Upload Chemicals

Once you have opened an account, login to PubChem Upload and click New Submission > Substances.


Format a File Or Fill Out a Web Form

If you have only a few records to upload, use our web form to fill in your information.


To input many chemical substances, like a product catalog, it is most convenient to prepare a file for upload. You can do this with either a standard spreadsheet file (like CSV) or a chemistry-specific SDF file.  In either case the main objectives are the same as outlined below.


You Can Upload a Spreadsheet

  • First row contains PubChem standard tags defining each column
  • Each subsequent row defines one substance record


Or You Can Upload a Chemical SDF File

Most chemical software packages output chemical structures in SDF


An SDF file can be used to define your structures in PubChem.


While SDF is more complicated than a spreadsheet, it offers the following advantages:

  • Annotation tags more easily support multi-line values
  • Chemical structures can be specified with detailed MOL format
  • Chemical software packages typically output data in SDF


Map Your Tags

The primary preparation required is to map your existing tags, e.g. Catalog-Number, to our PubChem standard tags, e.g. PUBCHEM_EXT_DATASOURCE_REGID, so that our parser can understand your content.  In some cases such as synonyms, multiple fields can be defined with the same tag.  Their values will be listed line by line.


Give Each Record a Unique Identifier

Provide a unique identifier to track your record for future updates and revokes


Use the following tag in your file:


Each of your records in PubChem must contain a unique identifier (registry-id):

  • Use any combination of numbers and/or letters
  • Keep it simple and easy for you to keep track of (e.g. a catalog number).


PubChem is an archive keeping track of multiple versions of each record based on your registry-id:

  • Replace your PubChem record if an uploaded record has the same registry-id
  • Use your registry-id to revoke a record.
  • Avoid using the same registry-id multiple times in one submission.



Add a Structure If You Have One

Expose your information on our highly-visible Compound page


If you have a chemical structure that we can standardize, we will link your information to a highly-visible Compound summary page for that structure.


If you provide something like 'tea extract', then you won't have a structure, which is fine. We do not accept molecular formulas to define your structure. We accept three structure tags:


In addition, with an SDF file, you can use the MOL section to define your structure instead of using a tag.


List Common Synonyms

Synonyms, listed one per line, associate your structure with common names for text search


Use the following tag in your file:


Synonyms including common names, registry-ids (like CAS), chemical names and trade names. This tag can have multiple synonyms by putting each on a separate line or by repeating this tag with a different synonym for each tag occurrence.

Example entry (one synonym per line):


2-acetoxybenzoic acid


Synonyms are the primary keywords by which a substance is known and found via text search. They are collected to name our aggregated PubChem Compound records. Your records are most frequently discovered through your high-quality synonyms and chemical structure. Synonyms must be ASCII text; as with other input, all special characters and HTML tags will be converted to text or stripped out as appropriate.


Provide a URL To a Specific Page On Your Site

Drive web traffic back to your site


If your website has a specific page for each molecule, use the following tag to provide the URLs:



Here are some guidelines for this type of URL:

  • Make it specific to the record, not a general location like a home page.
  • Keep the page outside of a login or paywall mechanism.
  • Point to a page on your website, not a third party.
Was this information helpful?


National Library of Medicine
8600 Rockville Pike
Bethesda, MD 20894


PubChem Help
HHS Vulnerability Disclosure


The page cannot be found

The page you are looking for might have been removed, had its name changed, or is temporarily unavailable. Please make sure you spelled the page name correctly or use the search box.