I reported earlier how to I uploaded the ChemPedia (RIP) data onto Kasabi. But for ChEMBL-RDF I have used the pytassium tool, not just because it has a cool name :) I discovered yesterday, however, that I did not write down in this lab notebook, what steps I needed to take to reproduce it. And I just wanted to uploaded new triples to the ChEMBL-RDF data set on Kasabi.

The new triples I wanted to upload, link the new public CHEMBL identifiers (like CHEMBL25 for aspirin) to the internal ChEMBL database identifier I used for ChEMBL 09 for the URIs. So, I am adding a lot of triples like:

<http://data.kasabi.com/dataset/chembl-rdf/09/molecule/m517180> <http://www.w3.org/2002/07/owl#sameAs>
<http://data.kasabi.com/dataset/chembl-rdf/09/chemblid/CHEMBL1>

And the pytassium code I use to upload this to Kasabi looks like:

import pytassium
import time

dataset = pytassium.Dataset('chembl-rdf','XXX')

# Store the contents of a turtle file
dataset.store_file('chemblids.nt', media_type='text/plain')

So, that omission in my log book has been corrected now.

This post was originally posted as https://chem-bla-ics.blogspot.com/2011/10/chembl-rdf-uploading-data-to-kasabi.html.