PubChem Standardization Service

This document describes how to use the PubChem standardization web service.


What is Standardization?

Standardization in PubChem is the validation and determination of a unique chemical structure that is used to create a PubChem Compound from one or more submitted Substance records. Standardization is part of the PubChem Upload pipeline for submitted records with valid chemical structures. It allows PubChem to display one Compound page for aspirin (for example) that includes information from many submitted aspirin Substance records.


Read about the details of PubChem standardization or view a schematic:



Can I Test My Chemical Structure?

Yes! We provide the PubChem Standardization web service to let you see how PubChem would handle any structure you would like to upload. (This functionality is also available though PubChem's PUG service.)


Note that this does not include the computation of all the properties normally associated with a PubChem compound, as many of these are computationally expensive. For more thorough processing of your structure data, please use PubChem Upload.


Standardization through this service is limited to a single structure at a time, though any number of requests may be submitted. Requests are processed in the order received. All requests are kept private; without your unique 64-bit key, nobody else can see what structures you have submitted.


Steps to Use Web Service Standardization

1) Input your structure in one of these formats:

  • SMILES: Standard SMILES string.
  • InChI: An InChI string.
  • SDF: Upload an SDF file.

2) Select an output format:

  • SMILES: Standard SMILES string.
  • InChI: An InChI string.
  • SDF: Returns an SDF format chemical structure, which will contain both SMILES and InChI tags, and a tag with the PubChem CID if this is a structure present in PubChem.

3) Initiate the request:

  • Submit Job: Begin processing this structure. You will be taken to a self-refreshing waiting page while your request is queued on NCBI's servers. When done, the output will appear as plain text in the desired format.
  • Save Job: Save the XML specification of this request, mainly for use with PubChem's PUG service.
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