PubChem BioAssay Tools to be replaced

PubChem BioAssay Tools (, a legacy collection of bioactivity analysis services, are being retired as part of an on-going technology refresh.  Alternative approaches now exist to perform most of the same tasks, and these newer technologies provide expanded features and capabilities.  The PubChem BioAssay Tools services will be no longer accessible after November 1, 2018.

Why are we phasing out the BioAssay Tools?

The BioAssay tools were developed when PubChem was much smaller.  At PubChem’s current size, the tools do not scale sufficiently to handle most analysis tasks.  Consequently, many users download data for use in their assay analysis workflows instead of using the tools.  Deprecating these BioAssay Tools will free up resources allowing PubChem to develop new and better approaches to accessing bioactivity content.


What replaces the BioAssay Tools?

BioAssay Assay Results for CID 2244 There are easier-to-find PubChem services that offer the same or similar functionalities for most BioAssay Tools.  For instance, let’s say you have a compound, like aspirin, for which you would like to analyze all reported bioactivity data.  In the past, you would need to first find the dedicated tool (the BioActivity Summary service) to retrieve the data. Now you will find this information in a BioAssay Results section on the widely accessed Compound Summary page:

Though some tools (like Structure Clustering and Structure-Activity Relationship Analysis) do not currently have direct alternatives in PubChem, most PubChem pages indicate related records such as structurally similar chemicals or assays performed against a given target.  They can be further aggregated using commonly available third-party tools.

Will my old link work to the BioAssay Tools?

URL redirection from BioAssay Tools to their corresponding replacement will be provided for a period beyond November 1, 2018.  Eventually, the redirection links will be removed.

For more detailed information on this topic, please visit this PubChem Help document: