PubChem Taxonomies

The taxonomy page presents PubChem data associated with a given taxon (organism). 

 

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]

 

You can access a PubChem pathway via a URL of this form:

 

https://pubchem.ncbi.nlm.nih.gov/taxonomy/TAXON

 

where TAXON is the name of a taxon.  It can be a common name (e.g., rat or Norway rat) or a scientific name (Rattus norvegicus).  A taxon identifier used in the NCBI Taxonomy database (10116 for norway rat) can also be used as TAXON.  For example, the following URLs lead to the PubChem Pathway page for norway rat:

 

https://pubchem.ncbi.nlm.nih.gov/taxonomy/rat

https://pubchem.ncbi.nlm.nih.gov/taxonomy/Norway rat

https://pubchem.ncbi.nlm.nih.gov/taxonomy/Rattus norvegicus

https://pubchem.ncbi.nlm.nih.gov/taxonomy/10116

 

Programmatic access

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

The PUG-View request URLs contain an NCBI Taxonomy ID, as shown in the following example:

 

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