Uploading Structured Chemical Data to Wikidata

Coming back to consistent blogging. Wikidata is becoming a common way to transmit structured chemical data across different communities. More available data there is the more we can incite discussions and research. For this showcase, I uploaded the Cannabis Sativa Template

To accomplish this, I started off with the data import guide:

This step is pretty easy and then you arrive at this page.

The data is structured in a Wikidata format, however, in GlobalChem all the formatting is in JSON.

class CannabisAlcohols(object):

  def __init__(self):

    self.name = 'cannabis_alcohols'

  @staticmethod
  def get_smiles():

    smiles = {
      'methanol': 'CO',
      'ethanol': 'CCO',
      'octanol-1': 'CCCCCCCC(O)',
      'octanol-3': 'CCCCCC(O)CC',
      'nonanol-1': 'CCCCCCCCC(O)',
      'hexadecanol-1': 'CCCCCCCC(O)CCCCCC',
    }

    return smiles

  @staticmethod
  def get_smarts():

    smarts = {
    }

    return smarts

Conveniently the conversion was pretty easy with this tool:

This allowed for easy flexibility between the data tables. Moving forward, there is probably a more programmatic way of accomplishing this but I found this little conversion and uploading data to be a bit of a tricky endeavor.

I’m more happy with the result of the page in where it looks cleaner to the average consumer and in a format they are used too because of Wikipedia.

Happy Cheminformatics!