PubChem Pathways

PubChem integrates pathway related information. What is a pathway? Wikipedia defines a biological pathway as "a series of interactions among molecules in a cell that leads to a certain product or a change in a cell". A pathway involves the interactions between chemicals, proteins (gene products, enzymes), and genes. Some pathways are known to be directly involved in diseases. This integration helps to improve access to and highlight available pathway resources as well as to provide a context for a given chemical or target. PubChem pathways are searchable within PubChem Search.

 

More detailed information on PubChem Pathway can be found in the following paper:

Kim S, Cheng T, He S, Thiessen PA, Li Q, Gindulyte A, Bolton EE. PubChem Protein, Gene, Pathway, and Taxonomy Data Collections: Bridging Biology and Chemistry through Target-Centric Views of PubChem Data. J Mol Biol. 2022 Feb 25:167514. doi:10.1016/j.jmb.2022.167514. Epub ahead of print. PMID: 35227770.
[PubMed PMID: 35227770] [Free Full Text]

 

To get a list of available pathway data sources, please visit the PubChem Sources page.

 

You can access a PubChem pathway via a URL of this form: https://pubchem.ncbi.nlm.nih.gov/pathway/SOURCE:ExternalID. For instance, https://pubchem.ncbi.nlm.nih.gov/pathway/PathBank:SMP0000001. PathBank is the SOURCE that provides the pathway and SMP0000001 is the ExternalID used by PathBank.

 

The noticeable added merit by PubChem pathways is that we extracted the interactions/reactions involved in a pathway (if any), as shown in the following example:

https://pubchem.ncbi.nlm.nih.gov/pathway/PathBank:SMP0000001#section=Interactions

Interaction controls such as inhibition and activation are also provided. Pathways entities like small molecules, proteins, and genes are linked to PubChem pages and external source pages, as well as NCBI pages.

 

PubChem is superseding the NCBI BioSystems database which will soon be retired. If you have a NCBI BioSystems identifier (BSID), you can access the corresponding PubChem pathway page via, e.g.:
https://pubchem.ncbi.nlm.nih.gov/pathway/BSID:703092

 

Programmatic access

The annotation data presented on the Pathway pages can be downloaded programmatically through PubChem's REST-like interface called PUG-View

The PUG-View request URL contains a pathway record identifier (e.g., SOURCE:ExternalID), as shown in the following example:

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