Introducing PubChem Pathway Pages


Posted on March 31, 2020


PubChem PathwaysPubChem Pathway Pages are now available. Each PubChem Pathway page provides information about chemicals, proteins, genes, and diseases involved in or associated with the biological pathway, which can be very important to provide a context to observed biological activity. In addition, all pathways associated with a given chemical, protein or gene are summarized on the corresponding page.


All content comes from existing Pathway resources without any attempt to merge or combine them.  Each page for a given pathway can be accessed via an URL of this form:


where SOURCE is the information source for the pathway and PATHID is the record identifier used by the source.  For example, the following URL directs to the pathway page for the citric acid cycle in human and mouse (ID: SMP0000057 and SMP0063477, respectively) from PathBank:  (for human)  (for mouse)


PubChem Pathways supersedes the NCBI BioSystems database, which is no longer being updated. If you have a NCBI BioSystems identifier (BSID) and the page exists in PubChem Pathways, you can access the corresponding PubChem Pathway page via, for example:


Chemicals, proteins, and genes presented on PubChem Pathway pages are linked to corresponding PubChem pages, providing quick access to more detailed information on these entities.  In addition, the Pathway page provides information on the interactions or reactions among these entities.  The PubChem Pathway pages are searchable within PubChem Search.


Lastly, PubChem Pathway information is integrated with the NCBI Gene database (  For instance, the following web page presents all pathways associated with the human EGFR (NCBI Gene ID: 1956) in PubChem Pathways:


To learn more about the PubChem Pathway page, please read this Help page (

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