem Target Summary
Posted on September 12, 2017
Have you ever wanted a convenient way to access information stored in PubChem about a particular biological target? We’ve created the PubChem Target Summary page to help you easily explore PubChem content.
PubChem contains a wealth of information about chemical substances. Included in this massive corpus is more than 230 million biological activity data results from more than one million biological experiments deposited in the BioAssay database. Finding all relevant information for a given target can involve a lot of clicking!
This new page provides the means to readily navigate and download PubChem content using a gene-centric data view. In addition, other pertinent annotation is provided to help give context to the biological target relative to the available PubChem content. This includes information such as:
- Protein targets encoded by the gene (i.e., protein gene-products)
- Known drugs, chemical probes, ligands, and compounds tested against the gene or gene-products
- Available small molecule and RNAi biological assay experiments for the gene or gene-products
- Annotated information about the gene and gene-products, such as: biological function, relevance to disease, gene/protein family classifications, gene-gene interactions, and pathways
Each PubChem BioAssay Record page with a gene/protein target now has a link to its corresponding PubChem Target Summary page. This can be located under the “BioAssay Target” section of the Assay Record page. (See image)
In addition, the PubChem Target Summary page for a given gene can be accessed via a web URL that contains the corresponding NCBI Gene ID or Gene Symbol. For example, the following URLs will give the same PubChem Target Summary page for human epidermal growth factor receptor (EGFR) gene (Gene ID 1956):
In this URL scheme, by default, using a gene symbol will yield the corresponding human gene target. If PubChem does not have content for the human gene, an orthologous gene with available content will be provided. If there is more than one orthologous gene, the orthologue with the smallest NCBI Taxonomy identifier is used. One can navigate between PubChem Target Summary pages for orthologous genes using the “Orthologs” link provided in the summary table at the top of each target page. (See image)
The types of targets covered by the PubChem Target Summary page may be expanded to include other known target types, such as cell lines and pathways. In addition, improvements may be made to expand the annotation content and utility of the PubChem Target Summary page.