Legacy BioAssay/BioActivity Tools

The PubChem BioAssay Tools (https://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi) are now legacy (end of life). These services will no longer be accessible after Nov. 1, 2018. Please consult PubChem Help (pubchem-help@ncbi.nlm.nih.gov) on how to achieve the same or similar functionality that these pages offer.

 

Why are we phasing these tools out? These were developed over a period time when PubChem was smaller. While useful, they are not scalable and are expensive to maintain. In addition, their utility to PubChem users has decreased to the point that they are infrequently used. Deprecating these tools will help PubChem to continue working in new and interesting directions.

 

What will replace these BioAssay Tool services? Fortunately, there are alternatives for most tools. PubChem data view pages, including the new PubChem Target pages (see this blog), as well as new and improved bioassay and target-based sections in compound pages are now available.

 

Will my old links work to these BioAssay Tools? URL redirection will be provided during a transitionary period of time. Eventually links to these legacy tools will be removed.

 

BioAssay Classification

As part of the entire PubChem classification system, which can be accessed at PubChem Classification Browser (see help document), the BioAssay-specific classification is under the sub-menu Select classification > PubChem > PubChem BioAssay Classification, allowing to browse the PubChem BioAssay contents in a hierarchical way. It also can be accessed directly at: https://pubchem.ncbi.nlm.nih.gov/classification/#hid=80.

 

Advanced Search

This is directly accessible from the NCBI's Entrez portal for PubChem BioAssay : https://www.ncbi.nlm.nih.gov/pcassay/limits.

 

BioActivity Summary

This service reports the biological screening results (e.g. tested bioassays and protein targets) for a single or a set of chemical samples.

  • For single-compound input, it's could be mostly replaced by the BioAssay Results section on a PubChem Compound summary page. For example, the biological test results for aspirin (CID 2244) can be obtained at: https://pubchem.ncbi.nlm.nih.gov/compound/2244#section=BioAssay-Results. More information on tested bioassays and targets are available therein. The results could be saved as a CSV file.
  • For multiple-compound input, the support will be dropped. The issue with multiple compound inputs is that it does not scale with the growth of PubChem content. As a workaround, user can download the data for individual compound, aggregate, and analyze offline.

 

BioActivity Data Table

This service reports the test results for a single bioassay record. This is equivalent to the Data Table section on a PubChem BioAssay record page, e.g. https://pubchem.ncbi.nlm.nih.gov/bioassay/450#section=Data-Table.

 

SAR

The Structure-Activity Relationship (SAR) analysis service clusters compounds and bioassays simultaneously using chemical structure, biological outcome, and target information. Unfortunately, there is no alternative currently.

 

Structure Clustering

This tool clusters compounds based on the two-dimension (2D) structural similarity using the single linkage algorithm. The same functionality could be achieved in two steps: 1) obtaining the 2D similarity scores using Score Matrix Service (see help document); 2) clustering with third-party tools such as R.

 

BioAssay Download

The old assay download page is deprecated, but assays  - either search results or user-specified AIDs - can be downloaded through the main PubChem search page, see https://pubchemdocs.ncbi.nlm.nih.gov/downloads for more information. For single bioassay record, more options can be found under the Download button on the top of a BioAssay record page, e.g. https://pubchem.ncbi.nlm.nih.gov/bioassay/450.

 

BioAssay FTP

The BioAssay FTP is accessible at: https://ftp.ncbi.nlm.nih.gov/pubchem/Bioassay/.

 

Plot Service

Two types of plot services are provided:

  1. Scatter Plot / Histogram for the column(s) provided in the data table for a single bioassay record. User needs first download the entire Data Table on a BioAssay record page (e.g. https://pubchem.ncbi.nlm.nih.gov/bioassay/450#section=Data-Table), then import the data in tools like Excel, where they can create their own plots.
  2. Dose-response Curve for a pair of a substance tested in a bioassay. This is accessible from Dose-response Data section (if any) on the AID-SID dyad summary page, e.g. https://pubchem.ncbi.nlm.nih.gov/bioassay/2244#sid=85256217&section=Dose-response-Data. The dyad page could be launched from the Data Table on the BioAssay record page (e.g. https://pubchem.ncbi.nlm.nih.gov/bioassay/2244#section=Data-Table) by clicking the structure image or the Outcome column.

 

BioActivity Data Analysis

This tool (https://pubchem.ncbi.nlm.nih.gov/assay/bioactivity.html) provides fast retrieval, filter, and analysis of bioactivity data for a single substance (SID), compound (CID), a bioassay (AID), protein target (GI/Accession/UniProt), gene target (GeneID/Gene Symbol), and publication (PMID).

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