Upload Chemicals

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

substance_submission.sdf

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

Use the following tag in your file:

• PUBCHEM_EXT_DATASOURCE_REGID

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.

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:

•  PUBCHEM_EXT_DATASOURCE_SMILES
  CC(=O)C

   
•  PUBCHEM_EXT_DATASOURCE_INCHI:
  InChI=1S/C3H6O/c1-3(2)4/h1-2H3

   
•  PUBCHEM_EXT_DATASOURCE_CID
  180

   

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

Use the following tag in your file:

• PUBCHEM_SUBSTANCE_SYNONYM

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):

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.

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

• PUBCHEM_EXT_SUBSTANCE_URL

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.